Starting phenix.real_space_refine on Sun Jul 5 11:16:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srk_40734/07_2026/8srk_40734.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srk_40734/07_2026/8srk_40734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8srk_40734/07_2026/8srk_40734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srk_40734/07_2026/8srk_40734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8srk_40734/07_2026/8srk_40734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srk_40734/07_2026/8srk_40734.map" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 8 5.49 5 S 104 5.16 5 C 17420 2.51 5 N 4836 2.21 5 O 4952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27328 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 6710 Classifications: {'peptide': 1071} Incomplete info: {'truncation_to_alanine': 524} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 1031} Chain breaks: 2 Unresolved non-hydrogen bonds: 1910 Unresolved non-hydrogen angles: 2391 Unresolved non-hydrogen dihedrals: 1560 Unresolved non-hydrogen chiralities: 156 Planarities with less than four sites: {'GLU:plan': 51, 'ASN:plan1': 26, 'ASP:plan': 52, 'ARG:plan': 37, 'GLN:plan1': 30, 'PHE:plan': 36, 'HIS:plan': 14, 'TYR:plan': 8, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 1094 Chain: "D" Number of atoms: 6710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 6710 Classifications: {'peptide': 1071} Incomplete info: {'truncation_to_alanine': 524} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 1031} Chain breaks: 2 Unresolved non-hydrogen bonds: 1910 Unresolved non-hydrogen angles: 2391 Unresolved non-hydrogen dihedrals: 1560 Unresolved non-hydrogen chiralities: 156 Planarities with less than four sites: {'GLU:plan': 51, 'ASN:plan1': 26, 'ASP:plan': 52, 'ARG:plan': 37, 'GLN:plan1': 30, 'PHE:plan': 36, 'HIS:plan': 14, 'TYR:plan': 8, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 1094 Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'APR': 1, 'CLR': 3} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 2 Chain: "D" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'APR': 1, 'CLR': 3} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 2 Restraints were copied for chains: B, C Time building chain proxies: 9.59, per 1000 atoms: 0.35 Number of scatterers: 27328 At special positions: 0 Unit cell: (149.64, 149.64, 153.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 104 16.00 P 8 15.00 O 4952 8.00 N 4836 7.00 C 17420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 609 " distance=0.00 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 676 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B 997 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B1006 " distance=0.00 Simple disulfide: pdb=" SG CYS B1060 " - pdb=" SG CYS B1060 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C 997 " - pdb=" SG CYS C1006 " distance=2.03 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: 2.39 Conformation dependent library (CDL) restraints added in 1.5 seconds 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8136 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 12 sheets defined 66.9% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.536A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 175 Processing helix chain 'A' and resid 187 through 203 removed outlier: 3.537A pdb=" N LEU A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.683A pdb=" N PHE A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.782A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'A' and resid 410 through 419 removed outlier: 3.535A pdb=" N MET A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 439 through 457 removed outlier: 4.194A pdb=" N ILE A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.550A pdb=" N GLU A 475 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 476' Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'A' and resid 513 through 521 removed outlier: 3.564A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.673A pdb=" N LEU A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.942A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR A 581 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 582 " --> pdb=" O THR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 577 through 582' Processing helix chain 'A' and resid 590 through 610 Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 640 Processing helix chain 'A' and resid 651 through 680 removed outlier: 3.788A pdb=" N LEU A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 689 removed outlier: 3.603A pdb=" N HIS A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.718A pdb=" N LEU A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 728 Processing helix chain 'A' and resid 735 through 745 removed outlier: 3.511A pdb=" N VAL A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 799 Processing helix chain 'A' and resid 801 through 826 Processing helix chain 'A' and resid 833 through 856 removed outlier: 3.532A pdb=" N TRP A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.649A pdb=" N TYR A 863 " --> pdb=" O GLY A 859 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 864 " --> pdb=" O ILE A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.530A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 911 removed outlier: 4.156A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP A 911 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.587A pdb=" N ALA A 919 " --> pdb=" O ARG A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 