Starting phenix.real_space_refine on Sat Sep 28 17:36:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl8_40575/09_2024/8sl8_40575.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl8_40575/09_2024/8sl8_40575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl8_40575/09_2024/8sl8_40575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl8_40575/09_2024/8sl8_40575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl8_40575/09_2024/8sl8_40575.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl8_40575/09_2024/8sl8_40575.cif" } resolution = 4.2 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= 0.022 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 48 5.16 5 C 12460 2.51 5 N 3516 2.21 5 O 3664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19688 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 4922 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 393} Link IDs: {'PTRANS': 28, 'TRANS': 759} Chain breaks: 14 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1547 Unresolved non-hydrogen angles: 1961 Unresolved non-hydrogen dihedrals: 1298 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 12, 'TYR:plan': 11, 'ASN:plan1': 8, 'TRP:plan': 7, 'ASP:plan': 23, 'PHE:plan': 27, 'GLU:plan': 40, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 878 Restraints were copied for chains: C, B, D Time building chain proxies: 11.75, per 1000 atoms: 0.60 Number of scatterers: 19688 At special positions: 0 Unit cell: (141.48, 141.48, 155.52, 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 48 16.00 O 3664 8.00 N 3516 7.00 C 12460 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.47 Conformation dependent library (CDL) restraints added in 3.1 seconds 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6032 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 4 sheets defined 79.3% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'B' and resid 48 through 58 removed outlier: 3.719A pdb=" N LEU B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 262 through 272 removed outlier: 4.003A pdb=" N GLY B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 329 through 345 removed outlier: 3.785A pdb=" N HIS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 345 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 362 removed outlier: 3.892A pdb=" N ASP B 353 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 379 through 393 removed outlier: 3.599A pdb=" N LEU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU B 385 " --> pdb=" O CYS B 381 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 405 removed outlier: 4.028A pdb=" N VAL B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 414 through 424 Processing helix chain 'B' and resid 429 through 446 Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.501A pdb=" N ASP B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 removed outlier: 3.511A pdb=" N MET B 539 " --> pdb=" O TYR B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 561 removed outlier: 3.540A pdb=" N ALA B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS B 559 " --> pdb=" O LYS B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 571 Processing helix chain 'B' and resid 574 through 590 removed outlier: 3.885A pdb=" N LEU B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 609 through 618 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 645 through 655 removed outlier: 3.912A pdb=" N CYS B 655 " --> pdb=" O GLY B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 719 through 727 Processing helix chain 'B' and resid 729 through 757 removed outlier: 3.810A pdb=" N LEU B 753 " --> pdb=" O SER B 749 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL B 754 " --> pdb=" O TYR B 750 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 786 removed outlier: 4.563A pdb=" N PHE B 775 " --> pdb=" O TYR B 771 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N THR B 776 " --> pdb=" O PHE B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 826 removed outlier: 3.586A pdb=" N PHE B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 818 " --> pdb=" O ILE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 851 removed outlier: 4.283A pdb=" N LEU B 837 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE B 844 " --> pdb=" O ASP B 840 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR B 845 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS B 850 " --> pdb=" O LEU B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 868 removed outlier: 4.483A pdb=" N LYS B 861 " --> pdb=" O GLN B 857 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 863 " --> pdb=" O GLY B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 895 removed outlier: 3.687A pdb=" N PHE B 875 " --> pdb=" O ASP B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 