Starting phenix.real_space_refine on Sun Aug 24 06:11:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sle_40577/08_2025/8sle_40577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sle_40577/08_2025/8sle_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/cci-nas-00/data/ceres_data/8sle_40577/08_2025/8sle_40577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sle_40577/08_2025/8sle_40577.map" model { file = "/net/cci-nas-00/data/ceres_data/8sle_40577/08_2025/8sle_40577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sle_40577/08_2025/8sle_40577.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 53, 'ASN:plan1': 20, 'PHE:plan': 57, 'ARG:plan': 49, 'TRP:plan': 20, 'HIS:plan': 26, 'ASP:plan': 44, 'GLN:plan1': 31, 'TYR:plan': 20} 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: {'GLU:plan': 53, 'ASN:plan1': 20, 'PHE:plan': 57, 'ARG:plan': 49, 'TRP:plan': 20, 'HIS:plan': 26, 'ASP:plan': 44, 'GLN:plan1': 31, 'TYR:plan': 20} 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: {'GLU:plan': 53, 'ASN:plan1': 20, 'PHE:plan': 57, 'ARG:plan': 49, 'TRP:plan': 20, 'HIS:plan': 26, 'ASP:plan': 44, 'GLN:plan1': 31, 'TYR:plan': 20} 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: {'GLU:plan': 53, 'ASN:plan1': 20, 'PHE:plan': 57, 'ARG:plan': 49, 'TRP:plan': 20, 'HIS:plan': 26, 'ASP:plan': 44, 'GLN:plan1': 31, 'TYR:plan': 20} Unresolved non-hydrogen planarities: 1565 Time building chain proxies: 3.96, per 1000 atoms: 0.23 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: 1.76 Conformation dependent library (CDL) restraints added in 855.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.50 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: 3.05 Time building geometry restraints manager: 2.21 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: 0.07 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: 4.090 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.730 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- 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= 0.390 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.018 0.001 TYR C 979 PHE 0.009 0.000 PHE C 40 TRP 0.005 0.001 TRP B 537 HIS 0.001 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00513 (17344) covalent geometry : angle 0.89817 (24068) hydrogen bonds : bond 0.18397 ( 1698) hydrogen bonds : angle 7.16363 ( 5025) *********************** 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 : 0.375 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0764 time to fit residues: 12.0027 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 : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.084195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.055446 restraints weight = 133330.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055533 restraints weight = 125772.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.055642 restraints weight = 120117.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.055755 restraints weight = 114738.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.055802 restraints weight = 110798.152| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17344 Z= 0.273 Angle : 0.549 11.742 24068 Z= 0.354 Chirality : 0.039 0.151 3332 Planarity : 0.004 0.018 3416 Dihedral : 4.762 20.541 3400 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.14), residues: 3324 helix: -0.08 (0.10), residues: 2500 sheet: -1.17 (0.46), residues: 144 loop : -2.15 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR A 979 PHE 0.002 0.000 PHE B 40 TRP 0.020 0.002 TRP A 537 HIS 0.001 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00393 (17344) covalent geometry : angle 0.54857 (24068) hydrogen bonds : bond 0.04857 ( 1698) hydrogen bonds : angle 5.27855 ( 5025) *********************** 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 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.551 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0592 time to fit residues: 9.4281 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 : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 50 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 18 optimal weight: 40.0000 chunk 90 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 240 optimal weight: 30.0000 chunk 296 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 overall best weight: 15.9998 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.079975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.053542 restraints weight = 132513.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.053702 restraints weight = 124793.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.053805 restraints weight = 117301.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053947 restraints weight = 111527.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053947 restraints weight = 107088.495| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 17344 Z= 0.499 Angle : 0.828 14.708 24068 Z= 0.552 Chirality : 0.045 0.232 3332 Planarity : 0.006 0.033 3416 Dihedral : 6.965 26.124 3400 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.23 % Favored : 89.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.81 (0.13), residues: 3324 helix: -1.47 (0.09), residues: 2372 sheet: -1.70 (0.44), residues: 152 loop : -2.54 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.001 TYR C 979 PHE 0.027 0.001 PHE B 40 TRP 0.049 0.003 TRP B 537 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00713 (17344) covalent geometry : angle 0.82813 (24068) hydrogen bonds : bond 0.07899 ( 1698) hydrogen bonds : angle 7.38091 ( 5025) *********************** 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 : 0.607 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0671 time to fit residues: 10.7253 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 : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 215 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 100 optimal weight: 50.0000 chunk 142 optimal weight: 2.9990 chunk 245 optimal weight: 50.0000 chunk 58 optimal weight: 20.0000 chunk 303 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 chunk 251 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.082937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.054399 restraints weight = 131434.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.054622 restraints weight = 122425.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.054702 restraints weight = 112746.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.054702 restraints weight = 109020.