4.149A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 980 removed outlier: 3.648A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 3.604A pdb=" N LEU A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1066 removed outlier: 3.732A pdb=" N ILE A1034 " --> pdb=" O VAL A1030 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1072 No H-bonds generated for 'chain 'A' and resid 1070 through 1072' Processing helix chain 'A' and resid 1073 through 1090 Processing helix chain 'A' and resid 1102 through 1129 removed outlier: 3.557A pdb=" N GLN A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1168 removed outlier: 3.911A pdb=" N ARG A1135 " --> pdb=" O MET A1131 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A1168 " --> pdb=" O LEU A1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.536A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 187 through 203 removed outlier: 3.537A pdb=" N LEU B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.683A pdb=" N PHE B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 312 removed outlier: 3.782A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 346 through 358 Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 395 through 406 Processing helix chain 'B' and resid 410 through 419 removed outlier: 3.535A pdb=" N MET B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 437 Processing helix chain 'B' and resid 439 through 457 removed outlier: 4.195A pdb=" N ILE B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.550A pdb=" N GLU B 475 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'B' and resid 513 through 521 removed outlier: 3.564A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.674A pdb=" N LEU B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 582 removed outlier: 3.942A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 582 " --> pdb=" O THR B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 577 through 582' Processing helix chain 'B' and resid 590 through 610 Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 640 Processing helix chain 'B' and resid 651 through 680 removed outlier: 3.788A pdb=" N LEU B 668 " --> pdb=" O LYS B 664 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 669 " --> pdb=" O PHE B 665 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 689 removed outlier: 3.603A pdb=" N HIS B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'B' and resid 709 through 714 removed outlier: 3.718A pdb=" N LEU B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 728 Processing helix chain 'B' and resid 735 through 745 removed outlier: 3.511A pdb=" N VAL B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 799 Processing helix chain 'B' and resid 801 through 826 Processing helix chain 'B' and resid 833 through 856 removed outlier: 3.532A pdb=" N TRP B 837 " --> pdb=" O SER B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 866 removed outlier: 3.649A pdb=" N TYR B 863 " --> pdb=" O GLY B 859 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 864 " --> pdb=" O ILE B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.530A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 911 removed outlier: 4.156A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP B 911 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 919 removed outlier: 3.587A pdb=" N ALA B 919 " --> pdb=" O ARG B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 4.149A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 980 removed outlier: 3.648A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1013 through 1028 removed outlier: 3.604A pdb=" N LEU B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1066 removed outlier: 3.733A pdb=" N ILE B1034 " --> pdb=" O VAL B1030 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1072 No H-bonds generated for 'chain 'B' and resid 1070 through 1072' Processing helix chain 'B' and resid 1073 through 1090 Processing helix chain 'B' and resid 1102 through 1129 removed outlier: 3.557A pdb=" N GLN B1129 " --> pdb=" O GLU B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1168 removed outlier: 3.911A pdb=" N ARG B1135 " --> pdb=" O MET B1131 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B1168 " --> pdb=" O LEU B1164 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.536A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 175 Processing helix chain 'C' and resid 187 through 203 removed outlier: 3.537A pdb=" N LEU C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 271 through 286 removed outlier: 3.683A pdb=" N PHE C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 312 removed outlier: 3.782A pdb=" N LEU C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 303 " --> pdb=" O PRO C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 335 Processing helix chain 'C' and resid 346 through 358 Processing helix chain 'C' and resid 362 through 377 Processing helix chain 'C' and resid 395 through 406 Processing helix chain 'C' and resid 410 through 419 removed outlier: 3.535A pdb=" N MET C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 437 Processing helix chain 'C' and resid 439 through 457 removed outlier: 4.194A pdb=" N ILE C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 444 " --> pdb=" O HIS C 440 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.550A pdb=" N GLU C 475 " --> pdb=" O LYS C 472 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 476' Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 Processing helix chain 'C' and resid 513 through 521 removed outlier: 3.564A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.673A pdb=" N