Starting phenix.real_space_refine on Tue Mar 19 13:49:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baj_7074/03_2024/6baj_7074_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baj_7074/03_2024/6baj_7074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baj_7074/03_2024/6baj_7074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baj_7074/03_2024/6baj_7074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baj_7074/03_2024/6baj_7074_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baj_7074/03_2024/6baj_7074_neut_updated.pdb" } resolution = 3.2 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= 0.003 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 131 5.16 5 C 15802 2.51 5 N 3829 2.21 5 O 4527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ARG 540": "NH1" <-> "NH2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "B ARG 818": "NH1" <-> "NH2" Residue "B ARG 867": "NH1" <-> "NH2" Residue "B ARG 1030": "NH1" <-> "NH2" Residue "B ARG 1032": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C ARG 620": "NH1" <-> "NH2" Residue "C ARG 767": "NH1" <-> "NH2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 818": "NH1" <-> "NH2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 867": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 1032": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24318 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 7786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7786 Classifications: {'peptide': 1024} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 978} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 7777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7777 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 977} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 7544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7544 Classifications: {'peptide': 995} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 949} Chain breaks: 1 Chain: "B" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 391 Unusual residues: {'D12': 6, 'PTY': 9} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 127 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 410 Unusual residues: {'D12': 5, 'PTY': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PTY:plan-1': 2, 'PTY:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 409 Unusual residues: {'PTY': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 141 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 12.50, per 1000 atoms: 0.51 Number of scatterers: 24318 At special positions: 0 Unit cell: (114.4, 122.1, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 29 15.00 O 4527 8.00 N 3829 7.00 C 15802 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: 9.02 Conformation dependent library (CDL) restraints added in 4.2 seconds 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5578 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 23 sheets defined 44.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.40 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 24 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 166 No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 208 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 299 through 311 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 330 through 359 removed outlier: 4.202A pdb=" N VAL B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 398 No H-bonds generated for 'chain 'B' and resid 395 through 398' Processing helix chain 'B' and resid 402 through 422 removed outlier: 4.334A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 437 Processing helix chain 'B' and resid 439 through 449 removed outlier: 3.974A pdb=" N VAL B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 466 through 485 removed outlier: 3.919A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 515 through 534 Processing helix chain 'B' and resid 539 through 557 Processing helix chain 'B' and resid 584 through 601 removed outlier: 3.530A pdb=" N THR B 600 " --> pdb=" O HIS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 654 removed outlier: 3.928A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 677 No H-bonds generated for 'chain 'B' and resid 675 through 677' Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 743 through 753 removed outlier: 4.061A pdb=" N ALA B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 788 removed outlier: 3.927A pdb=" N ILE B 786 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY B 787 " --> pdb=" O ASP B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 847 Processing helix chain 'B' and resid 861 through 867 removed outlier: 4.684A pdb=" N GLN B 865 " --> pdb=" O MET B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 891 removed outlier: 4.172A pdb=" N ILE B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 882 " --> pdb=" O ALA B 878 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 883 " --> pdb=" O ILE B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 901 Processing helix chain 'B' and resid 907 through 919 removed outlier: 4.409A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 952 removed outlier: 3.712A pdb=" N GLY B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 970 Processing helix chain 'B' and resid 973 through 