Starting phenix.real_space_refine on Sun Jun 15 16:33:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sle_40577/06_2025/8sle_40577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sle_40577/06_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_40577/06_2025/8sle_40577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sle_40577/06_2025/8sle_40577.map" model { file = "/net/cci-nas-00/data/ceres_data/8sle_40577/06_2025/8sle_40577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sle_40577/06_2025/8sle_40577.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 4 5.16 5 C 10424 2.51 5 N 3484 2.21 5 O 3476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17388 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 4347 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 749} Link IDs: {'PTRANS': 32, 'TRANS': 834} Chain breaks: 17 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 2845 Unresolved non-hydrogen angles: 3677 Unresolved non-hydrogen dihedrals: 2411 Unresolved non-hydrogen chiralities: 277 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 44, 'TYR:plan': 20, 'ASN:plan1': 20, 'TRP:plan': 20, 'HIS:plan': 26, 'PHE:plan': 57, 'GLU:plan': 53, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1565 Chain: "B" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 4347 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 749} Link IDs: {'PTRANS': 32, 'TRANS': 834} Chain breaks: 17 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 2845 Unresolved non-hydrogen angles: 3677 Unresolved non-hydrogen dihedrals: 2411 Unresolved non-hydrogen chiralities: 277 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 44, 'TYR:plan': 20, 'ASN:plan1': 20, 'TRP:plan': 20, 'HIS:plan': 26, 'PHE:plan': 57, 'GLU:plan': 53, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1565 Chain: "C" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 4347 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 749} Link IDs: {'PTRANS': 32, 'TRANS': 834} Chain breaks: 17 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 2845 Unresolved non-hydrogen angles: 3677 Unresolved non-hydrogen dihedrals: 2411 Unresolved non-hydrogen chiralities: 277 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 44, 'TYR:plan': 20, 'ASN:plan1': 20, 'TRP:plan': 20, 'HIS:plan': 26, 'PHE:plan': 57, 'GLU:plan': 53, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1565 Chain: "D" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 4347 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 749} Link IDs: {'PTRANS': 32, 'TRANS': 834} Chain breaks: 17 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 2845 Unresolved non-hydrogen angles: 3677 Unresolved non-hydrogen dihedrals: 2411 Unresolved non-hydrogen chiralities: 277 Planarities with less than four sites: {'GLN:plan1': 31, 'ASP:plan': 44, 'TYR:plan': 20, 'ASN:plan1': 20, 'TRP:plan': 20, 'HIS:plan': 26, 'PHE:plan': 57, 'GLU:plan': 53, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1565 Time building chain proxies: 12.50, per 1000 atoms: 0.72 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: 4.87 Conformation dependent library (CDL) restraints added in 3.5 seconds 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6640 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 16 sheets defined 73.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 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: 7.30 Time building geometry restraints manager: 5.54 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 47.220 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3324 helix: -0.99 (0.10), residues: 2308 sheet: -1.89 (0.35), residues: 152 loop : -1.62 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 537 HIS 0.001 0.001 HIS D 184 PHE 0.009 0.000 PHE C 40 TYR 0.018 0.001 TYR C 979 Details of bonding type rmsd hydrogen bonds : bond 0.18397 ( 1698) hydrogen bonds : angle 7.16363 ( 5025) covalent geometry : bond 0.00513 (17344) covalent geometry : angle 0.89817 (24068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.909 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1549 time to fit residues: 25.8369 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 9.9990 chunk 260 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 175 optimal weight: 40.0000 chunk 139 optimal weight: 3.9990 chunk 269 optimal weight: 0.0970 chunk 104 optimal weight: 30.0000 chunk 163 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 312 optimal weight: 50.0000 overall best weight: 3.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.098388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.063905 restraints weight = 135774.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.062707 restraints weight = 124220.