LEU C 567 " --> pdb=" O ILE C 563 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 582 removed outlier: 3.941A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR C 581 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 582 " --> pdb=" O THR C 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 577 through 582' Processing helix chain 'C' and resid 590 through 610 Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 640 Processing helix chain 'C' and resid 651 through 680 removed outlier: 3.788A pdb=" N LEU C 668 " --> pdb=" O LYS C 664 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA C 669 " --> pdb=" O PHE C 665 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL C 670 " --> pdb=" O GLU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 689 removed outlier: 3.603A pdb=" N HIS C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 Processing helix chain 'C' and resid 709 through 714 removed outlier: 3.718A pdb=" N LEU C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 728 Processing helix chain 'C' and resid 735 through 745 removed outlier: 3.511A pdb=" N VAL C 739 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 799 Processing helix chain 'C' and resid 801 through 826 Processing helix chain 'C' and resid 833 through 856 removed outlier: 3.531A pdb=" N TRP C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 866 removed outlier: 3.650A pdb=" N TYR C 863 " --> pdb=" O GLY C 859 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 864 " --> pdb=" O ILE C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.530A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 911 removed outlier: 4.156A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP C 911 " --> pdb=" O VAL C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 919 removed outlier: 3.587A pdb=" N ALA C 919 " --> pdb=" O ARG C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 4.149A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 980 removed outlier: 3.648A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG C 977 " --> pdb=" O GLY C 973 " (cutoff:3.500A) Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1013 through 1028 removed outlier: 3.604A pdb=" N LEU C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1066 removed outlier: 3.733A pdb=" N ILE C1034 " --> pdb=" O VAL C1030 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1072 No H-bonds generated for 'chain 'C' and resid 1070 through 1072' Processing helix chain 'C' and resid 1073 through 1090 Processing helix chain 'C' and resid 1102 through 1129 removed outlier: 3.557A pdb=" N GLN C1129 " --> pdb=" O GLU C1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 1131 through 1168 removed outlier: 3.911A pdb=" N ARG C1135 " --> pdb=" O MET C1131 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.536A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 175 Processing helix chain 'D' and resid 187 through 203 removed outlier: 3.537A pdb=" N LEU D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.683A pdb=" N PHE D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 312 removed outlier: 3.782A pdb=" N LEU D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 335 Processing helix chain 'D' and resid 346 through 358 Processing helix chain 'D' and resid 362 through 377 Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'D' and resid 410 through 419 removed outlier: 3.535A pdb=" N MET D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 437 Processing helix chain 'D' and resid 439 through 457 removed outlier: 4.194A pdb=" N ILE D 443 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 444 " --> pdb=" O HIS D 440 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.550A pdb=" N GLU D 475 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 472 through 476' Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 Processing helix chain 'D' and resid 513 through 521 removed outlier: 3.564A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.674A pdb=" N LEU D 567 " --> pdb=" O ILE D 563 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 582 removed outlier: 3.941A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR D 581 " --> pdb=" O PHE D 578 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP D 582 " --> pdb=" O THR D 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 577 through 582' Processing helix chain 'D' and resid 590 through 610 Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 640 Processing helix chain 'D' and resid 651 through 680 removed outlier: 3.788A pdb=" N LEU D 668 " --> pdb=" O LYS D 664 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA D 669 " --> pdb=" O PHE D 665 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 689 removed outlier: 3.603A pdb=" N HIS D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 696 removed outlier: 4.076A pdb=" N ASN D 696 " --> pdb=" O ASP D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 708 Processing helix chain 'D' and resid 709 through 714 removed outlier: 3.718A pdb=" N LEU D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 728 Processing helix chain 'D' and resid 735 through 745 removed outlier: 3.511A pdb=" N VAL D 739 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 799 Processing helix chain 'D' and resid 801 through 826 Processing helix chain 'D' and resid 833 through 856 removed outlier: 3.532A pdb=" N TRP D 837 " --> pdb=" O SER D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 866 removed outlier: 3.650A pdb=" N TYR D 863 " --> pdb=" O GLY D 859 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 864 " --> pdb=" O