980 removed outlier: 3.689A pdb=" N MET B 977 " --> pdb=" O ARG B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 991 Processing helix chain 'B' and resid 999 through 1016 removed outlier: 4.445A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET B1011 " --> pdb=" O VAL B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1031 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.599A pdb=" N ILE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 100 through 113 removed outlier: 4.182A pdb=" N LYS C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.661A pdb=" N ARG C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 299 through 310 Processing helix chain 'C' and resid 331 through 359 removed outlier: 3.503A pdb=" N ILE C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'C' and resid 371 through 385 removed outlier: 4.091A pdb=" N LEU C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 423 removed outlier: 4.775A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.620A pdb=" N MET C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 448 removed outlier: 3.641A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 485 removed outlier: 4.104A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 Processing helix chain 'C' and resid 514 through 532 removed outlier: 4.441A pdb=" N ARG C 518 " --> pdb=" O GLY C 514 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N MET C 519 " --> pdb=" O TRP C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 557 removed outlier: 4.230A pdb=" N LEU C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR C 545 " --> pdb=" O TYR C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 600 Processing helix chain 'C' and resid 634 through 636 No H-bonds generated for 'chain 'C' and resid 634 through 636' Processing helix chain 'C' and resid 644 through 654 removed outlier: 3.719A pdb=" N MET C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 697 removed outlier: 3.529A pdb=" N GLN C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 693 through 697' Processing helix chain 'C' and resid 699 through 705 Processing helix chain 'C' and resid 733 through 738 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 784 through 788 removed outlier: 3.706A pdb=" N ASP C 788 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 847 Processing helix chain 'C' and resid 862 through 869 removed outlier: 3.524A pdb=" N GLU C 866 " --> pdb=" O MET C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 892 removed outlier: 3.776A pdb=" N LEU C 891 " --> pdb=" O CYS C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 900 No H-bonds generated for 'chain 'C' and resid 898 through 900' Processing helix chain 'C' and resid 905 through 918 removed outlier: 4.102A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 956 removed outlier: 4.331A pdb=" N ALA C 939 " --> pdb=" O ILE C 935 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 940 " --> pdb=" O GLY C 936 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN C 941 " --> pdb=" O LEU C 937 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 942 " --> pdb=" O SER C 938 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 970 removed outlier: 3.775A pdb=" N MET C 970 " --> pdb=" O ASP C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 983 removed outlier: 3.863A pdb=" N PHE C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 990 No H-bonds generated for 'chain 'C' and resid 987 through 990' Processing helix chain 'C' and resid 999 through 1016 removed outlier: 4.528A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C1009 " --> pdb=" O THR C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1021 No H-bonds generated for 'chain 'C' and resid 1018 through 1021' Processing helix chain 'C' and resid 1024 through 1027 No H-bonds generated for 'chain 'C' and resid 1024 through 1027' Processing helix chain 'C' and resid 1029 through 1032 No H-bonds generated for 'chain 'C' and resid 1029 through 1032' Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.743A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.808A pdb=" N GLN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.934A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.748A pdb=" N GLY A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 248' Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 330 through 357 removed outlier: 3.748A pdb=" N LYS A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 386 removed outlier: 3.761A pdb=" N LEU A 366 " --> pdb=" O ARG A 363 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE A 367 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 4.680A pdb=" N VAL A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Proline residue: A 373 - end of helix removed outlier: 3.977A pdb=" N LEU A 376 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA A 384 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 386 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.587A pdb=" N LYS A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 464 through 496 removed outlier: 4.026A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 4.042A pdb=" N THR A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 556 removed outlier: 3.833A pdb=" N VAL A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 