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.062175 restraints weight = 133189.094| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 17344 Z= 0.159 Angle : 0.430 6.944 24068 Z= 0.274 Chirality : 0.038 0.126 3332 Planarity : 0.003 0.015 3416 Dihedral : 4.138 19.606 3400 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3324 helix: 0.74 (0.10), residues: 2464 sheet: -1.21 (0.38), residues: 192 loop : -1.49 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 806 HIS 0.000 0.000 HIS C 184 PHE 0.003 0.000 PHE D 40 TYR 0.013 0.001 TYR A 979 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 1698) hydrogen bonds : angle 4.62316 ( 5025) covalent geometry : bond 0.00234 (17344) covalent geometry : angle 0.42965 (24068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.693 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2270 time to fit residues: 40.4109 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 28 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 161 optimal weight: 50.0000 chunk 206 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 303 optimal weight: 7.9990 chunk 87 optimal weight: 50.0000 chunk 195 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 270 optimal weight: 40.0000 chunk 113 optimal weight: 5.9990 overall best weight: 8.7994 ------------------------------------------------------------------------------- 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 = 0.083348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.055789 restraints weight = 132305.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.055831 restraints weight = 125409.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.055891 restraints weight = 119693.694| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17344 Z= 0.293 Angle : 0.564 10.877 24068 Z= 0.366 Chirality : 0.040 0.138 3332 Planarity : 0.004 0.020 3416 Dihedral : 4.874 21.398 3400 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3324 helix: 0.26 (0.10), residues: 2468 sheet: -0.88 (0.47), residues: 144 loop : -1.73 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 537 HIS 0.002 0.001 HIS C 184 PHE 0.007 0.000 PHE B 40 TYR 0.016 0.001 TYR C 979 Details of bonding type rmsd hydrogen bonds : bond 0.05264 ( 1698) hydrogen bonds : angle 5.27138 ( 5025) covalent geometry : bond 0.00414 (17344) covalent geometry : angle 0.56426 (24068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.934 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1907 time to fit residues: 31.6512 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 103 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 252 optimal weight: 40.0000 chunk 38 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 285 optimal weight: 9.9990 chunk 94 optimal weight: 40.0000 chunk 166 optimal weight: 30.0000 chunk 154 optimal weight: 20.0000 chunk 299 optimal weight: 7.9990 overall best weight: 9.5994 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.082126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.054081 restraints weight = 132576.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.054168 restraints weight = 124054.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.054243 restraints weight = 116973.995| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 17344 Z= 0.295 Angle : 0.551 11.844 24068 Z= 0.358 Chirality : 0.039 0.150 3332 Planarity : 0.003 0.020 3416 Dihedral : 4.965 19.638 3400 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3324 helix: 0.16 (0.10), residues: 2460 sheet: -1.10 (0.45), residues: 144 loop : -2.09 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 537 HIS 0.001 0.001 HIS C 184 PHE 0.018 0.000 PHE B 40 TYR 0.014 0.001 TYR C 979 Details of bonding type rmsd hydrogen bonds : bond 0.04928 ( 1698) hydrogen bonds : angle 5.37871 ( 5025) covalent geometry : bond 0.00424 (17344) covalent geometry : angle 0.55104 (24068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.134 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1789 time to fit residues: 29.8851 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 167 optimal weight: 8.9990 chunk 12 optimal weight: 50.0000 chunk 201 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 15 optimal weight: 40.0000 chunk 281 optimal weight: 20.0000 chunk 159 optimal weight: 50.0000 chunk 101 optimal weight: 50.0000 chunk 339 optimal weight: 20.0000 chunk 328 optimal weight: 20.0000 chunk 153 optimal weight: 30.0000 overall best weight: 15.7996 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.079293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.053084 restraints weight = 133150.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.053253 restraints weight = 124581.