ILE D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.530A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 911 removed outlier: 4.157A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP D 911 " --> pdb=" O VAL D 907 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 919 removed outlier: 3.587A pdb=" N ALA D 919 " --> pdb=" O ARG D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 4.149A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER D 961 " --> pdb=" O GLN D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 980 removed outlier: 3.649A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 978 - end of helix Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1013 through 1028 removed outlier: 3.603A pdb=" N LEU D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1066 removed outlier: 3.733A pdb=" N ILE D1034 " --> pdb=" O VAL D1030 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1072 No H-bonds generated for 'chain 'D' and resid 1070 through 1072' Processing helix chain 'D' and resid 1073 through 1090 Processing helix chain 'D' and resid 1102 through 1129 removed outlier: 3.557A pdb=" N GLN D1129 " --> pdb=" O GLU D1125 " (cutoff:3.500A) Processing helix chain 'D' and resid 1131 through 1168 removed outlier: 3.910A pdb=" N ARG D1135 " --> pdb=" O MET D1131 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA D1168 " --> pdb=" O LEU D1164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 236 removed outlier: 6.581A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL A 316 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR A 292 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A 318 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL A 294 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 315 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR A 386 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A 317 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 236 removed outlier: 6.581A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL B 316 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR B 292 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL B 318 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 294 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 315 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR B 386 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL B 317 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'C' and resid 232 through 236 removed outlier: 6.582A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL C 316 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR C 292 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 318 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL C 294 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 315 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR C 386 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL C 317 " --> pdb=" O TYR C 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'D' and resid 232 through 236 removed outlier: 6.581A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL D 316 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR D 292 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL D 318 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL D 294 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 315 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N TYR D 386 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL D 317 " --> pdb=" O TYR D 386 " (cutoff:3.500A) 2033 hydrogen bonds defined for protein. 6036 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: 5.84 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4587 1.32 - 1.44: 7210 1.44 - 1.57: 15903 1.57 - 1.69: 16 1.69 - 1.81: 188 Bond restraints: 27904 Sorted by residual: bond pdb=" CA SER A1025 " pdb=" CB SER A1025 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.78e+01 bond pdb=" CA SER D1025 " pdb=" CB SER D1025 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.78e+01 bond pdb=" CA SER B1025 " pdb=" CB SER B1025 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.78e+01 bond pdb=" CA SER C1025 " pdb=" CB SER C1025 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.78e+01 bond pdb=" C4 APR D6003 " pdb=" C5 APR D6003 " ideal model delta sigma weight residual 1.386 1.467 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 27899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 35545 2.05 - 4.10: 2307 4.10 - 6.15: 561 6.15 - 8.20: 165 8.20 - 10.25: 34 Bond angle restraints: 38612 Sorted by residual: angle pdb=" N TYR A 216 " pdb=" CA TYR A 216 " pdb=" C TYR A 216 " ideal model delta sigma weight residual 113.28 103.25 10.03 1.22e+00 6.72e-01 6.75e+01 angle pdb=" N TYR C 216 " pdb=" CA TYR C 216 " pdb=" C TYR C 216 " ideal model delta sigma weight residual 113.28 103.25 10.03 1.22e+00 6.72e-01 6.75e+01 angle pdb=" N TYR B 216 " pdb=" CA TYR B 216 " pdb=" C TYR B 216 " ideal model delta sigma weight residual 113.28 103.25 10.03 1.22e+00 6.72e-01 6.75e+01 angle pdb=" N TYR D 216 " pdb=" CA TYR D 216 " pdb=" C TYR D 216 " ideal model delta sigma weight residual 113.28 103.30 9.98 1.22e+00 6.72e-01 6.69e+01 angle pdb=" N GLN A1055 " pdb=" CA GLN A1055 " pdb=" C GLN A1055 " ideal model delta sigma weight residual 111.82 103.23 8.59 1.16e+00 7.43e-01 5.48e+01 ... (remaining 38607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 16171 23.50 - 47.01: 533 47.01 - 70.51: 151 70.51 - 94.02: 16 94.02 - 117.52: 12 Dihedral angle restraints: 16883 sinusoidal: 4379 harmonic: 12504 Sorted by residual: dihedral pdb=" CA