601 removed outlier: 4.025A pdb=" N VAL A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 644 through 653 removed outlier: 4.300A pdb=" N MET A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR A 652 " --> pdb=" O THR A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 707 removed outlier: 3.662A pdb=" N ALA A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN A 701 " --> pdb=" O GLN A 697 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 703 " --> pdb=" O ARG A 699 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 707 " --> pdb=" O LEU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 743 through 754 Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 801 through 803 No H-bonds generated for 'chain 'A' and resid 801 through 803' Processing helix chain 'A' and resid 862 through 864 No H-bonds generated for 'chain 'A' and resid 862 through 864' Processing helix chain 'A' and resid 873 through 892 removed outlier: 4.026A pdb=" N ALA A 878 " --> pdb=" O PRO A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 905 through 919 removed outlier: 4.149A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 916 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 919 " --> pdb=" O ALA A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 935 No H-bonds generated for 'chain 'A' and resid 932 through 935' Processing helix chain 'A' and resid 938 through 955 removed outlier: 3.639A pdb=" N LEU A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N MET A 953 " --> pdb=" O ALA A 949 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP A 954 " --> pdb=" O LYS A 950 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 955 " --> pdb=" O ASP A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 989 removed outlier: 3.585A pdb=" N LEU A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Proline residue: A 974 - end of helix removed outlier: 4.177A pdb=" N ALA A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 997 through 1016 removed outlier: 4.548A pdb=" N ALA A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1032 removed outlier: 3.943A pdb=" N VAL A1027 " --> pdb=" O PRO A1023 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A1028 " --> pdb=" O VAL A1024 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 128 through 131 removed outlier: 3.682A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 77 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 286 through 288 Processing sheet with id= C, first strand: chain 'B' and resid 183 through 188 removed outlier: 8.937A pdb=" N MET B 184 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS B 770 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE B 186 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR B 772 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET B 188 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N MET B 774 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 662 through 666 Processing sheet with id= E, first strand: chain 'B' and resid 824 through 827 Processing sheet with id= F, first strand: chain 'B' and resid 725 through 728 Processing sheet with id= G, first strand: chain 'B' and resid 790 through 792 Processing sheet with id= H, first strand: chain 'B' and resid 250 through 253 removed outlier: 7.225A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.485A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 83 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 77 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 286 through 291 Processing sheet with id= K, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.679A pdb=" N VAL C 768 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N MET C 184 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LYS C 770 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE C 186 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR C 772 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N MET C 188 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET C 774 " --> pdb=" O MET C 188 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 278 through 281 Processing sheet with id= M, first strand: chain 'C' and resid 724 through 731 Processing sheet with id= N, first strand: chain 'C' and resid 790 through 792 Processing sheet with id= O, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= P, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.581A pdb=" N LYS A 322 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 175 through 177 Processing sheet with id= R, first strand: chain 'A' and resid 266 through 272 Processing sheet with id= S, first strand: chain 'A' and resid 278 through 280 removed outlier: 3.745A pdb=" N MET A 573 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 723 through 731 Processing sheet with id= U, first strand: chain 'A' and resid 761 through 764 Processing sheet with id= V, first strand: chain 'A' and resid 790 through 792 Processing sheet with id= W, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.943A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2742 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: 8.06 Time building geometry restraints manager: 9.