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.053360 restraints weight = 114855.439| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 17344 Z= 0.486 Angle : 0.791 17.807 24068 Z= 0.525 Chirality : 0.044 0.238 3332 Planarity : 0.006 0.030 3416 Dihedral : 6.629 30.300 3400 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.89 % Favored : 88.75 % 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 : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.13), residues: 3324 helix: -1.25 (0.09), residues: 2440 sheet: -1.80 (0.45), residues: 144 loop : -2.76 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 537 HIS 0.002 0.001 HIS A 184 PHE 0.025 0.001 PHE B 40 TYR 0.018 0.001 TYR C 979 Details of bonding type rmsd hydrogen bonds : bond 0.07326 ( 1698) hydrogen bonds : angle 7.17708 ( 5025) covalent geometry : bond 0.00690 (17344) covalent geometry : angle 0.79086 (24068) *********************** 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 : 2.641 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1746 time to fit residues: 29.3613 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 272 optimal weight: 40.0000 chunk 21 optimal weight: 0.0870 chunk 230 optimal weight: 30.0000 chunk 292 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 19 optimal weight: 40.0000 chunk 163 optimal weight: 30.0000 chunk 112 optimal weight: 20.0000 chunk 53 optimal weight: 0.0070 chunk 101 optimal weight: 40.0000 chunk 307 optimal weight: 0.0670 overall best weight: 4.8320 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.083169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.054429 restraints weight = 132968.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.054593 restraints weight = 122057.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.054767 restraints weight = 113568.181| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17344 Z= 0.173 Angle : 0.442 11.576 24068 Z= 0.275 Chirality : 0.038 0.128 3332 Planarity : 0.002 0.017 3416 Dihedral : 4.731 22.015 3400 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3324 helix: 0.43 (0.10), residues: 2400 sheet: -2.04 (0.47), residues: 124 loop : -2.12 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 537 HIS 0.003 0.001 HIS C 184 PHE 0.008 0.000 PHE B 40 TYR 0.011 0.001 TYR C 979 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 1698) hydrogen bonds : angle 4.96859 ( 5025) covalent geometry : bond 0.00242 (17344) covalent geometry : angle 0.44215 (24068) *********************** 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 : 3.326 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1897 time to fit residues: 32.0988 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 : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 243 optimal weight: 20.0000 chunk 176 optimal weight: 40.0000 chunk 56 optimal weight: 7.9990 chunk 276 optimal weight: 30.0000 chunk 292 optimal weight: 9.9990 chunk 194 optimal weight: 50.0000 chunk 187 optimal weight: 30.0000 chunk 14 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 240 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 overall best weight: 10.3992 ------------------------------------------------------------------------------- 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 = 0.081069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053826 restraints weight = 128888.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.054002 restraints weight = 121467.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.054053 restraints weight = 111320.207| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17344 Z= 0.329 Angle : 0.585 14.615 24068 Z= 0.383 Chirality : 0.040 0.165 3332 Planarity : 0.004 0.019 3416 Dihedral : 5.424 22.769 3400 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3324 helix: -0.12 (0.10), residues: 2404 sheet: -2.12 (0.47), residues: 124 loop : -2.20 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 806 HIS 0.002 0.001 HIS C 184 PHE 0.014 0.000 PHE B 40 TYR 0.016 0.001 TYR C 979 Details of bonding type rmsd hydrogen bonds : bond 0.05584 ( 1698) hydrogen bonds : angle 5.92287 ( 5025) covalent geometry : bond 0.00468 (17344) covalent geometry : angle 0.58477 (24068) *********************** 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 : 2.037 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2812 time to fit residues: 47.0719 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 208 optimal weight: 40.0000 chunk 25 optimal weight: 20.0000 chunk 254 optimal weight: 20.0000 chunk 219 optimal weight: 20.0000 chunk 240 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 40.0000 chunk 162 optimal weight: 40.0000 chunk 301 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.082239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.053929 restraints weight = 131392.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.054092 restraints weight = 122671.