917 removed outlier: 4.824A pdb=" N ARG B 911 " --> pdb=" O ARG B 907 " (cutoff:3.500A) Proline residue: B 912 - end of helix Processing helix chain 'B' and resid 921 through 926 Processing helix chain 'B' and resid 959 through 1006 removed outlier: 3.537A pdb=" N PHE B 977 " --> pdb=" O LEU B 973 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 981 " --> pdb=" O PHE B 977 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLN B 982 " --> pdb=" O SER B 978 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY B 986 " --> pdb=" O GLN B 982 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET B 990 " --> pdb=" O GLY B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1027 removed outlier: 3.748A pdb=" N LEU B1015 " --> pdb=" O PRO B1011 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1071 Processing helix chain 'B' and resid 1072 through 1092 Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.719A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 262 through 272 removed outlier: 4.003A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 329 through 345 removed outlier: 3.785A pdb=" N HIS A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 removed outlier: 3.892A pdb=" N ASP A 353 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.598A pdb=" N LEU A 383 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 removed outlier: 4.028A pdb=" N VAL A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 429 through 446 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.501A pdb=" N ASP A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.512A pdb=" N MET A 539 " --> pdb=" O TYR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 561 removed outlier: 3.540A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 Processing helix chain 'A' and resid 574 through 590 removed outlier: 3.885A pdb=" N LEU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 606 Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 645 through 655 removed outlier: 3.912A pdb=" N CYS A 655 " --> pdb=" O GLY A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 729 through 757 removed outlier: 3.810A pdb=" N LEU A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 754 " --> pdb=" O TYR A 750 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 786 removed outlier: 4.564A pdb=" N PHE A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N THR A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 826 removed outlier: 3.586A pdb=" N PHE A 817 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 851 removed outlier: 4.283A pdb=" N LEU A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE A 844 " --> pdb=" O ASP A 840 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR A 845 " --> pdb=" O PHE A 841 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 removed outlier: 4.483A pdb=" N LYS A 861 " --> pdb=" O GLN A 857 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 863 " --> pdb=" O GLY A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 895 removed outlier: 3.687A pdb=" N PHE A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 917 removed outlier: 4.824A pdb=" N ARG A 911 " --> pdb=" O ARG A 907 " (cutoff:3.500A) Proline residue: A 912 - end of helix Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 959 through 1006 removed outlier: 3.537A pdb=" N PHE A 977 " --> pdb=" O LEU A 973 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLN A 982 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 983 " --> pdb=" O TYR A 979 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY A 986 " --> pdb=" O GLN A 982 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 990 " --> pdb=" O GLY A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1027 removed outlier: 3.748A pdb=" N LEU A1015 " --> pdb=" O PRO A1011 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1071 Processing helix chain 'A' and resid 1072 through 1092 Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.719A pdb=" N LEU C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 239 through 249 Processing helix chain 'C' and resid 262 through 272 removed outlier: 4.003A pdb=" N GLY C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 289 Processing helix chain 'C' and resid 296 through 310 Processing helix chain 'C' and resid 329 through 345 removed outlier: 3.785A pdb=" N HIS C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 345 " --> pdb=" O CYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 362 removed outlier: 3.892A pdb=" N ASP C 353 " --> pdb=" O GLN C 349 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU C 354 " --> pdb=" O ASP C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 379 through 393 removed outlier: 3.599A pdb=" N LEU C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 405 