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3900 1.30 - 1.43: 5920 1.43 - 1.56: 14573 1.56 - 1.68: 60 1.68 - 1.81: 256 Bond restraints: 24709 Sorted by residual: bond pdb=" C GLU A 314 " pdb=" N PRO A 315 " ideal model delta sigma weight residual 1.337 1.385 -0.049 9.80e-03 1.04e+04 2.49e+01 bond pdb=" C GLU C 314 " pdb=" N PRO C 315 " ideal model delta sigma weight residual 1.337 1.382 -0.046 9.80e-03 1.04e+04 2.17e+01 bond pdb=" C MET A 987 " pdb=" N PRO A 988 " ideal model delta sigma weight residual 1.334 1.370 -0.036 8.40e-03 1.42e+04 1.84e+01 bond pdb=" C8 PTY A1101 " pdb=" O7 PTY A1101 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C8 PTY C1108 " pdb=" O7 PTY C1108 " ideal model delta sigma weight residual 1.331 1.405 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 24704 not shown) Histogram of bond angle deviations from ideal: 96.23 - 103.82: 396 103.82 - 111.40: 10532 111.40 - 118.98: 9645 118.98 - 126.56: 12453 126.56 - 134.14: 253 Bond angle restraints: 33279 Sorted by residual: angle pdb=" O11 PTY B1107 " pdb=" P1 PTY B1107 " pdb=" O14 PTY B1107 " ideal model delta sigma weight residual 92.90 111.24 -18.34 3.00e+00 1.11e-01 3.74e+01 angle pdb=" O11 PTY C1101 " pdb=" P1 PTY C1101 " pdb=" O14 PTY C1101 " ideal model delta sigma weight residual 92.90 110.78 -17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" O11 PTY A1108 " pdb=" P1 PTY A1108 " pdb=" O14 PTY A1108 " ideal model delta sigma weight residual 92.90 110.56 -17.66 3.00e+00 1.11e-01 3.46e+01 angle pdb=" O11 PTY A1110 " pdb=" P1 PTY A1110 " pdb=" O14 PTY A1110 " ideal model delta sigma weight residual 92.90 110.32 -17.42 3.00e+00 1.11e-01 3.37e+01 angle pdb=" O11 PTY B1104 " pdb=" P1 PTY B1104 " pdb=" O14 PTY B1104 " ideal model delta sigma weight residual 92.90 110.32 -17.42 3.00e+00 1.11e-01 3.37e+01 ... (remaining 33274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 14527 34.98 - 69.96: 420 69.96 - 104.94: 53 104.94 - 139.92: 16 139.92 - 174.91: 3 Dihedral angle restraints: 15019 sinusoidal: 6325 harmonic: 8694 Sorted by residual: dihedral pdb=" CA PRO B 579 " pdb=" C PRO B 579 " pdb=" N ALA B 580 " pdb=" CA ALA B 580 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA ALA B 704 " pdb=" C ALA B 704 " pdb=" N GLU B 705 " pdb=" CA GLU B 705 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ILE B 207 " pdb=" C ILE B 207 " pdb=" N LYS B 208 " pdb=" CA LYS B 208 " ideal model delta harmonic sigma weight residual 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 15016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2937 0.066 - 0.131: 751 0.131 - 0.197: 109 0.197 - 0.263: 11 0.263 - 0.328: 7 Chirality restraints: 3815 Sorted by residual: chirality pdb=" CA LEU C 75 " pdb=" N LEU C 75 " pdb=" C LEU C 75 " pdb=" CB LEU C 75 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA ASN C 74 " pdb=" N ASN C 74 " pdb=" C ASN C 74 " pdb=" CB ASN C 74 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE B 729 " pdb=" CA ILE B 729 " pdb=" CG1 ILE B 729 " pdb=" CG2 ILE B 729 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 3812 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 671 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE B 671 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE B 671 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL B 672 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 982 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.94e+00 pdb=" C PHE B 982 " 0.049 2.00e-02 2.50e+03 pdb=" O PHE B 982 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE B 983 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 822 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO C 823 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 823 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 823 " 0.035 5.00e-02 4.00e+02 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 557 2.68 - 3.24: 21706 3.24 - 3.79: 36739 3.79 - 4.35: 48990 4.35 - 4.90: 82697 Nonbonded interactions: 190689 Sorted by model distance: nonbonded pdb=" O ILE B 268 " pdb=" O GLU B 269 " model vdw 2.131 3.040 nonbonded pdb=" O ASN C 820 " pdb=" ND2 ASN C 820 " model vdw 2.151 2.520 nonbonded pdb=" NZ LYS B 958 " pdb=" OD2 ASP B 966 " model vdw 2.199 2.520 nonbonded pdb=" O THR B 676 " pdb=" CB ALA B 677 " model vdw 2.205 3.460 nonbonded pdb=" NH2 ARG B 307 " pdb=" OD2 ASP B 328 " model vdw 2.219 2.520 ... (remaining 190684 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 1 through 341 or (resid 342 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE )) or resid 343 through \ 452 or (resid 453 and (name N or name CA or name C or name CB or name CG or nam \ e CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 454 or (resid 4 \ 55 and (name N or name CA or name C or name O or name CB or name CG )) or resid \ 456 through 1033 or (resid 1101 and (name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C2 or name C3 or name C \ 30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 1102 and (name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C18 or name C19 or name C2 or name C3 or name C5 or name C6 or name C8 or na \ me N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O7 or \ name P1 )) or (resid 1103 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C17 or name C18 or name C2 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C5 