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.054702 restraints weight = 108993.581| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17344 Z= 0.196 Angle : 0.462 11.060 24068 Z= 0.293 Chirality : 0.038 0.131 3332 Planarity : 0.003 0.019 3416 Dihedral : 4.893 19.648 3400 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 3324 helix: 0.07 (0.10), residues: 2432 sheet: -1.58 (0.44), residues: 144 loop : -2.28 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR C 979 PHE 0.012 0.000 PHE B 40 TRP 0.010 0.001 TRP A 806 HIS 0.002 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00279 (17344) covalent geometry : angle 0.46153 (24068) hydrogen bonds : bond 0.04574 ( 1698) hydrogen bonds : angle 5.13717 ( 5025) *********************** 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 : 0.592 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0668 time to fit residues: 10.7271 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 : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 171 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 22 optimal weight: 50.0000 chunk 308 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 294 optimal weight: 30.0000 chunk 250 optimal weight: 20.0000 chunk 271 optimal weight: 40.0000 chunk 20 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 overall best weight: 9.9592 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.081337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.053948 restraints weight = 129374.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.054071 restraints weight = 122129.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.054071 restraints weight = 113796.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.054071 restraints weight = 113795.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.054071 restraints weight = 113795.707| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17344 Z= 0.299 Angle : 0.590 15.539 24068 Z= 0.381 Chirality : 0.040 0.160 3332 Planarity : 0.004 0.022 3416 Dihedral : 5.490 22.431 3400 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.08 % Favored : 89.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.14), residues: 3324 helix: -0.37 (0.10), residues: 2436 sheet: -2.16 (0.48), residues: 124 loop : -2.50 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR C 979 PHE 0.017 0.000 PHE B 40 TRP 0.010 0.001 TRP C 806 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00429 (17344) covalent geometry : angle 0.58985 (24068) hydrogen bonds : bond 0.05688 ( 1698) hydrogen bonds : angle 5.97348 ( 5025) *********************** 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 : 0.384 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0624 time to fit residues: 10.0853 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 : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 18 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 187 optimal weight: 30.0000 chunk 312 optimal weight: 50.0000 chunk 296 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 288 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.082577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.054371 restraints weight = 129931.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054481 restraints weight = 122251.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.054606 restraints weight = 113741.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.054606 restraints weight = 106860.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.054606 restraints weight = 106860.915| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17344 Z= 0.217 Angle : 0.477 12.451 24068 Z= 0.302 Chirality : 0.038 0.132 3332 Planarity : 0.003 0.019 3416 Dihedral : 4.685 19.156 3400 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.15), residues: 3324 helix: 0.40 (0.10), residues: 2440 sheet: -2.12 (0.47), residues: 124 loop : -2.37 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR C 979 PHE 0.008 0.000 PHE B 40 TRP 0.011 0.001 TRP C 806 HIS 0.002 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00304 (17344) covalent geometry : angle 0.47665 (24068) hydrogen bonds : bond 0.04467 ( 1698) hydrogen bonds : angle 5.10747 ( 5025) *********************** 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 : 0.457 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0711 time to fit residues: 11.2834 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 : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 204 optimal weight: 0.4980 chunk 21 optimal weight: 50.0000 chunk 44 optimal weight: 40.0000 chunk 61 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 268 optimal weight: 50.0000 chunk 30 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 149 optimal weight: 40.0000 chunk 110 optimal weight: 0.8980 chunk 317 optimal weight: 9.9990 overall best weight: 8.0788 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.082162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.054284 restraints weight = 130813.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.054451 restraints weight = 121991.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054522 restraints weight = 113178.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.054557 restraints weight = 108712.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.054557 restraints weight = 108104.637| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17344 Z= 0.268 Angle : 0.520 13.072 24068 Z= 0.335 Chirality : 0.039 0.139 3332 Planarity : 0.003 0.019 3416 Dihedral : 4.915 21.379 3400 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.15), residues: 3324 helix: 0.37 (0.10), residues: 2416 sheet: -2.69 (0.52), residues: 84 loop : -1.97 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR C 979 PHE 0.013 0.000 PHE B 40 TRP 0.011 0.001 TRP C 806 HIS 0.001 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00376 (17344) covalent geometry : angle 0.52049 (24068) hydrogen bonds : bond 0.04850 ( 1698) hydrogen bonds : angle 5.40546 ( 5025) *********************** 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 : 0.538 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0641 time to fit residues: 10.2900 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 : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 26 optimal weight: 20.0000 chunk 304 optimal weight: 20.0000 chunk 294 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 177 optimal weight: 0.7980 chunk 155 optimal weight: 50.0000 chunk 3 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 overall best weight: 7.3590 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.082527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.054311 restraints weight = 130591.