removed outlier: 4.029A pdb=" N VAL C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 414 through 424 Processing helix chain 'C' and resid 429 through 446 Processing helix chain 'C' and resid 465 through 478 Processing helix chain 'C' and resid 515 through 527 removed outlier: 3.501A pdb=" N ASP C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 539 removed outlier: 3.511A pdb=" N MET C 539 " --> pdb=" O TYR C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 561 removed outlier: 3.540A pdb=" N ALA C 546 " --> pdb=" O GLU C 542 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS C 559 " --> pdb=" O LYS C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 571 Processing helix chain 'C' and resid 574 through 590 removed outlier: 3.885A pdb=" N LEU C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 599 Processing helix chain 'C' and resid 602 through 606 Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 637 Processing helix chain 'C' and resid 645 through 655 removed outlier: 3.912A pdb=" N CYS C 655 " --> pdb=" O GLY C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 662 Processing helix chain 'C' and resid 719 through 727 Processing helix chain 'C' and resid 729 through 757 removed outlier: 3.810A pdb=" N LEU C 753 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL C 754 " --> pdb=" O TYR C 750 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 786 removed outlier: 4.563A pdb=" N PHE C 775 " --> pdb=" O TYR C 771 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR C 776 " --> pdb=" O PHE C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 826 removed outlier: 3.586A pdb=" N PHE C 817 " --> pdb=" O ALA C 813 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 818 " --> pdb=" O ILE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 851 removed outlier: 4.284A pdb=" N LEU C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE C 844 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR C 845 " --> pdb=" O PHE C 841 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS C 850 " --> pdb=" O LEU C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 868 removed outlier: 4.482A pdb=" N LYS C 861 " --> pdb=" O GLN C 857 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 863 " --> pdb=" O GLY C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 895 removed outlier: 3.688A pdb=" N PHE C 875 " --> pdb=" O ASP C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 917 removed outlier: 4.823A pdb=" N ARG C 911 " --> pdb=" O ARG C 907 " (cutoff:3.500A) Proline residue: C 912 - end of helix Processing helix chain 'C' and resid 921 through 926 Processing helix chain 'C' and resid 959 through 1006 removed outlier: 3.537A pdb=" N PHE C 977 " --> pdb=" O LEU C 973 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 981 " --> pdb=" O PHE C 977 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLN C 982 " --> pdb=" O SER C 978 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL C 983 " --> pdb=" O TYR C 979 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 984 " --> pdb=" O THR C 980 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY C 986 " --> pdb=" O GLN C 982 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET C 990 " --> pdb=" O GLY C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1027 removed outlier: 3.749A pdb=" N LEU C1015 " --> pdb=" O PRO C1011 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU C1016 " --> pdb=" O PRO C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1044 through 1071 Processing helix chain 'C' and resid 1072 through 1092 Processing helix chain 'D' and resid 48 through 58 removed outlier: 3.719A pdb=" N LEU D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 97 Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 239 through 249 Processing helix chain 'D' and resid 262 through 272 removed outlier: 4.003A pdb=" N GLY D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 289 Processing helix chain 'D' and resid 296 through 310 Processing helix chain 'D' and resid 329 through 345 removed outlier: 3.784A pdb=" N HIS D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 345 " --> pdb=" O CYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 362 removed outlier: 3.892A pdb=" N ASP D 353 " --> pdb=" O GLN D 349 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU D 354 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 379 through 393 removed outlier: 3.599A pdb=" N LEU D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU D 385 " --> pdb=" O CYS D 381 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 405 removed outlier: 4.028A pdb=" N VAL D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 414 through 424 Processing helix chain 'D' and resid 429 through 446 Processing helix chain 'D' and resid 465 through 478 Processing helix chain 'D' and resid 515 through 527 removed outlier: 3.500A pdb=" N ASP D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.511A pdb=" N MET D 539 " --> pdb=" O TYR D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 561 removed outlier: 3.540A pdb=" N ALA D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS D 559 " --> pdb=" O LYS D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 571 Processing helix chain 'D' and resid 574 through 590 removed outlier: 3.885A pdb=" N LEU D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 599 Processing helix chain 'D' and resid 602 through 606 Processing helix chain 'D' and resid 609 through 618 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 645 through 655 removed outlier: 3.911A pdb=" N CYS D 655 " --> pdb=" O GLY D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 662 Processing helix chain 'D' and resid 719 through 727 Processing helix chain 'D' and resid 729 through 757 removed outlier: 3.811A pdb=" N LEU D 753 " --> pdb=" O SER D 749 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL D 754 " --> pdb=" O TYR D 750 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG D 757 " --> pdb=" O LEU D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 786 removed outlier: 4.564A pdb=" N PHE D 775 " --> pdb=" O TYR D 771 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N THR D 776 " --> pdb=" O PHE D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 826 removed outlier: 3.586A pdb=" N PHE D 817 " --> pdb=" O ALA D 813 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 818 " --> pdb=" O ILE D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 851 removed outlier: 4.284A pdb=" N LEU D 837 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET D 842 " --> pdb=" O ALA D 838 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL D 843 " --> pdb=" O ILE D 839 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE D 844 " --> pdb=" O ASP D 840 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR D 845 " --> pdb=" O PHE D 841 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS D 850 " --> pdb=" O LEU D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 868 removed outlier: 4.483A pdb=" N LYS D 861 " --> pdb=" O GLN D 857 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 863 " --> pdb=" O GLY D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 895 removed outlier: 3.687A pdb=" N PHE D 875 " --> pdb=" O ASP D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 917 removed outlier: 4.824A pdb=" N ARG D 911 " --> pdb=" O ARG D 907 " (cutoff:3.500A) Proline residue: D 912 - end of helix Processing helix chain 'D' and resid 921 through 926 Processing helix chain 'D' and resid 959 through 1006 removed outlier: 3.537A pdb=" N PHE D 977 " --> pdb=" O LEU D 973 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 981 " --> pdb=" O PHE D 977 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLN D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL D 983 " --> pdb=" O TYR D 979 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 984 " --> pdb=" O THR D 980 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY D 986 " --> pdb=" O GLN D 982 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET D 990 " --> pdb=" O GLY D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1027 removed outlier: 3.748A pdb=" N LEU D1015 " --> pdb=" O PRO D1011 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU D1016 " --> pdb=" O PRO D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1044 through 1071 Processing helix chain 'D' and resid 1072 through 1092 Processing sheet with id=AA1, first strand: chain 'B' and resid 103 through 104 removed outlier: 6.126A pdb=" N VAL B 69 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 317 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 removed outlier: 6.126A pdb=" N VAL A 69 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 317 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 103 through 104 removed outlier: 6.127A pdb=" N VAL C 69 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 317 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 103 through 104 removed outlier: 6.126A pdb=" N VAL D 69 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 317 " --> pdb=" O TRP D 253 " (cutoff:3.500A) 1656 hydrogen bonds defined for protein. 4944 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: 6.90 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6790 1.34 - 1.46: 3551 1.46 - 1.57: 9611 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 20024 Sorted by residual: bond pdb=" CG1 ILE A 554 " pdb=" CD1 ILE A 554 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.83e+00 bond pdb=" CG1 ILE C 554 " pdb=" CD1 ILE C 554 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.81e+00 bond pdb=" CG1 ILE D 554 " pdb=" CD1 ILE D 554 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.81e+00 bond pdb=" CG1 ILE B 554 " pdb=" CD1 ILE B 554 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.81e+00 bond pdb=" CB ILE B 554 " pdb=" CG2 ILE B 554 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.41e+00 ... (remaining 20019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 26570 1.51 - 3.03: 910 3.03 - 4.54: 78 4.54 - 6.06: 58 6.06 - 7.57: 16 Bond angle restraints: 27632 Sorted by residual: angle pdb=" N ALA C 641 " pdb=" CA ALA C 641 " pdb=" C ALA C 641 " ideal model delta sigma weight residual 111.28 116.82 -5.54 1.09e+00 8.42e-01 2.58e+01 angle pdb=" N ALA B 641 " pdb=" CA ALA B 641 " pdb=" C ALA B 641 " ideal model delta sigma weight residual 111.28 116.80 -5.52 1.09e+00 8.42e-01 2.56e+01 angle pdb=" N ALA A 641 " pdb=" CA ALA A 641 " pdb=" C ALA A 641 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" C LEU B 229 " pdb=" N CYS B 230 " pdb=" CA CYS B 230 " ideal model delta sigma weight residual 122.94 115.37 7.57 1.50e+00 4.44e-01 2.55e+01 angle pdb=" C LEU C 229 " pdb=" N CYS C 230 " pdb=" CA CYS C 230 " ideal model delta sigma weight residual 122.94 115.37 7.57 1.50e+00 4.44e-01 2.55e+01 ... (remaining 27627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 10808 15.04 - 30.08: 504 30.08 - 45.13: 140 45.13 - 60.17: 28 60.17 - 75.21: 12 Dihedral angle restraints: 11492 sinusoidal: 2336 harmonic: 9156 Sorted by residual: dihedral pdb=" CA GLU A 377 " pdb=" C GLU A 377 " pdb=" N TRP A 378 " pdb=" CA TRP A 378 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA GLU D 377 " pdb=" C GLU D 377 " pdb=" N TRP D 378 " pdb=" CA TRP D 378 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA GLU B 377 " pdb=" C GLU B 377 " pdb=" N TRP B 378 " pdb=" CA TRP B 378 " ideal model delta harmonic sigma weight residual -180.00 -158.16 -21.84 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 11489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3311 0.076 - 0.152: 155 0.152 - 0.229: 6 0.229 - 0.305: 8 0.305 - 0.381: 4 Chirality restraints: 3484 Sorted by residual: chirality pdb=" CB ILE D 554 " pdb=" CA ILE D 554 " pdb=" CG1 ILE D 554 " pdb=" CG2 ILE D 554 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB ILE B 554 " pdb=" CA ILE B 554 " pdb=" CG1 ILE B 554 " pdb=" CG2 ILE B 554 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE C 554 " pdb=" CA ILE C 554 " pdb=" CG1 ILE C 554 " pdb=" CG2 ILE C 554 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 3481 not shown) Planarity restraints: 3636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 570 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C MET A 570 " 0.030 2.00e-02 2.50e+03 pdb=" O MET A 570 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 571 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 570 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C MET B 570 " 0.029 2.00e-02 2.50e+03 pdb=" O MET B 570 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 571 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 570 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C MET C 570 " -0.029 2.00e-02 2.50e+03 pdb=" O MET C 570 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG C 571 " 0.010 2.00e-02 2.50e+03 ... (remaining 3633 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2293 2.74 - 3.28: 22208 3.28 - 3.82: 33919 3.82 - 4.36: 32984 4.36 - 4.90: 56147 Nonbonded interactions: 147551 Sorted by model distance: nonbonded pdb=" O GLU A 385 " pdb=" OG1 THR A 388 " model vdw 2.201 3.040 nonbonded pdb=" O GLU B 385 " pdb=" OG1 THR B 388 " model vdw 2.202 3.040 nonbonded pdb=" O GLU C 385 " pdb=" OG1 THR C 388 " model vdw 2.202 3.040 nonbonded pdb=" O GLU D 385 " pdb=" OG1 THR D 388 " model vdw 2.202 3.040 nonbonded pdb=" N VAL A 68 " pdb=" O PRO A 227 " model vdw 2.212 3.120 ... (remaining 147546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 3.860 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: 0.710 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 44.970 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.004 0.066 20024 Z= 0.250 Angle : 0.678 7.570 27632 Z= 0.451 Chirality : 0.041 0.381 3484 Planarity : 0.003 0.034 3636 Dihedral : 10.975 75.209 5460 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3032 helix: -0.16 (0.10), residues: 2316 sheet: 0.41 (0.58), residues: 84 loop : -1.89 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 636 HIS 0.005 0.001 HIS A 998 PHE 0.014 0.001 PHE C 994 TYR 0.010 0.001 TYR D 535 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 773 TRP cc_start: 0.7613 (m100) cc_final: 0.6918 (m100) REVERT: B 882 TRP cc_start: 0.9269 (t-100) cc_final: 0.9051 (t-100) REVERT: B 1050 ILE cc_start: 0.9615 (mt) cc_final: 0.9382 (tp) REVERT: B 1057 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8379 (tp40) REVERT: A 398 PHE cc_start: 0.8067 (m-80) cc_final: 0.7864 (m-80) REVERT: A 409 MET cc_start: 0.8650 (mmm) cc_final: 0.8428 (mmp) REVERT: A 420 GLN cc_start: 0.8872 (tt0) cc_final: 0.8310 (tp-100) REVERT: A 773 TRP cc_start: 0.7624 (m100) cc_final: 0.6705 (m100) REVERT: A 1050 ILE cc_start: 0.9593 (mt) cc_final: 0.9323 (tp) REVERT: A 1057 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8401 (tp40) REVERT: C 773 TRP cc_start: 0.7538 (m100) cc_final: 0.6735 (m100) REVERT: C 1050 ILE cc_start: 0.9590 (mt) cc_final: 0.9318 (tp) REVERT: C 1057 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8510 (tp40) REVERT: D 773 TRP cc_start: 0.7450 (m100) cc_final: 0.6597 (m100) REVERT: D 845 THR cc_start: 0.9495 (p) cc_final: 0.9290 (p) REVERT: D 1050 ILE cc_start: 0.9604 (mt) cc_final: 0.9309 (tp) REVERT: D 1057 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8507 (tp40) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2347 time to fit residues: 76.7030 Evaluate side-chains 149 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 10.0000 chunk 236 optimal weight: 40.0000 chunk 131 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 50.0000 chunk 126 optimal weight: 50.0000 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 283 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 HIS B 528 ASN B 602 ASN A 439 HIS A 528 ASN A 602 ASN C 439 HIS C 528 ASN C 602 ASN C1048 GLN D 439 HIS D 528 ASN D 602 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20024 Z= 0.174 Angle : 0.472 6.437 27632 Z= 0.262 Chirality : 0.036 0.163 3484 Planarity : 0.003 0.037 3636 Dihedral : 3.951 23.156 3172 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.34 % Allowed : 4.83 % Favored : 94.83 % 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: 1.84 (0.15), residues: 3032 helix: 1.87 (0.10), residues: 2360 sheet: 0.32 (0.58), residues: 84 loop : -1.34 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 605 HIS 0.005 0.001 HIS C 998 PHE 0.011 0.001 PHE B 631 TYR 0.012 0.001 TYR A 535 ARG 0.004 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 194 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 422 TYR cc_start: 0.8232 (m-80) cc_final: 0.7223 (m-80) REVERT: B 773 TRP cc_start: 0.7855 (m100) cc_final: 0.7195 (m100) REVERT: B 1057 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8367 (tp40) REVERT: A 1057 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8375 (tp40) REVERT: C 422 TYR cc_start: 0.8240 (m-80) cc_final: 0.7231 (m-80) REVERT: C 773 TRP cc_start: 0.7814 (m100) cc_final: 0.6982 (m100) REVERT: C 1057 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8412 (tp40) REVERT: D 422 TYR cc_start: 0.8367 (m-80) cc_final: 0.7363 (m-80) REVERT: D 773 TRP cc_start: 0.7733 (m100) cc_final: 0.6908 (m100) REVERT: D 1057 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8428 (tp40) outliers start: 4 outliers final: 0 residues processed: 198 average time/residue: 0.2585 time to fit residues: 86.2012 Evaluate side-chains 146 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 235 optimal weight: 7.9990 chunk 192 optimal weight: 0.6980 chunk 78 optimal weight: 70.0000 chunk 283 optimal weight: 5.9990 chunk 306 optimal weight: 30.0000 chunk 252 optimal weight: 0.0470 chunk 281 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 overall best weight: 2.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN C 528 ASN D 528 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20024 Z= 0.193 Angle : 0.476 6.539 27632 Z= 0.261 Chirality : 0.036 0.185 3484 Planarity : 0.003 0.037 3636 Dihedral : 3.816 23.186 3172 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.25 % Allowed : 4.24 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.15), residues: 3032 helix: 2.45 (0.11), residues: 2344 sheet: 0.64 (0.62), residues: 84 loop : -1.34 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 361 HIS 0.004 0.001 HIS C 998 PHE 0.014 0.001 PHE A 631 TYR 0.016 0.001 TYR D 535 ARG 0.002 0.000 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 2.332 Fit side-chains REVERT: B 422 TYR cc_start: 0.8346 (m-80) cc_final: 0.7346 (m-80) REVERT: B 773 TRP cc_start: 0.7940 (m100) cc_final: 0.7268 (m100) REVERT: B 1057 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8432 (tp40) REVERT: A 1057 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8430 (tp40) REVERT: C 422 TYR cc_start: 0.8350 (m-80) cc_final: 0.7343 (m-80) REVERT: C 842 MET cc_start: 0.8551 (mmp) cc_final: 0.8340 (mmp) REVERT: C 1057 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8464 (tp40) REVERT: D 422 TYR cc_start: 0.8470 (m-80) cc_final: 0.8255 (m-80) REVERT: D 842 MET cc_start: 0.8706 (mmp) cc_final: 0.8490 (mmp) REVERT: D 1057 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8471 (tp40) outliers start: 3 outliers final: 3 residues processed: 176 average time/residue: 0.2208 time to fit residues: 68.6898 Evaluate side-chains 143 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 5.9990 chunk 213 optimal weight: 40.0000 chunk 147 optimal weight: 7.9990 chunk 31 optimal weight: 0.0980 chunk 135 optimal weight: 20.0000 chunk 190 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 301 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 chunk 81 optimal weight: 50.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 612 HIS A 612 HIS C 612 HIS D 612 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20024 Z= 0.226 Angle : 0.512 8.019 27632 Z= 0.277 Chirality : 0.037 0.175 3484 Planarity : 0.004 0.037 3636 Dihedral : 3.951 22.302 3172 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.15), residues: 3032 helix: 2.45 (0.11), residues: 2360 sheet: 0.53 (0.65), residues: 84 loop : -1.23 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 517 HIS 0.005 0.001 HIS C 998 PHE 0.017 0.002 PHE A 631 TYR 0.019 0.002 TYR D 535 ARG 0.004 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.189 Fit side-chains REVERT: B 634 LYS cc_start: 0.9346 (tmtt) cc_final: 0.9129 (tptp) REVERT: B 842 MET cc_start: 0.8810 (mmp) cc_final: 0.8584 (mmp) REVERT: B 1057 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8477 (tp40) REVERT: A 1057 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8505 (tp40) REVERT: C 1057 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8527 (tp40) REVERT: D 422 TYR cc_start: 0.8561 (m-80) cc_final: 0.8332 (m-80) REVERT: D 1057 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8542 (tp40) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2424 time to fit residues: 70.7808 Evaluate side-chains 137 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 4 optimal weight: 50.0000 chunk 224 optimal weight: 2.9990 chunk 124 optimal weight: 0.0870 chunk 257 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 0 optimal weight: 90.0000 chunk 153 optimal weight: 5.9990 chunk 270 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20024 Z= 0.158 Angle : 0.461 6.415 27632 Z= 0.247 Chirality : 0.035 0.128 3484 Planarity : 0.003 0.036 3636 Dihedral : 3.717 20.941 3172 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.16), residues: 3032 helix: 2.63 (0.11), residues: 2368 sheet: 0.70 (0.65), residues: 84 loop : -1.32 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D1053 HIS 0.003 0.001 HIS C 612 PHE 0.010 0.001 PHE D 631 TYR 0.013 0.001 TYR B 535 ARG 0.002 0.000 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.660 Fit side-chains revert: symmetry clash REVERT: B 422 TYR cc_start: 0.8399 (m-80) cc_final: 0.7320 (m-80) REVERT: C 422 TYR cc_start: 0.8359 (m-80) cc_final: 0.7268 (m-80) REVERT: D 422 TYR cc_start: 0.8509 (m-80) cc_final: 0.8236 (m-80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1950 time to fit residues: 60.2943 Evaluate side-chains 142 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 301 optimal weight: 4.9990 chunk 250 optimal weight: 50.0000 chunk 139 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1060 ASN C1060 ASN D1060 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20024 Z= 0.275 Angle : 0.555 6.531 27632 Z= 0.305 Chirality : 0.037 0.138 3484 Planarity : 0.004 0.040 3636 Dihedral : 4.054 23.188 3172 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: 2.53 (0.15), residues: 3032 helix: 2.40 (0.11), residues: 2356 sheet: 0.50 (0.66), residues: 84 loop : -1.26 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 773 HIS 0.007 0.001 HIS D 612 PHE 0.022 0.002 PHE B 631 TYR 0.023 0.002 TYR B 535 ARG 0.004 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.292 Fit side-chains REVERT: A 398 PHE cc_start: 0.8077 (m-80) cc_final: 0.7799 (m-80) REVERT: C 398 PHE cc_start: 0.8077 (m-80) cc_final: 0.7807 (m-80) REVERT: D 398 PHE cc_start: 0.8061 (m-80) cc_final: 0.7826 (m-80) REVERT: D 422 TYR cc_start: 0.8515 (m-80) cc_final: 0.8204 (m-80) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2214 time to fit residues: 66.1550 Evaluate side-chains 139 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 300 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 HIS D 423 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20024 Z= 0.363 Angle : 0.636 9.026 27632 Z= 0.353 Chirality : 0.039 0.131 3484 Planarity : 0.004 0.045 3636 Dihedral : 4.572 25.263 3172 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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: 1.85 (0.15), residues: 3032 helix: 1.94 (0.11), residues: 2360 sheet: -0.16 (0.67), residues: 84 loop : -1.57 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 361 HIS 0.012 0.002 HIS C 612 PHE 