Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 16:17:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhl_24465/04_2023/7rhl_24465.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhl_24465/04_2023/7rhl_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_24465/04_2023/7rhl_24465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhl_24465/04_2023/7rhl_24465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhl_24465/04_2023/7rhl_24465.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhl_24465/04_2023/7rhl_24465.pdb" } resolution = 3.03 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 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-1.21rc1-4938/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: 8.47, per 1000 atoms: 0.55 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: 6.56 Conformation dependent library (CDL) restraints added in 2.2 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: 0.74 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: 4.93 Time building geometry restraints manager: 6.97 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.650 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 42.130 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.390 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.752 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2857 time to fit residues: 87.2115 Evaluate side-chains 168 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1558 ------------------------------------------------------------------------------- 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: 5.9990 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.8145 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 15713 Z= 0.233 Angle : 0.478 6.442 21308 Z= 0.259 Chirality : 0.039 0.185 2407 Planarity : 0.004 0.044 2659 Dihedral : 3.703 19.595 2127 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 0.56 % 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: 2.32 (0.19), residues: 1914 helix: 2.06 (0.14), residues: 1298 sheet: 0.68 (0.72), residues: 47 loop : 0.52 (0.27), residues: 569 *********************** 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 : 2.066 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 187 average time/residue: 0.2920 time to fit residues: 81.6903 Evaluate side-chains 179 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1372 time to fit residues: 4.6522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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** D 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1191 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= 0.153 Angle : 0.431 9.209 21308 Z= 0.231 Chirality : 0.037 0.162 2407 Planarity : 0.003 0.034 2659 Dihedral : 3.554 19.013 2127 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.19), residues: 1914 helix: 2.38 (0.14), residues: 1296 sheet: 0.94 (0.69), residues: 44 loop : 0.53 (0.27), residues: 574 *********************** 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 181 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 1.885 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 179 average time/residue: 0.2868 time to fit residues: 77.0619 Evaluate side-chains 166 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.738 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- 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** A 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 15713 Z= 0.210 Angle : 0.454 6.210 21308 Z= 0.244 Chirality : 0.038 0.164 2407 Planarity : 0.003 0.030 2659 Dihedral : 3.616 18.417 2127 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.19), residues: 1914 helix: 2.40 (0.14), residues: 1300 sheet: 0.85 (0.67), residues: 44 loop : 0.52 (0.26), residues: 570 *********************** 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 185 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 1.829 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 179 average time/residue: 0.2874 time to fit residues: 77.3554 Evaluate side-chains 172 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1489 time to fit residues: 4.5542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 B 953 ASN D 468 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 15713 Z= 0.150 Angle : 0.427 7.708 21308 Z= 0.228 Chirality : 0.037 0.198 2407 Planarity : 0.003 0.027 2659 Dihedral : 3.514 18.215 2127 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.37 % 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: 2.86 (0.19), residues: 1914 helix: 2.54 (0.14), residues: 1299 sheet: 0.72 (0.68), residues: 44 loop : 0.55 (0.26), residues: 571 *********************** 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 172 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.946 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 169 average time/residue: 0.2730 time to fit residues: 69.9574 Evaluate side-chains 164 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1352 time to fit residues: 3.1924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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: 0.8172 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 15713 Z= 0.222 Angle : 0.466 6.748 21308 Z= 0.249 Chirality : 0.039 0.211 2407 Planarity : 0.003 0.033 2659 Dihedral : 3.630 17.734 2127 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.50 % 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: 2.77 (0.19), residues: 1914 helix: 2.46 (0.14), residues: 1301 sheet: 0.92 (0.71), residues: 44 loop : 0.51 (0.26), residues: 569 *********************** 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 173 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 2.133 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 171 average time/residue: 0.2890 time to fit residues: 76.0607 Evaluate side-chains 166 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 162 time to evaluate : 2.135 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1563 time to fit residues: 3.9467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 104 optimal weight: 0.5980 chunk 155 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 84 optimal weight: 0.0970 overall best weight: 1.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1692 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 : 0.436 7.011 21308 Z= 0.233 Chirality : 0.038 0.204 2407 Planarity : 0.003 0.028 2659 Dihedral : 3.557 17.948 2127 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 0.19 % 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: 2.85 (0.19), residues: 1914 helix: 2.53 (0.14), residues: 1300 sheet: 0.93 (0.72), residues: 44 loop : 0.51 (0.26), residues: 570 *********************** 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 167 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 2.042 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 166 average time/residue: 0.2867 time to fit residues: 72.0782 Evaluate side-chains 162 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.064 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 144 optimal weight: 0.0970 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 15713 Z= 0.287 Angle : 0.506 8.054 21308 Z= 0.270 Chirality : 0.040 0.206 2407 Planarity : 0.004 0.034 2659 Dihedral : 3.783 17.423 2127 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.19), residues: 1914 helix: 2.37 (0.14), residues: 1293 sheet: 0.83 (0.71), residues: 44 loop : 0.46 (0.26), residues: 577 *********************** 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 168 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 2.018 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 167 average time/residue: 0.2914 time to fit residues: 73.7788 Evaluate side-chains 162 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 1.915 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1528 time to fit residues: 3.4375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 103 optimal weight: 0.0670 chunk 74 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.2920 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1831 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= 0.168 Angle : 0.446 8.669 21308 Z= 0.236 Chirality : 0.038 0.206 2407 Planarity : 0.003 0.028 2659 Dihedral : 3.611 18.180 2127 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 0.06 % 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: 2.81 (0.19), residues: 1914 helix: 2.53 (0.14), residues: 1289 sheet: 0.82 (0.70), residues: 44 loop : 0.48 (0.26), residues: 581 *********************** 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 166 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 2.015 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.2958 time to fit residues: 74.6298 Evaluate side-chains 162 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.905 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.7980 chunk 181 optimal weight: 0.0060 chunk 110 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 126 optimal weight: 0.9980 chunk 190 optimal weight: 30.0000 chunk 175 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 15713 Z= 0.129 Angle : 0.428 8.533 21308 Z= 0.224 Chirality : 0.037 0.200 2407 Planarity : 0.003 0.028 2659 Dihedral : 3.453 18.159 2127 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.19), residues: 1914 helix: 2.68 (0.14), residues: 1288 sheet: 0.80 (0.69), residues: 44 loop : 0.57 (0.26), residues: 582 ********************** 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 171 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 1.952 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.2809 time to fit residues: 73.2885 Evaluate side-chains 160 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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 422 HIS D 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.089750 restraints weight = 22283.934| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.18 r_work: 0.2892 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 15713 Z= 0.342 Angle : 0.541 9.566 21308 Z= 0.285 Chirality : 0.041 0.218 2407 Planarity : 0.004 0.037 2659 Dihedral : 3.804 17.165 2127 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.19 % 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: 2.63 (0.19), residues: 1914 helix: 2.37 (0.14), residues: 1292 sheet: 0.86 (0.71), residues: 44 loop : 0.46 (0.26), residues: 578 =============================================================================== Job complete usr+sys time: 2915.31 seconds wall clock time: 54 minutes 25.49 seconds (3265.49 seconds total)