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.054163 restraints weight = 114998.509| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.6888 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= 0.230 Angle : 0.487 11.812 24068 Z= 0.314 Chirality : 0.038 0.127 3332 Planarity : 0.003 0.019 3416 Dihedral : 4.766 20.538 3400 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3324 helix: 0.42 (0.11), residues: 2408 sheet: -2.54 (0.52), residues: 84 loop : -2.02 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 806 HIS 0.002 0.001 HIS C 184 PHE 0.007 0.000 PHE B 40 TYR 0.011 0.001 TYR C 979 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 1698) hydrogen bonds : angle 5.23293 ( 5025) covalent geometry : bond 0.00323 (17344) covalent geometry : angle 0.48685 (24068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.900 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1610 time to fit residues: 26.9274 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 96 optimal weight: 50.0000 chunk 319 optimal weight: 40.0000 chunk 308 optimal weight: 20.0000 chunk 257 optimal weight: 30.0000 chunk 291 optimal weight: 9.9990 chunk 224 optimal weight: 50.0000 chunk 269 optimal weight: 6.9990 chunk 284 optimal weight: 30.0000 chunk 317 optimal weight: 5.9990 chunk 335 optimal weight: 40.0000 chunk 209 optimal weight: 8.9990 overall best weight: 10.3992 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.080769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.053683 restraints weight = 130555.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.053846 restraints weight = 122271.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.053897 restraints weight = 114636.020| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.7544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 17344 Z= 0.328 Angle : 0.588 12.863 24068 Z= 0.390 Chirality : 0.040 0.168 3332 Planarity : 0.004 0.022 3416 Dihedral : 5.620 24.842 3400 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.59 % Favored : 89.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3324 helix: -0.20 (0.10), residues: 2400 sheet: -2.73 (0.53), residues: 84 loop : -2.10 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 806 HIS 0.002 0.001 HIS C 184 PHE 0.016 0.000 PHE B 40 TYR 0.015 0.001 TYR C 979 Details of bonding type rmsd hydrogen bonds : bond 0.05752 ( 1698) hydrogen bonds : angle 6.16939 ( 5025) covalent geometry : bond 0.00467 (17344) covalent geometry : angle 0.58848 (24068) *********************** 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 : 2.023 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1653 time to fit residues: 27.6819 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 115 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 282 optimal weight: 50.0000 chunk 315 optimal weight: 20.0000 chunk 86 optimal weight: 40.0000 chunk 153 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 overall best weight: 5.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.082514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.054422 restraints weight = 128846.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.054518 restraints weight = 120007.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.054574 restraints weight = 112895.415| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.7622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17344 Z= 0.201 Angle : 0.448 9.530 24068 Z= 0.290 Chirality : 0.038 0.121 3332 Planarity : 0.003 0.019 3416 Dihedral : 4.640 19.668 3400 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3324 helix: 0.58 (0.11), residues: 2432 sheet: -2.63 (0.53), residues: 84 loop : -1.99 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 537 HIS 0.001 0.000 HIS D 184 PHE 0.007 0.000 PHE B 40 TYR 0.011 0.001 TYR C 979 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 1698) hydrogen bonds : angle 5.06967 ( 5025) covalent geometry : bond 0.00281 (17344) covalent geometry : angle 0.44811 (24068) ********************** 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 : 1.869 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1597 time to fit residues: 26.5634 Evaluate side-chains 80 residues out of total 3036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 230 optimal weight: 4.9990 chunk 217 optimal weight: 0.7980 chunk 181 optimal weight: 40.0000 chunk 291 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 235 optimal weight: 40.0000 chunk 122 optimal weight: 40.0000 chunk 27 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.082788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.054557 restraints weight = 129923.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.054678 restraints weight = 121025.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.054730 restraints weight = 113871.950| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.7883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17344 Z= 0.191 Angle : 0.422 7.271 24068 Z= 0.276 Chirality : 0.038 0.122 3332 Planarity : 0.002 0.020 3416 Dihedral : 4.265 18.528 3400 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3324 helix: 1.11 (0.11), residues: 2444 sheet: -2.61 (0.53), residues: 84 loop : -1.90 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 806 HIS 0.001 0.000 HIS C 184 PHE 0.007 0.000 PHE B 40 TYR 0.012 0.001 TYR C 979 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 1698) hydrogen bonds : angle 4.72966 ( 5025) covalent geometry : bond 0.00269 (17344) covalent geometry : angle 0.42211 (24068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6530.52 seconds wall clock time: 116 minutes 42.61 seconds (7002.61 seconds total)