THR B1001 " pdb=" C THR B1001 " pdb=" N PRO B1002 " pdb=" CA PRO B1002 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA THR C1001 " pdb=" C THR C1001 " pdb=" N PRO C1002 " pdb=" CA PRO C1002 " ideal model delta harmonic sigma weight residual -180.00 -150.48 -29.52 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA THR A1001 " pdb=" C THR A1001 " pdb=" N PRO A1002 " pdb=" CA PRO A1002 " ideal model delta harmonic sigma weight residual 180.00 -150.48 -29.52 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 16880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4131 0.088 - 0.175: 525 0.175 - 0.263: 96 0.263 - 0.351: 24 0.351 - 0.438: 8 Chirality restraints: 4784 Sorted by residual: chirality pdb=" CB VAL C 907 " pdb=" CA VAL C 907 " pdb=" CG1 VAL C 907 " pdb=" CG2 VAL C 907 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CB VAL D 907 " pdb=" CA VAL D 907 " pdb=" CG1 VAL D 907 " pdb=" CG2 VAL D 907 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CB VAL B 907 " pdb=" CA VAL B 907 " pdb=" CG1 VAL B 907 " pdb=" CG2 VAL B 907 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 4781 not shown) Planarity restraints: 5048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 905 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C PHE D 905 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE D 905 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU D 906 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 905 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.52e+00 pdb=" C PHE B 905 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE B 905 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU B 906 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B1024 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.52e+00 pdb=" C GLY B1024 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY B1024 " 0.020 2.00e-02 2.50e+03 pdb=" N SER B1025 " 0.018 2.00e-02 2.50e+03 ... (remaining 5045 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 124 2.60 - 3.18: 19964 3.18 - 3.75: 44887 3.75 - 4.33: 52718 4.33 - 4.90: 86692 Nonbonded interactions: 204385 Sorted by model distance: nonbonded pdb=" SG CYS D 997 " pdb=" SG CYS D1006 " model vdw 2.029 3.760 nonbonded pdb=" O ARG A1135 " pdb=" OG1 THR A1139 " model vdw 2.364 3.040 nonbonded pdb=" O ARG C1135 " pdb=" OG1 THR C1139 " model vdw 2.364 3.040 nonbonded pdb=" O ARG B1135 " pdb=" OG1 THR B1139 " model vdw 2.364 3.040 nonbonded pdb=" O ARG D1135 " pdb=" OG1 THR D1139 " model vdw 2.364 3.040 ... (remaining 204380 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: 0.10 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 52 through 1168 or resid 1706)) selection = (chain 'B' and (resid 52 through 1168 or resid 1706)) selection = (chain 'C' and (resid 52 through 1168 or resid 1706)) selection = (chain 'D' and (resid 52 through 1168 or resid 6006)) } 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: 1.780 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 30.010 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 27907 Z= 0.455 Angle : 1.228 10.253 38623 Z= 0.759 Chirality : 0.065 0.438 4784 Planarity : 0.009 0.058 5048 Dihedral : 14.145 117.520 8728 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.50 % Allowed : 2.18 % Favored : 97.32 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.16 (0.09), residues: 4260 helix: -4.06 (0.05), residues: 2780 sheet: -0.55 (0.37), residues: 224 loop : -1.68 (0.15), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 614 TYR 0.028 0.003 TYR B 952 PHE 0.037 0.004 PHE C 941 TRP 0.037 0.003 TRP B 842 HIS 0.010 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00815 / 0.45 (27904) covalent geometry : angle 1.22806 / 0.76 (38612) SS BOND : bond 0.00211 / 0.10 ( 3) SS BOND : angle 0.25836 / 0.17 ( 11) hydrogen bonds : bond 0.14245 / 10.55 ( 2033) hydrogen bonds : angle 7.96058 / 5.71 ( 6036) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 328 time to evaluate : 1.065 Fit side-chains REVERT: A 456 MET cc_start: 0.9028 (tpp) cc_final: 0.8786 (tpp) REVERT: A 683 MET cc_start: 0.8864 (mmm) cc_final: 0.8419 (tpp) REVERT: A 874 ILE cc_start: 0.9534 (mm) cc_final: 0.9294 (tt) REVERT: A 1021 TYR cc_start: 0.9310 (t80) cc_final: 0.9089 (t80) REVERT: A 1150 MET cc_start: 0.9072 (tpp) cc_final: 0.8634 (tmm) REVERT: B 456 MET cc_start: 0.9025 (tpp) cc_final: 0.8794 (tpp) REVERT: B 683 MET cc_start: 0.8862 (mmm) cc_final: 0.8419 (tpp) REVERT: B 874 ILE cc_start: 0.9533 (mm) cc_final: 0.9292 (tt) REVERT: B 1021 TYR cc_start: 0.9325 (t80) cc_final: 0.9112 (t80) REVERT: B 1150 MET cc_start: 0.9072 (tpp) cc_final: 0.8119 (mmp) REVERT: C 456 MET cc_start: 0.9025 (tpp) cc_final: 0.8794 (tpp) REVERT: C 683 MET cc_start: 0.8858 (mmm) cc_final: 0.8423 (tpp) REVERT: C 874 ILE cc_start: 0.9534 (mm) cc_final: 0.9294 (tt) REVERT: C 1021 TYR cc_start: 0.9325 (t80) cc_final: 0.9111 (t80) REVERT: C 1150 MET cc_start: 0.9072 (tpp) cc_final: 0.8200 (mmm) REVERT: D 456 MET cc_start: 0.9025 (tpp) cc_final: 0.8794 (tpp) REVERT: D 683 MET cc_start: 0.8860 (mmm) cc_final: 0.8426 (tpp) REVERT: D 874 ILE cc_start: 0.9534 (mm) cc_final: 0.9292 (tt) REVERT: D 1021 TYR cc_start: 0.9324 (t80) cc_final: 0.9114 (t80) REVERT: D 1150 MET cc_start: 0.9072 (tpp) cc_final: 0.8853 (mmm) outliers start: 8 outliers final: 0 residues processed: 332 average time/residue: 0.1591 time to fit residues: 88.7159 Evaluate side-chains 256 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS B 592 GLN B1078 HIS ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1078 HIS ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1078 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.045005 restraints weight = 197249.