or name C6 or name C8 or \ name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 \ or name O4 or name O7 or name P1 )) or (resid 1104 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C8 )) or resid 1105 or (re \ sid 1106 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C16 or name C5 or name C6 or name C8 or name N1 or name O10 or name O1 \ 1 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or (resid 1107 and (name C1 or name C11 or name C2 or name C3 or name C30 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name C5 or name C6 or name C8 or name N1 or name O10 or name \ O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or nam \ e P1 )) or (resid 1108 and (name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or na \ me C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or \ name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 ) \ ))) selection = (chain 'B' and (resid 1 through 454 or (resid 455 and (name N or name CA or name \ C or name O or name CB or name CG )) or resid 456 through 499 or resid 539 thro \ ugh 1033 or resid 1102 or (resid 1103 and (name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 o \ r name C3 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or \ name O12 or name O13 or name O14 or name O7 or name P1 )) or (resid 1104 and (n \ ame C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C17 or name C18 or name C2 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 \ or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P \ 1 )) or (resid 1105 and (name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C16 or name C8 )) or (resid 1106 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or nam \ e C33 or name C34 or name C5 or name C6 or name C8 or name N1 or name O10 or nam \ e O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or n \ ame P1 )) or (resid 1107 and (name C1 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C5 or name C6 or name C8 or name N1 or nam \ e O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or \ name O7 or name P1 )) or (resid 1108 and (name C1 or name C11 or name C2 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name N1 or n \ ame O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 o \ r name O7 or name P1 )) or (resid 1109 and (name C1 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name C5 or name C6 or name C8 or name N1 or name O1 \ 0 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name \ O7 or name P1 )))) selection = (chain 'C' and (resid 1 through 341 or (resid 342 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE )) or resid 343 through \ 452 or (resid 453 and (name N or name CA or name C or name CB or name CG or nam \ e CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 454 through 499 \ or resid 539 through 1033 or (resid 1102 and (name C1 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name \ O13 or name O14 or name O30 or name O4 or name O7 or name P1 )) or resid 1103 o \ r (resid 1104 and (name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C16 or name C17 or name C18 or name C2 or name C3 or name C30 or \ name C31 or name C32 or name C33 or name C5 or name C6 or name C8 or name N1 or \ name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 \ or name O7 or name P1 )) or (resid 1105 and (name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C8 )) or (resid 1106 and (name C1 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C20 or name C3 or name C30 or name C3 \ 1 or name C32 or name C33 or name C34 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 1107 and (name C1 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C5 or name C6 or name \ C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or nam \ e O30 or name O4 or name O7 or name P1 )) or (resid 1108 and (name C1 or name C1 \ 1 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C5 or name C6 or nam \ e C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or n \ ame O30 or name O4 or name O7 or name P1 )) or (resid 1109 and (name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C18 or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C5 or name C6 or name C8 o \ r name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O3 \ 0 or name O4 or name O7 or name P1 )))) } 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: 0.350 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: 0.030 Extract box with map and model: 3.140 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 62.390 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 : 0.008 0.087 24709 Z= 0.526 Angle : 1.401 18.343 33279 Z= 0.637 Chirality : 0.059 0.328 3815 Planarity : 0.008 0.065 4144 Dihedral : 16.650 174.905 9441 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.57 % Favored : 93.00 % Rotamer: Outliers : 1.74 % Allowed : 6.91 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -4.66 (0.12), residues: 3030 helix: -3.10 (0.09), residues: 1492 sheet: -2.44 (0.23), residues: 407 loop : -3.03 (0.15), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 754 HIS 0.004 0.001 HIS C 338 PHE 0.037 0.003 PHE A 572 TYR 0.039 0.003 TYR A 49 ARG 0.013 0.001 ARG C 717 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 604 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable