Starting phenix.real_space_refine on Mon Nov 18 21:37:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sle_40577/11_2024/8sle_40577.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sle_40577/11_2024/8sle_40577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sle_40577/11_2024/8sle_40577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sle_40577/11_2024/8sle_40577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sle_40577/11_2024/8sle_40577.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sle_40577/11_2024/8sle_40577.cif" } resolution = 4.3 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 4 5.16 5 C 10424 2.51 5 N 3484 2.21 5 O 3476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17388 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 4347 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 749} Link IDs: {'PTRANS': 32, 'TRANS': 834} Chain breaks: 17 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 2845 Unresolved non-hydrogen angles: 3677 Unresolved non-hydrogen dihedrals: 2411 Unresolved non-hydrogen chiralities: 277 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 44, 'TYR:plan': 20, 'ASN:plan1': 20, 'TRP:plan': 20, 'HIS:plan': 26, 'PHE:plan': 57, 'GLU:plan': 53, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1565 Chain: "B" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 4347 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 749} Link IDs: {'PTRANS': 32, 'TRANS': 834} Chain breaks: 17 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 2845 Unresolved non-hydrogen angles: 3677 Unresolved non-hydrogen dihedrals: 2411 Unresolved non-hydrogen chiralities: 277 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 44, 'TYR:plan': 20, 'ASN:plan1': 20, 'TRP:plan': 20, 'HIS:plan': 26, 'PHE:plan': 57, 'GLU:plan': 53, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1565 Chain: "C" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 4347 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 749} Link IDs: {'PTRANS': 32, 'TRANS': 834} Chain breaks: 17 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 2845 Unresolved non-hydrogen angles: 3677 Unresolved non-hydrogen dihedrals: 2411 Unresolved non-hydrogen chiralities: 277 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 44, 'TYR:plan': 20, 'ASN:plan1': 20, 'TRP:plan': 20, 'HIS:plan': 26, 'PHE:plan': 57, 'GLU:plan': 53, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1565 Chain: "D" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 4347 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 749} Link IDs: {'PTRANS': 32, 'TRANS': 834} Chain breaks: 17 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 2845 Unresolved non-hydrogen angles: 3677 Unresolved non-hydrogen dihedrals: 2411 Unresolved non-hydrogen chiralities: 277 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 44, 'TYR:plan': 20, 'ASN:plan1': 20, 'TRP:plan': 20, 'HIS:plan': 26, 'PHE:plan': 57, 'GLU:plan': 53, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1565 Time building chain proxies: 11.57, per 1000 atoms: 0.67 Number of scatterers: 17388 At special positions: 0 Unit cell: (137.16, 137.16, 147.96, 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 4 16.00 O 3476 8.00 N 3484 7.00 C 10424 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: 5.04 Conformation dependent library (CDL) restraints added in 3.4 seconds 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6640 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 16 sheets defined 73.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.858A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 removed outlier: 4.229A pdb=" N ARG A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.714A pdb=" N LEU A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 238 through 249 removed outlier: 3.722A pdb=" N ARG A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 removed outlier: 3.738A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 329 through 345 removed outlier: 3.636A pdb=" N SER A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 removed outlier: 3.657A pdb=" N ASP A 353 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 4.467A 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: 4.772A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 removed outlier: 3.711A 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 528 removed outlier: 4.228A pdb=" N ASP A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 543 through 561 removed outlier: 4.042A pdb=" N ALA A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 603 through 606 Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 638 removed outlier: 3.665A pdb=" N GLN A 629 " --> pdb=" O HIS A 625 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TRP A 637 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 729 through 755 removed outlier: 3.769A pdb=" N LEU A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 754 " --> pdb=" O TYR A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 787 removed outlier: 4.307A pdb=" N PHE A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N THR A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN A 784 " --> pdb=" O GLU A 780 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLY A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 Processing helix chain 'A' and resid 804 through 825 removed outlier: 3.631A pdb=" N LYS A 808 " --> pdb=" O ASP A 804 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP A 810 " --> pdb=" O TRP A 806 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 813 " --> pdb=" O CYS A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 849 removed outlier: 3.930A pdb=" N LEU A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A 844 " --> pdb=" O ASP A 840 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 845 " --> pdb=" O PHE A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 860 through 894 removed outlier: 3.930A pdb=" N GLU A 866 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 878 " --> pdb=" O PHE A 874 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 894 " --> pdb=" O THR A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 916 removed outlier: 4.595A 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 990 removed outlier: 4.081A pdb=" N ASN A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET A 970 " --> pdb=" O ASN A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1006 removed outlier: 3.814A pdb=" N GLY A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1027 removed outlier: 3.758A pdb=" N LEU A1015 " --> pdb=" O PRO A1011 " (cutoff:3.500A) removed outlier: 4.361A 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 'B' and resid 48 through 59 removed outlier: 3.859A pdb=" N LEU B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE B 53 " --> pdb=" O PRO B 49 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 removed outlier: 4.229A pdb=" N ARG B 89 " --> pdb=" O ARG B 85 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.714A pdb=" N LEU B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.722A pdb=" N ARG B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 removed outlier: 3.738A pdb=" N VAL B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'B' and resid 295 through 310 Processing helix chain 'B' and resid 329 through 345 removed outlier: 3.636A pdb=" N SER B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 345 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 362 removed outlier: 3.657A pdb=" N ASP B 353 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 4.467A 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: 4.772A pdb=" N GLU B 385 " --> pdb=" O CYS B 381 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 405 removed outlier: 3.711A 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 528 removed outlier: 4.228A pdb=" N ASP B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 543 through 561 removed outlier: 4.043A pdb=" N ALA B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 571 Processing helix chain 'B' and resid 574 through 590 Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 603 through 606 Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 638 removed outlier: 3.665A pdb=" N GLN B 629 " --> pdb=" O HIS B 625 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TRP B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 655 Processing helix chain 'B' and resid 719 through 727 Processing helix chain 'B' and resid 729 through 755 removed outlier: 3.769A pdb=" N LEU B 753 " --> pdb=" O SER B 749 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 754 " --> pdb=" O TYR B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 787 removed outlier: 4.307A pdb=" N PHE B 775 " --> pdb=" O TYR B 771 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N THR B 776 " --> pdb=" O PHE B 772 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN B 784 " --> pdb=" O GLU B 780 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 802 Processing helix chain 'B' and resid 804 through 825 removed outlier: 3.631A pdb=" N LYS B 808 " --> pdb=" O ASP B 804 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS B 809 " --> pdb=" O ASN B 805 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP B 810 " --> pdb=" O TRP B 806 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 813 " --> pdb=" O CYS B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 849 removed outlier: 3.930A pdb=" N LEU B 837 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B 844 " --> pdb=" O ASP B 840 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR B 845 " --> pdb=" O PHE B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 860 through 895 removed outlier: 3.930A pdb=" N GLU B 866 " --> pdb=" O ILE B 862 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE B 875 " --> pdb=" O ASP B 871 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 878 " --> pdb=" O PHE B 874 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 893 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 916 removed outlier: 4.594A 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 990 removed outlier: 4.080A pdb=" N ASN B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET B 970 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1006 removed outlier: 3.814A pdb=" N GLY B1005 " --> pdb=" O VAL B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1027 removed outlier: 3.758A pdb=" N LEU B1015 " --> pdb=" O PRO B1011 " (cutoff:3.500A) removed outlier: 4.360A 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 'C' and resid 48 through 59 removed outlier: 3.887A pdb=" N LEU C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 53 " --> pdb=" O PRO C 49 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 98 removed outlier: 4.229A pdb=" N ARG C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL C 93 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.714A pdb=" N LEU C 125 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 238 through 249 removed outlier: 3.721A pdb=" N ARG C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 removed outlier: 3.738A pdb=" N VAL C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 295 through 310 Processing helix chain 'C' and resid 329 through 345 removed outlier: 3.636A pdb=" N SER C 343 " --> pdb=" O LYS C 339 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER C 345 " --> pdb=" O CYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 362 removed outlier: 3.657A pdb=" N ASP C 353 " --> pdb=" O GLN C 349 " (cutoff:3.500A) removed outlier: 4.468A 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: 4.773A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 405 removed outlier: 3.711A 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 528 removed outlier: 4.228A pdb=" N ASP C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 540 Processing helix chain 'C' and resid 543 through 561 removed outlier: 4.042A pdb=" N ALA C 547 " --> pdb=" O GLY C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 571 Processing helix chain 'C' and resid 574 through 590 Processing helix chain 'C' and resid 592 through 599 Processing helix chain 'C' and resid 603 through 606 Processing helix chain 'C' and resid 610 through 617 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 638 removed outlier: 3.664A pdb=" N GLN C 629 " --> pdb=" O HIS C 625 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TRP C 637 " --> pdb=" O THR C 633 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 655 Processing helix chain 'C' and resid 719 through 727 Processing helix chain 'C' and resid 729 through 755 removed outlier: 3.768A pdb=" N LEU C 753 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 754 " --> pdb=" O TYR C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 787 removed outlier: 4.307A pdb=" N PHE C 775 " --> pdb=" O TYR C 771 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N THR C 776 " --> pdb=" O PHE C 772 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN C 784 " --> pdb=" O GLU C 780 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY C 785 " --> pdb=" O GLU C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 802 Processing helix chain 'C' and resid 804 through 825 removed outlier: 3.631A pdb=" N LYS C 808 " --> pdb=" O ASP C 804 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS C 809 " --> pdb=" O ASN C 805 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP C 810 " --> pdb=" O TRP C 806 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 813 " --> pdb=" O CYS C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 849 removed outlier: 3.929A pdb=" N LEU C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N MET C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE C 844 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR C 845 " --> pdb=" O PHE C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 854 Processing helix chain 'C' and resid 860 through 895 removed outlier: 3.930A pdb=" N GLU C 866 " --> pdb=" O ILE C 862 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG C 867 " --> pdb=" O ILE C 863 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE C 874 " --> pdb=" O LYS C 870 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE C 875 " --> pdb=" O ASP C 871 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE C 878 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 916 removed outlier: 4.595A 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 990 removed outlier: 4.081A pdb=" N ASN C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET C 970 " --> pdb=" O ASN C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1006 removed outlier: 3.814A pdb=" N GLY C1005 " --> pdb=" O VAL C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1027 removed outlier: 3.758A pdb=" N LEU C1015 " --> pdb=" O PRO C1011 " (cutoff:3.500A) removed outlier: 4.361A 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 59 removed outlier: 3.864A pdb=" N LEU D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE D 53 " --> pdb=" O PRO D 49 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 removed outlier: 4.229A pdb=" N ARG D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.715A pdb=" N LEU D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 238 through 249 removed outlier: 3.722A pdb=" N ARG D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 removed outlier: 3.738A pdb=" N VAL D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'D' and resid 295 through 310 Processing helix chain 'D' and resid 329 through 345 removed outlier: 3.636A pdb=" N SER D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER D 345 " --> pdb=" O CYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 362 removed outlier: 3.657A pdb=" N ASP D 353 " --> pdb=" O GLN D 349 " (cutoff:3.500A) removed outlier: 4.467A 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: 4.773A pdb=" N GLU D 385 " --> pdb=" O CYS D 381 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.711A 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 528 removed outlier: 4.228A pdb=" N ASP D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 543 through 561 removed outlier: 4.043A pdb=" N ALA D 547 " --> pdb=" O GLY D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 571 Processing helix chain 'D' and resid 574 through 590 Processing helix chain 'D' and resid 592 through 599 Processing helix chain 'D' and resid 603 through 606 Processing helix chain 'D' and resid 610 through 617 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 625 through 638 removed outlier: 3.665A pdb=" N GLN D 629 " --> pdb=" O HIS D 625 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY D 638 " --> pdb=" O LYS D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 655 Processing helix chain 'D' and resid 719 through 727 Processing helix chain 'D' and resid 729 through 755 removed outlier: 3.768A pdb=" N LEU D 753 " --> pdb=" O SER D 749 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL D 754 " --> pdb=" O TYR D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 787 removed outlier: 4.306A pdb=" N PHE D 775 " --> pdb=" O TYR D 771 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N THR D 776 " --> pdb=" O PHE D 772 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN D 784 " --> pdb=" O GLU D 780 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY D 785 " --> pdb=" O GLU D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 802 Processing helix chain 'D' and resid 804 through 825 removed outlier: 3.631A pdb=" N LYS D 808 " --> pdb=" O ASP D 804 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP D 810 " --> pdb=" O TRP D 806 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 813 " --> pdb=" O CYS D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 849 removed outlier: 3.930A pdb=" N LEU D 837 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET D 842 " --> pdb=" O ALA D 838 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL D 843 " --> pdb=" O ILE D 839 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE D 844 " --> pdb=" O ASP D 840 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR D 845 " --> pdb=" O PHE D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 854 Processing helix chain 'D' and resid 860 through 895 removed outlier: 3.930A pdb=" N GLU D 866 " --> pdb=" O ILE D 862 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG D 867 " --> pdb=" O ILE D 863 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE D 874 " --> pdb=" O LYS D 870 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE D 875 " --> pdb=" O ASP D 871 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE D 878 " --> pdb=" O PHE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 916 removed outlier: 4.595A 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 990 removed outlier: 4.081A pdb=" N ASN D 966 " --> pdb=" O LEU D 962 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET D 970 " --> pdb=" O ASN D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 1006 removed outlier: 3.813A pdb=" N GLY D1005 " --> pdb=" O VAL D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1027 removed outlier: 3.758A pdb=" N LEU D1015 " --> pdb=" O PRO D1011 " (cutoff:3.500A) removed outlier: 4.361A 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 'A' and resid 25 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.344A pdb=" N CYS A 230 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU A 256 " --> pdb=" O CYS A 230 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 232 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TYR A 319 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 255 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 141 removed outlier: 3.569A pdb=" N VAL A 188 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 602 Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 28 Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.344A pdb=" N CYS B 230 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU B 256 " --> pdb=" O CYS B 230 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 232 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TYR B 319 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 255 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.568A pdb=" N VAL B 188 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 601 through 602 Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 28 Processing sheet with id=AB1, first strand: chain 'C' and resid 102 through 104 removed outlier: 6.709A pdb=" N VAL C 68 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU C 231 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER C 70 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS C 230 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU C 256 " --> pdb=" O CYS C 230 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU C 232 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TYR C 319 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE C 255 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 139 through 141 removed outlier: 3.569A pdb=" N VAL C 188 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 601 through 602 Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 28 Processing sheet with id=AB5, first strand: chain 'D' and resid 102 through 104 removed outlier: 6.344A pdb=" N CYS D 230 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU D 256 " --> pdb=" O CYS D 230 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU D 232 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR D 319 " --> pdb=" O TRP D 253 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE D 255 " --> pdb=" O TYR D 319 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 139 through 141 removed outlier: 3.569A pdb=" N VAL D 188 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 601 through 602 1698 hydrogen bonds defined for protein. 5025 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: 8.00 Time building geometry restraints manager: 5.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3518 1.32 - 1.44: 3514 1.44 - 1.56: 10300 1.56 - 1.68: 4 1.68 - 1.80: 8 Bond restraints: 17344 Sorted by residual: bond pdb=" CA TRP B 992 " pdb=" C TRP B 992 " ideal model delta sigma weight residual 1.523 1.567 -0.044 1.34e-02 5.57e+03 1.06e+01 bond pdb=" CA TRP A 992 " pdb=" C TRP A 992 " ideal model delta sigma weight residual 1.523 1.566 -0.043 1.34e-02 5.57e+03 1.04e+01 bond pdb=" CA TRP D 992 " pdb=" C TRP D 992 " ideal model delta sigma weight residual 1.523 1.566 -0.043 1.34e-02 5.57e+03 1.03e+01 bond pdb=" C THR A 980 " pdb=" O THR A 980 " ideal model delta sigma weight residual 1.237 1.199 0.037 1.17e-02 7.31e+03 1.02e+01 bond pdb=" C THR B 980 " pdb=" O THR B 980 " ideal model delta sigma weight residual 1.237 1.199 0.037 1.17e-02 7.31e+03 1.02e+01 ... (remaining 17339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 23162 1.98 - 3.96: 771 3.96 - 5.94: 67 5.94 - 7.92: 51 7.92 - 9.89: 17 Bond angle restraints: 24068 Sorted by residual: angle pdb=" N LEU B 779 " pdb=" CA LEU B 779 " pdb=" C LEU B 779 " ideal model delta sigma weight residual 111.14 103.27 7.87 1.08e+00 8.57e-01 5.30e+01 angle pdb=" N LEU D 779 " pdb=" CA LEU D 779 " pdb=" C LEU D 779 " ideal model delta sigma weight residual 111.14 103.28 7.86 1.08e+00 8.57e-01 5.29e+01 angle pdb=" N LEU A 779 " pdb=" CA LEU A 779 " pdb=" C LEU A 779 " ideal model delta sigma weight residual 111.14 103.29 7.85 1.08e+00 8.57e-01 5.28e+01 angle pdb=" N LEU C 779 " pdb=" CA LEU C 779 " pdb=" C LEU C 779 " ideal model delta sigma weight residual 111.14 103.32 7.82 1.08e+00 8.57e-01 5.25e+01 angle pdb=" N PHE C 815 " pdb=" CA PHE C 815 " pdb=" C PHE C 815 " ideal model delta sigma weight residual 111.36 103.59 7.77 1.09e+00 8.42e-01 5.08e+01 ... (remaining 24063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.92: 9596 6.92 - 13.84: 400 13.84 - 20.76: 116 20.76 - 27.68: 4 27.68 - 34.60: 4 Dihedral angle restraints: 10120 sinusoidal: 80 harmonic: 10040 Sorted by residual: dihedral pdb=" CA ASP A 375 " pdb=" C ASP A 375 " pdb=" N VAL A 376 " pdb=" CA VAL A 376 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ASP C 375 " pdb=" C ASP C 375 " pdb=" N VAL C 376 " pdb=" CA VAL C 376 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ASP B 375 " pdb=" C ASP B 375 " pdb=" N VAL B 376 " pdb=" CA VAL B 376 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 10117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2535 0.049 - 0.099: 624 0.099 - 0.148: 129 0.148 - 0.197: 32 0.197 - 0.246: 12 Chirality restraints: 3332 Sorted by residual: chirality pdb=" CA MET B 990 " pdb=" N MET B 990 " pdb=" C MET B 990 " pdb=" CB MET B 990 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA MET C 990 " pdb=" N MET C 990 " pdb=" C MET C 990 " pdb=" CB MET C 990 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA MET A 990 " pdb=" N MET A 990 " pdb=" C MET A 990 " pdb=" CB MET A 990 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3329 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 778 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C VAL C 778 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL C 778 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU C 779 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 778 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C VAL A 778 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL A 778 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 779 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 778 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C VAL B 778 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL B 778 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 779 " -0.014 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 264 2.66 - 3.22: 19772 3.22 - 3.78: 27255 3.78 - 4.34: 29161 4.34 - 4.90: 43815 Nonbonded interactions: 120267 Sorted by model distance: nonbonded pdb=" N THR B 216 " pdb=" O ILE B 224 " model vdw 2.106 3.120 nonbonded pdb=" N THR D 216 " pdb=" O ILE D 224 " model vdw 2.106 3.120 nonbonded pdb=" N THR C 216 " pdb=" O ILE C 224 " model vdw 2.106 3.120 nonbonded pdb=" N THR A 216 " pdb=" O ILE A 224 " model vdw 2.106 3.120 nonbonded pdb=" O PRO D1043 " pdb=" N ASP D1047 " model vdw 2.220 3.120 ... (remaining 120262 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 45.600 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.100 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 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 : 0.005 0.044 17344 Z= 0.377 Angle : 0.898 9.894 24068 Z= 0.654 Chirality : 0.048 0.246 3332 Planarity : 0.005 0.024 3416 Dihedral : 5.480 34.603 3480 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3324 helix: -0.99 (0.10), residues: 2308 sheet: -1.89 (0.35), residues: 152 loop : -1.62 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 537 HIS 0.001 0.001 HIS D 184 PHE 0.009 0.000 PHE C 40 TYR 0.018 0.001 TYR C 979 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.861 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1615 time to fit residues: 26.9070 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 9.9990 chunk 260 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 175 optimal weight: 40.0000 chunk 139 optimal weight: 3.9990 chunk 269 optimal weight: 0.0970 chunk 104 optimal weight: 30.0000 chunk 163 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 312 optimal weight: 50.0000 overall best weight: 3.9984 ------------------------------------------------------------------------------- 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: 0.6221 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 17344 Z= 0.172 Angle : 0.430 6.944 24068 Z= 0.274 Chirality : 0.038 0.126 3332 Planarity : 0.003 0.015 3416 Dihedral : 4.138 19.606 3400 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3324 helix: 0.74 (0.10), residues: 2464 sheet: -1.21 (0.38), residues: 192 loop : -1.49 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 806 HIS 0.000 0.000 HIS C 184 PHE 0.003 0.000 PHE D 40 TYR 0.013 0.001 TYR A 979 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.851 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1642 time to fit residues: 28.1242 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 50.0000 chunk 96 optimal weight: 30.0000 chunk 259 optimal weight: 50.0000 chunk 212 optimal weight: 10.0000 chunk 86 optimal weight: 50.0000 chunk 312 optimal weight: 50.0000 chunk 338 optimal weight: 20.0000 chunk 278 optimal weight: 0.8980 chunk 310 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 251 optimal weight: 30.0000 overall best weight: 10.1792 ------------------------------------------------------------------------------- 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: 0.6364 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17344 Z= 0.372 Angle : 0.653 11.608 24068 Z= 0.431 Chirality : 0.041 0.167 3332 Planarity : 0.004 0.021 3416 Dihedral : 5.572 23.604 3400 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.34 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3324 helix: -0.20 (0.10), residues: 2428 sheet: -0.95 (0.47), residues: 144 loop : -1.90 (0.25), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 537 HIS 0.001 0.001 HIS C 184 PHE 0.012 0.000 PHE B 40 TYR 0.018 0.001 TYR C 979 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.928 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1609 time to fit residues: 26.8975 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 10.0000 chunk 235 optimal weight: 40.0000 chunk 162 optimal weight: 50.0000 chunk 34 optimal weight: 9.9990 chunk 149 optimal weight: 30.0000 chunk 210 optimal weight: 20.0000 chunk 314 optimal weight: 8.9990 chunk 332 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 297 optimal weight: 2.9990 chunk 89 optimal weight: 50.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.6341 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17344 Z= 0.231 Angle : 0.461 10.742 24068 Z= 0.296 Chirality : 0.038 0.124 3332 Planarity : 0.003 0.019 3416 Dihedral : 4.360 17.838 3400 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3324 helix: 0.68 (0.10), residues: 2472 sheet: -0.90 (0.46), residues: 144 loop : -2.00 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 537 HIS 0.001 0.000 HIS A 184 PHE 0.010 0.000 PHE B 40 TYR 0.013 0.001 TYR C 979 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1581 time to fit residues: 26.7544 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 4 optimal weight: 50.0000 chunk 247 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 283 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 169 optimal weight: 20.0000 chunk 298 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- 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: 0.6389 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17344 Z= 0.341 Angle : 0.582 13.379 24068 Z= 0.383 Chirality : 0.040 0.154 3332 Planarity : 0.004 0.020 3416 Dihedral : 5.116 20.299 3400 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3324 helix: 0.10 (0.10), residues: 2492 sheet: -1.24 (0.44), residues: 144 loop : -2.44 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 537 HIS 0.002 0.001 HIS A 184 PHE 0.018 0.000 PHE B 40 TYR 0.016 0.001 TYR C 979 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.907 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1577 time to fit residues: 27.3473 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 20.0000 chunk 299 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 195 optimal weight: 40.0000 chunk 82 optimal weight: 1.9990 chunk 332 optimal weight: 6.9990 chunk 276 optimal weight: 30.0000 chunk 154 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.6335 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17344 Z= 0.157 Angle : 0.401 9.646 24068 Z= 0.252 Chirality : 0.037 0.124 3332 Planarity : 0.002 0.019 3416 Dihedral : 4.058 17.677 3400 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3324 helix: 1.27 (0.11), residues: 2456 sheet: -1.43 (0.37), residues: 184 loop : -2.06 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 537 HIS 0.002 0.001 HIS B 184 PHE 0.006 0.000 PHE B 40 TYR 0.011 0.001 TYR C 979 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.939 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1685 time to fit residues: 28.5519 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 50.0000 chunk 37 optimal weight: 8.9990 chunk 189 optimal weight: 50.0000 chunk 243 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 280 optimal weight: 50.0000 chunk 185 optimal weight: 5.9990 chunk 331 optimal weight: 50.0000 chunk 207 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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: 0.6369 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17344 Z= 0.255 Angle : 0.485 11.510 24068 Z= 0.315 Chirality : 0.039 0.127 3332 Planarity : 0.003 0.020 3416 Dihedral : 4.510 18.879 3400 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3324 helix: 0.93 (0.10), residues: 2444 sheet: -1.11 (0.43), residues: 144 loop : -2.13 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 537 HIS 0.002 0.001 HIS A 184 PHE 0.011 0.000 PHE B 40 TYR 0.014 0.001 TYR C 979 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.926 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1548 time to fit residues: 26.1296 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 chunk 65 optimal weight: 50.0000 chunk 64 optimal weight: 30.0000 chunk 210 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 163 optimal weight: 30.0000 chunk 30 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 overall best weight: 13.7996 ------------------------------------------------------------------------------- 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: 0.6433 moved from start: 0.6956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 17344 Z= 0.451 Angle : 0.700 14.254 24068 Z= 0.466 Chirality : 0.042 0.222 3332 Planarity : 0.005 0.028 3416 Dihedral : 6.080 29.764 3400 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.26 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3324 helix: -0.62 (0.10), residues: 2392 sheet: -1.95 (0.47), residues: 124 loop : -2.22 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 537 HIS 0.002 0.001 HIS A 184 PHE 0.021 0.001 PHE B 40 TYR 0.016 0.001 TYR C 979 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.903 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1685 time to fit residues: 28.0502 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 289 optimal weight: 8.9990 chunk 308 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 242 optimal weight: 50.0000 chunk 94 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 292 optimal weight: 8.9990 chunk 307 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.6367 moved from start: 0.7029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17344 Z= 0.210 Angle : 0.454 9.990 24068 Z= 0.293 Chirality : 0.038 0.127 3332 Planarity : 0.003 0.018 3416 Dihedral : 4.676 19.092 3400 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3324 helix: 0.46 (0.10), residues: 2440 sheet: -1.85 (0.47), residues: 124 loop : -2.15 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 537 HIS 0.002 0.001 HIS C 184 PHE 0.006 0.000 PHE D 40 TYR 0.011 0.001 TYR C 979 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.961 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1643 time to fit residues: 27.1209 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 5.9990 chunk 326 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 227 optimal weight: 0.5980 chunk 342 optimal weight: 10.0000 chunk 315 optimal weight: 30.0000 chunk 272 optimal weight: 50.0000 chunk 28 optimal weight: 20.0000 chunk 210 optimal weight: 30.0000 chunk 167 optimal weight: 20.0000 overall best weight: 8.1192 ------------------------------------------------------------------------------- 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: 0.6387 moved from start: 0.7441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17344 Z= 0.277 Angle : 0.502 10.245 24068 Z= 0.332 Chirality : 0.039 0.145 3332 Planarity : 0.003 0.019 3416 Dihedral : 4.868 21.031 3400 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3324 helix: 0.44 (0.10), residues: 2428 sheet: -2.50 (0.52), residues: 84 loop : -1.84 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 806 HIS 0.002 0.001 HIS D 184 PHE 0.011 0.000 PHE B 40 TYR 0.014 0.001 TYR C 979 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1661 time to fit residues: 27.9217 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 30.0000 chunk 290 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 273 optimal weight: 50.0000 chunk 114 optimal weight: 20.0000 chunk 280 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.080853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.053799 restraints weight = 128623.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.053951 restraints weight = 120414.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.054094 restraints weight = 113416.156| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.8121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17344 Z= 0.337 Angle : 0.574 9.381 24068 Z= 0.382 Chirality : 0.040 0.162 3332 Planarity : 0.004 0.019 3416 Dihedral : 5.383 23.173 3400 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3324 helix: -0.08 (0.10), residues: 2444 sheet: -2.61 (0.52), residues: 84 loop : -2.02 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 806 HIS 0.002 0.000 HIS C 184 PHE 0.012 0.000 PHE B 40 TYR 0.013 0.001 TYR C 979 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.71 seconds wall clock time: 45 minutes 52.89 seconds (2752.89 seconds total)