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.046095 restraints weight = 100769.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.046878 restraints weight = 63416.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.047380 restraints weight = 45424.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.047741 restraints weight = 36078.256| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27907 Z= 0.234 Angle : 0.630 6.190 38623 Z= 0.338 Chirality : 0.040 0.147 4784 Planarity : 0.005 0.038 5048 Dihedral : 8.402 85.272 5416 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.11), residues: 4260 helix: -0.75 (0.08), residues: 2840 sheet: -0.48 (0.39), residues: 232 loop : -1.00 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1135 TYR 0.018 0.002 TYR D 917 PHE 0.019 0.002 PHE D 905 TRP 0.020 0.001 TRP A 842 HIS 0.004 0.001 HIS C 715 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 (27904) covalent geometry : angle 0.63022 / 0.34 (38612) SS BOND : bond 0.00139 / 0.06 ( 3) SS BOND : angle 0.34941 / 0.23 ( 11) hydrogen bonds : bond 0.03877 / 2.81 ( 2033) hydrogen bonds : angle 4.29237 / 3.06 ( 6036) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 1.053 Fit side-chains REVERT: A 76 MET cc_start: 0.9018 (mmm) cc_final: 0.8453 (ppp) REVERT: A 602 MET cc_start: 0.9179 (mmm) cc_final: 0.8873 (mmp) REVERT: A 683 MET cc_start: 0.9274 (mmm) cc_final: 0.8856 (tpp) REVERT: A 1058 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8782 (mm-30) REVERT: A 1138 MET cc_start: 0.8794 (ppp) cc_final: 0.8514 (ppp) REVERT: A 1150 MET cc_start: 0.9197 (tpp) cc_final: 0.8675 (tmm) REVERT: B 76 MET cc_start: 0.9036 (mmm) cc_final: 0.8455 (ppp) REVERT: B 602 MET cc_start: 0.9183 (mmm) cc_final: 0.8878 (mmp) REVERT: B 683 MET cc_start: 0.9270 (mmm) cc_final: 0.8855 (tpp) REVERT: B 915 MET cc_start: 0.9257 (mmt) cc_final: 0.9028 (mmp) REVERT: B 1058 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8777 (mm-30) REVERT: B 1138 MET cc_start: 0.8793 (ppp) cc_final: 0.8515 (ppp) REVERT: B 1150 MET cc_start: 0.9197 (tpp) cc_final: 0.8671 (tmm) REVERT: C 76 MET cc_start: 0.9033 (mmm) cc_final: 0.8452 (ppp) REVERT: C 602 MET cc_start: 0.9184 (mmm) cc_final: 0.8880 (mmp) REVERT: C 683 MET cc_start: 0.9274 (mmm) cc_final: 0.8859 (tpp) REVERT: C 915 MET cc_start: 0.9248 (mmt) cc_final: 0.9033 (mmp) REVERT: C 1058 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8779 (mm-30) REVERT: C 1138 MET cc_start: 0.8794 (ppp) cc_final: 0.8514 (ppp) REVERT: C 1150 MET cc_start: 0.9212 (tpp) cc_final: 0.8667 (tmm) REVERT: D 76 MET cc_start: 0.9036 (mmm) cc_final: 0.8455 (ppp) REVERT: D 602 MET cc_start: 0.9181 (mmm) cc_final: 0.8879 (mmp) REVERT: D 683 MET cc_start: 0.9277 (mmm) cc_final: 0.8860 (tpp) REVERT: D 915 MET cc_start: 0.9250 (mmt) cc_final: 0.9026 (mmp) REVERT: D 1036 MET cc_start: 0.9451 (mmm) cc_final: 0.9185 (mmm) REVERT: D 1058 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8777 (mm-30) REVERT: D 1138 MET cc_start: 0.8795 (ppp) cc_final: 0.8515 (ppp) REVERT: D 1150 MET cc_start: 0.9211 (tpp) cc_final: 0.8667 (tmm) outliers start: 1 outliers final: 0 residues processed: 272 average time/residue: 0.1465 time to fit residues: 67.8389 Evaluate side-chains 225 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 115 optimal weight: 0.2980 chunk 24 optimal weight: 50.0000 chunk 99 optimal weight: 50.0000 chunk 184 optimal weight: 3.9990 chunk 230 optimal weight: 50.0000 chunk 74 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 341 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 371 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.059421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.041710 restraints weight = 182227.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.042826 restraints weight = 93362.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.043589 restraints weight = 58616.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.044106 restraints weight = 42274.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.044386 restraints weight = 33505.722| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27907 Z= 0.150 Angle : 0.503 5.608 38623 Z= 0.268 Chirality : 0.037 0.123 4784 Planarity : 0.004 0.035 5048 Dihedral : 7.453 86.321 5416 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 4260 helix: 1.09 (0.09), residues: 2844 sheet: -0.38 (0.39), residues: 232 loop : -0.62 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 614 TYR 0.019 0.001 TYR A1041 PHE 0.016 0.002 PHE C 905 TRP 0.016 0.001 TRP B 842 HIS 0.003 0.001 HIS A 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (27904) covalent geometry : angle 0.50262 / 0.27 (38612) SS BOND : bond 0.00054 / 0.02 ( 3) SS BOND : angle 0.10072 / 0.07 ( 11) hydrogen bonds : bond 0.03440 / 2.49 ( 2033) hydrogen bonds : angle 3.74367 / 2.66 ( 6036) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.747 Fit side-chains REVERT: A 76 MET cc_start: 0.9008 (mmm) cc_final: 0.8592 (ppp) REVERT: A 602 MET cc_start: 0.9185 (mmm) cc_final: 0.8888 (mmp) REVERT: A 683 MET cc_start: 0.9293 (mmm) cc_final: 0.8878 (tpp) REVERT: A 1036 MET cc_start: 0.9440 (mmt) cc_final: 0.8981 (mmt) REVERT: A 1058 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8786 (mm-30) REVERT: A 1138 MET cc_start: 0.8848 (ppp) cc_final: 0.8472 (ppp) REVERT: A 1150 MET cc_start: 0.9110 (tpp) cc_final: 0.8696 (tmm) REVERT: B 76 MET cc_start: 0.9001 (mmm) cc_final: 0.8577 (ppp) REVERT: B 602 MET cc_start: 0.9189 (mmm) cc_final: 0.8892 (mmp) REVERT: B 683 MET cc_start: 0.9285 (mmm) cc_final: 0.8872 (tpp) REVERT: B 927 LYS cc_start: 0.9601 (mmtm) cc_final: 0.9213 (mmtm) REVERT: B 933 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8907 (tm-30) REVERT: B 1058 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8776 (mm-30) REVERT: B 1138 MET cc_start: 0.8848 (ppp) cc_final: 0.8470 (ppp) REVERT: B 1150 MET cc_start: 0.9117 (tpp) cc_final: 0.8698 (tmm) REVERT: C 76 MET cc_start: 0.9005 (mmm) cc_final: 0.8575 (ppp) REVERT: C 602 MET cc_start: 0.9189 (mmm) cc_final: 0.8892 (mmp) REVERT: C 683 MET cc_start: 0.9285 (mmm) cc_final: 0.8874 (tpp) REVERT: C 933 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8901 (tm-30) REVERT: C 1036 MET cc_start: 0.9394 (mmt) cc_final: 0.8951 (mmt) REVERT: C 1058 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8783 (mm-30) REVERT: C 1138 MET cc_start: 0.8851 (ppp) cc_final: 0.8474 (ppp) REVERT: C 1150 MET cc_start: 0.9118 (tpp) cc_final: 0.8697 (tmm) REVERT: D 76 MET cc_start: 0.9006 (mmm) cc_final: 0.8572 (ppp) REVERT: D 602 MET cc_start: 0.9182 (mmm) cc_final: 0.8892 (mmp) REVERT: D 683 MET cc_start: 0.9298 (mmm) cc_final: 0.8884 (tpp) REVERT: D 933 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8895 (tm-30) REVERT: D 1058 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8780 (mm-30) REVERT: D 1138 MET cc_start: 0.8851 (ppp) cc_final: 0.8473 (ppp) REVERT: D 1150 MET cc_start: 0.9116 (tpp) cc_final: 0.8696 (tmm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1408 time to fit residues: 64.1835 Evaluate side-chains 224 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 144 optimal weight: 0.0770 chunk 78 optimal weight: 0.8980 chunk 309 optimal weight: 3.9990 chunk 352 optimal weight: 50.0000 chunk 62 optimal weight: 9.9990 chunk 213 optimal weight: 40.0000 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 119 optimal weight: 0.0270 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.064044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.045654 restraints weight = 196728.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.046793 restraints weight = 97337.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.047572 restraints weight = 59986.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.048085 restraints weight = 42724.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.048434 restraints weight = 33773.554| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27907 Z= 0.109 Angle : 0.481 8.151 38623 Z= 0.247 Chirality : 0.037 0.121 4784 Planarity : 0.003 0.032 5048 Dihedral : 7.040 87.373 5416 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.13), residues: 4260 helix: 1.85 (0.10), residues: 2848 sheet: -0.34 (0.39), residues: 232 loop : -0.38 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1135 TYR 0.014 0.001 TYR C1041 PHE 0.012 0.001 PHE B 948 TRP 0.029 0.001 TRP A 842 HIS 0.001 0.000 HIS C 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (27904) covalent geometry : angle 0.48083 / 0.25 (38612) SS BOND : bond 0.00016 / 0.01 ( 3) SS BOND : angle 0.09531 / 0.06 ( 11) hydrogen bonds : bond 0.03207 / 2.32 ( 2033) hydrogen bonds : angle 3.52556 / 2.51 ( 6036) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.9020 (mmm) cc_final: 0.8512 (ppp) REVERT: A 602 MET cc_start: 0.9224 (mmm) cc_final: 0.8845 (mmp) REVERT: A 683 MET cc_start: 0.9264 (mmm) cc_final: 0.8790 (tpp) REVERT: A 1036 MET cc_start: 0.9415 (mmt) cc_final: 0.8820 (mmt) REVERT: A 1043 LYS cc_start: 0.9390 (mmtp) cc_final: 0.9162 (mmtp) REVERT: A 1058 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8767 (mm-30) REVERT: A 1138 MET cc_start: 0.8806 (ppp) cc_final: 0.8550 (ppp) REVERT: A 1150 MET cc_start: 0.9019 (tpp) cc_final: 0.8658 (tmm) REVERT: B 76 MET cc_start: 0.9016 (mmm) cc_final: 0.8486 (ppp) REVERT: B 602 MET cc_start: 0.9225 (mmm) cc_final: 0.8846 (mmp) REVERT: B 683 MET cc_start: 0.9258 (mmm) cc_final: 0.8786 (tpp) REVERT: B 915 MET cc_start: 0.9154 (mmt) cc_final: 0.8950 (mmt) REVERT: B 927 LYS cc_start: 0.9594 (mmtm) cc_final: 0.9215 (mmtm) REVERT: B 1036 MET cc_start: 0.9450 (mmt) cc_final: 0.8870 (mmt) REVERT: B 1058 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8749 (mm-30) REVERT: B 1138 MET cc_start: 0.8804 (ppp) cc_final: 0.8550 (ppp) REVERT: B 1150 MET cc_start: 0.9022 (tpp) cc_final: 0.8658 (tmm) REVERT: C 76 MET cc_start: 0.9014 (mmm) cc_final: 0.8484 (ppp) REVERT: C 602 MET cc_start: 0.9227 (mmm) cc_final: 0.8849 (mmp) REVERT: C 683 MET cc_start: 0.9261 (mmm) cc_final: 0.8790 (tpp) REVERT: C 927 LYS cc_start: 0.9595 (mmtm) cc_final: 0.9221 (mmtm) REVERT: C 1058 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8762 (mm-30) REVERT: C 1138 MET cc_start: 0.8805 (ppp) cc_final: 0.8551 (ppp) REVERT: C 1150 MET cc_start: 0.9031 (tpp) cc_final: 0.8661 (tmm) REVERT: D 76 MET cc_start: 0.9015 (mmm) cc_final: 0.8484 (ppp) REVERT: D 602 MET cc_start: 0.9225 (mmm) cc_final: 0.8848 (mmp) REVERT: D 683 MET cc_start: 0.9265 (mmm) cc_final: 0.8791 (tpp) REVERT: D 915 MET cc_start: 0.9161 (mmt) cc_final: 0.8955 (mmt) REVERT: D 927 LYS cc_start: 0.9559 (mmtm) cc_final: 0.9341 (mmtm) REVERT: D 1036 MET cc_start: 0.9487 (mmm) cc_final: 0.9251 (mmm) REVERT: D 1058 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8761 (mm-30) REVERT: D 1138 MET cc_start: 0.8820 (ppp) cc_final: 0.8567 (ppp) REVERT: D 1150 MET cc_start: 0.9034 (tpp) cc_final: 0.8660 (tmm) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1505 time to fit residues: 68.6337 Evaluate side-chains 230 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 353 optimal weight: 0.0470 chunk 14 optimal weight: 20.0000 chunk 407 optimal weight: 10.0000 chunk 79 optimal weight: 0.0000 chunk 379 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 254 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 422 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 overall best weight: 2.