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.054439 restraints weight = 122489.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.054520 restraints weight = 114556.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.054520 restraints weight = 108959.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.054520 restraints weight = 108959.304| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.7148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17344 Z= 0.226 Angle : 0.470 10.932 24068 Z= 0.302 Chirality : 0.038 0.122 3332 Planarity : 0.003 0.021 3416 Dihedral : 4.586 19.217 3400 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.15), residues: 3324 helix: 0.64 (0.11), residues: 2440 sheet: -2.76 (0.51), residues: 84 loop : -1.89 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR C 979 PHE 0.005 0.000 PHE D 40 TRP 0.011 0.001 TRP C 806 HIS 0.001 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00319 (17344) covalent geometry : angle 0.46950 (24068) hydrogen bonds : bond 0.04378 ( 1698) hydrogen bonds : angle 5.05949 ( 5025) *********************** 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 : 0.659 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0753 time to fit residues: 12.2062 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 : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 304 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 338 optimal weight: 20.0000 chunk 36 optimal weight: 40.0000 chunk 43 optimal weight: 20.0000 chunk 289 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 308 optimal weight: 20.0000 chunk 336 optimal weight: 20.0000 chunk 271 optimal weight: 20.0000 overall best weight: 13.3994 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.079905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.053558 restraints weight = 127610.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053674 restraints weight = 120332.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.053731 restraints weight = 113822.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.053731 restraints weight = 110577.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.053731 restraints weight = 110577.292| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.7723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 17344 Z= 0.414 Angle : 0.660 13.575 24068 Z= 0.445 Chirality : 0.041 0.204 3332 Planarity : 0.004 0.025 3416 Dihedral : 5.809 24.588 3400 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.14), residues: 3324 helix: -0.39 (0.10), residues: 2388 sheet: -2.93 (0.52), residues: 84 loop : -2.18 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR C 979 PHE 0.017 0.000 PHE B 40 TRP 0.017 0.002 TRP C 806 HIS 0.002 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00587 (17344) covalent geometry : angle 0.66011 (24068) hydrogen bonds : bond 0.06147 ( 1698) hydrogen bonds : angle 6.49031 ( 5025) *********************** 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 : 0.663 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0761 time to fit residues: 12.2723 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 : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 339 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 8 optimal weight: 40.0000 chunk 6 optimal weight: 30.0000 chunk 191 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 54 optimal weight: 50.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.081276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053815 restraints weight = 128130.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.053977 restraints weight = 120119.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.054027 restraints weight = 113683.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.054073 restraints weight = 109826.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.054075 restraints weight = 107611.676| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.7927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17344 Z= 0.295 Angle : 0.542 10.835 24068 Z= 0.358 Chirality : 0.039 0.154 3332 Planarity : 0.003 0.019 3416 Dihedral : 5.247 22.049 3400 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.14), residues: 3324 helix: -0.09 (0.10), residues: 2428 sheet: -2.92 (0.52), residues: 84 loop : -2.30 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR C 979 PHE 0.010 0.000 PHE B 40 TRP 0.014 0.001 TRP C 806 HIS 0.001 0.000 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00416 (17344) covalent geometry : angle 0.54227 (24068) hydrogen bonds : bond 0.05143 ( 1698) hydrogen bonds : angle 5.81751 ( 5025) ********************** 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 : 0.668 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0738 time to fit residues: 11.9306 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 : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 313 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 94 optimal weight: 40.0000 chunk 255 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 203 optimal weight: 9.9990 chunk 172 optimal weight: 40.0000 overall best weight: 9.9990 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.080751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.053900 restraints weight = 128765.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053996 restraints weight = 120874.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053996 restraints weight = 114287.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053996 restraints weight = 114287.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053996 restraints weight = 114287.501| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.8579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17344 Z= 0.319 Angle : 0.571 10.450 24068 Z= 0.381 Chirality : 0.040 0.165 3332 Planarity : 0.004 0.020 3416 Dihedral : 5.529 23.896 3400 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.86 % Favored : 89.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.14), residues: 3324 helix: -0.25 (0.10), residues: 2452 sheet: -2.99 (0.52), residues: 84 loop : -2.57 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR C 979 PHE 0.011 0.000 PHE B 40 TRP 0.011 0.001 TRP A 806 HIS 0.002 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00449 (17344) covalent geometry : angle 0.57131 (24068) hydrogen bonds : bond 0.05447 ( 1698) hydrogen bonds : angle 6.06449 ( 5025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3027.78 seconds wall clock time: 52 minutes 11.19 seconds (3131.19 seconds total)