0.024 0.002 PHE D 631 TYR 0.026 0.003 TYR B 535 ARG 0.006 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.177 Fit side-chains REVERT: B 398 PHE cc_start: 0.8036 (m-80) cc_final: 0.7731 (m-80) REVERT: D 634 LYS cc_start: 0.9366 (tmtt) cc_final: 0.9165 (tptp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2169 time to fit residues: 61.8152 Evaluate side-chains 135 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 90 optimal weight: 30.0000 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 204 optimal weight: 30.0000 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 236 optimal weight: 0.3980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1060 ASN D1060 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20024 Z= 0.171 Angle : 0.505 7.393 27632 Z= 0.267 Chirality : 0.035 0.124 3484 Planarity : 0.003 0.036 3636 Dihedral : 3.956 23.070 3172 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 2.52 (0.16), residues: 3032 helix: 2.45 (0.11), residues: 2368 sheet: -0.20 (0.65), residues: 84 loop : -1.49 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 523 HIS 0.003 0.001 HIS D 612 PHE 0.013 0.001 PHE D 841 TYR 0.012 0.001 TYR D 422 ARG 0.002 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.160 Fit side-chains REVERT: B 422 TYR cc_start: 0.8410 (m-80) cc_final: 0.7277 (m-80) REVERT: C 422 TYR cc_start: 0.8314 (m-80) cc_final: 0.7201 (m-80) REVERT: D 634 LYS cc_start: 0.9335 (tmtt) cc_final: 0.9123 (tptp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2160 time to fit residues: 65.1461 Evaluate side-chains 136 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 1.9990 chunk 288 optimal weight: 20.0000 chunk 262 optimal weight: 1.9990 chunk 280 optimal weight: 20.0000 chunk 168 optimal weight: 0.4980 chunk 122 optimal weight: 0.2980 chunk 220 optimal weight: 30.0000 chunk 85 optimal weight: 50.0000 chunk 253 optimal weight: 20.0000 chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20024 Z= 0.158 Angle : 0.487 7.182 27632 Z= 0.254 Chirality : 0.035 0.124 3484 Planarity : 0.003 0.036 3636 Dihedral : 3.661 21.990 3172 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.16), residues: 3032 helix: 2.75 (0.11), residues: 2368 sheet: -0.24 (0.63), residues: 84 loop : -1.50 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 882 HIS 0.005 0.001 HIS B 314 PHE 0.011 0.001 PHE C 631 TYR 0.012 0.001 TYR A 535 ARG 0.003 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.304 Fit side-chains REVERT: B 316 LEU cc_start: 0.8306 (pp) cc_final: 0.8039 (mm) REVERT: B 398 PHE cc_start: 0.7817 (m-80) cc_final: 0.7531 (m-80) REVERT: B 422 TYR cc_start: 0.8395 (m-80) cc_final: 0.7306 (m-80) REVERT: B 1057 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8612 (tp40) REVERT: A 398 PHE cc_start: 0.7851 (m-80) cc_final: 0.7538 (m-80) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2219 time to fit residues: 67.1094 Evaluate side-chains 138 residues out of total 2752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.135 > 50: distance: 10 - 31: 25.459 distance: 13 - 16: 23.562 distance: 14 - 36: 33.826 distance: 16 - 17: 21.679 distance: 17 - 18: 33.752 distance: 17 - 20: 39.359 distance: 18 - 19: 48.851 distance: 18 - 23: 15.189 distance: 19 - 44: 52.146 distance: 20 - 21: 8.991 distance: 20 - 22: 33.521 distance: 23 - 24: 14.770 distance: 24 - 25: 57.221 distance: 24 - 27: 33.029 distance: 25 - 26: 36.453 distance: 25 - 31: 25.553 distance: 26 - 51: 39.510 distance: 27 - 28: 40.011 distance: 28 - 29: 20.367 distance: 28 - 30: 21.838 distance: 31 - 32: 43.245 distance: 32 - 33: 48.290 distance: 32 - 35: 54.278 distance: 33 - 34: 7.893 distance: 33 - 36: 8.567 distance: 36 - 37: 19.634 distance: 37 - 38: 43.400 distance: 37 - 40: 41.957 distance: 38 - 39: 5.688 distance: 38 - 44: 9.829 distance: 40 - 41: 61.314 distance: 41 - 42: 57.372 distance: 41 - 43: 34.929 distance: 44 - 45: 54.249 distance: 45 - 46: 58.356 distance: 45 - 48: 5.264 distance: 46 - 47: 20.694 distance: 46 - 51: 45.390 distance: 48 - 50: 38.834 distance: 51 - 52: 60.433 distance: 52 - 53: 44.433 distance: 52 - 55: 60.834 distance: 53 - 54: 54.680 distance: 55 - 56: 40.073 distance: 57 - 58: 22.083 distance: 58 - 59: 23.740 distance: 58 - 61: 17.123 distance: 59 - 60: 19.438 distance: 59 - 65: 15.560 distance: 61 - 62: 39.509 distance: 62 - 64: 12.982 distance: 65 - 66: 35.537 distance: 66 - 67: 35.863 distance: 66 - 69: 32.377 distance: 67 - 68: 12.962 distance: 67 - 70: 4.143 distance: 70 - 71: 45.656 distance: 70 - 76: 3.648 distance: 71 - 72: 26.348 distance: 71 - 74: 36.914 distance: 73 - 97: 34.636 distance: 74 - 75: 9.196 distance: 75 - 76: 58.984 distance: 77 - 78: 25.541 distance: 78 - 79: 6.639 distance: 78 - 81: 34.905 distance: 79 - 80: 14.006 distance: 79 - 82: 25.225 distance: 80 - 105: 21.415