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.044871 restraints weight = 196079.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.046012 restraints weight = 97710.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.046780 restraints weight = 60335.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.047302 restraints weight = 43135.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.047624 restraints weight = 34124.323| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27907 Z= 0.133 Angle : 0.494 5.827 38623 Z= 0.256 Chirality : 0.037 0.133 4784 Planarity : 0.003 0.031 5048 Dihedral : 6.721 88.282 5416 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.14), residues: 4260 helix: 2.30 (0.10), residues: 2852 sheet: -0.34 (0.39), residues: 232 loop : -0.15 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 614 TYR 0.025 0.001 TYR C1041 PHE 0.022 0.001 PHE A 665 TRP 0.022 0.001 TRP B 842 HIS 0.002 0.001 HIS D 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (27904) covalent geometry : angle 0.49368 / 0.26 (38612) SS BOND : bond 0.00065 / 0.03 ( 3) SS BOND : angle 0.06550 / 0.04 ( 11) hydrogen bonds : bond 0.03242 / 2.34 ( 2033) hydrogen bonds : angle 3.50220 / 2.50 ( 6036) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8981 (mmm) cc_final: 0.8483 (ppp) REVERT: A 602 MET cc_start: 0.9166 (mmm) cc_final: 0.8953 (mmt) REVERT: A 683 MET cc_start: 0.9261 (mmm) cc_final: 0.8763 (tpp) REVERT: A 1036 MET cc_start: 0.9440 (mmt) cc_final: 0.8935 (mmt) REVERT: A 1043 LYS cc_start: 0.9326 (mmtp) cc_final: 0.9116 (mmtm) REVERT: A 1058 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8773 (mm-30) REVERT: A 1150 MET cc_start: 0.9012 (tpp) cc_final: 0.8548 (tmm) REVERT: B 76 MET cc_start: 0.9014 (mmm) cc_final: 0.8471 (ppp) REVERT: B 602 MET cc_start: 0.9166 (mmm) cc_final: 0.8951 (mmt) REVERT: B 683 MET cc_start: 0.9261 (mmm) cc_final: 0.8767 (tpp) REVERT: B 1036 MET cc_start: 0.9435 (mmt) cc_final: 0.9196 (mmt) REVERT: B 1042 MET cc_start: 0.9131 (mmm) cc_final: 0.8850 (mmm) REVERT: B 1043 LYS cc_start: 0.9436 (mmtm) cc_final: 0.9112 (mmtp) REVERT: B 1058 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8766 (mm-30) REVERT: B 1150 MET cc_start: 0.9004 (tpp) cc_final: 0.8548 (tmm) REVERT: C 76 MET cc_start: 0.8981 (mmm) cc_final: 0.8479 (ppp) REVERT: C 602 MET cc_start: 0.9172 (mmm) cc_final: 0.8956 (mmt) REVERT: C 683 MET cc_start: 0.9260 (mmm) cc_final: 0.8769 (tpp) REVERT: C 1036 MET cc_start: 0.9363 (mmt) cc_final: 0.8908 (mmp) REVERT: C 1058 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8766 (mm-30) REVERT: C 1150 MET cc_start: 0.9014 (tpp) cc_final: 0.8551 (tmm) REVERT: D 76 MET cc_start: 0.8983 (mmm) cc_final: 0.8478 (ppp) REVERT: D 602 MET cc_start: 0.9167 (mmm) cc_final: 0.8953 (mmt) REVERT: D 683 MET cc_start: 0.9263 (mmm) cc_final: 0.8766 (tpp) REVERT: D 1036 MET cc_start: 0.9409 (mmm) cc_final: 0.9167 (mmm) REVERT: D 1058 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8768 (mm-30) REVERT: D 1150 MET cc_start: 0.9020 (tpp) cc_final: 0.8552 (tmm) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1640 time to fit residues: 74.0532 Evaluate side-chains 228 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 334 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 128 optimal weight: 50.0000 chunk 340 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 344 optimal weight: 6.9990 chunk 366 optimal weight: 10.0000 chunk 280 optimal weight: 6.9990 chunk 403 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.044375 restraints weight = 197020.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.045476 restraints weight = 98069.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.046258 restraints weight = 61263.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.046761 restraints weight = 43795.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.047057 restraints weight = 34774.837| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27907 Z= 0.153 Angle : 0.507 7.486 38623 Z= 0.264 Chirality : 0.038 0.145 4784 Planarity : 0.003 0.030 5048 Dihedral : 6.546 89.133 5416 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.14), residues: 4260 helix: 2.52 (0.10), residues: 2832 sheet: -0.26 (0.39), residues: 232 loop : -0.08 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1135 TYR 0.030 0.001 TYR A1041 PHE 0.014 0.001 PHE B 948 TRP 0.020 0.001 TRP A 842 HIS 0.002 0.001 HIS C 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (27904) covalent geometry : angle 0.50697 / 0.26 (38612) SS BOND : bond 0.00078 / 0.04 ( 3) SS BOND : angle 0.10289 / 0.07 ( 11) hydrogen bonds : bond 0.03276 / 2.37 ( 2033) hydrogen bonds : angle 3.46980 / 2.47 ( 6036) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8964 (mmm) cc_final: 0.8588 (mmm) REVERT: A 602 MET cc_start: 0.9154 (mmm) cc_final: 0.8943 (mmt) REVERT: A 683 MET cc_start: 0.9341 (mmm) cc_final: 0.8814 (tpp) REVERT: A 1043 LYS cc_start: 0.9430 (mmtp) cc_final: 0.9163 (mmtp) REVERT: A 1058 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8780 (mm-30) REVERT: A 1150 MET cc_start: 0.9018 (tpp) cc_final: 0.8554 (tmm) REVERT: B 76 MET cc_start: 0.8968 (mmm) cc_final: 0.8585 (mmm) REVERT: B 602 MET cc_start: 0.9156 (mmm) cc_final: 0.8945 (mmt) REVERT: B 683 MET cc_start: 0.9341 (mmm) cc_final: 0.8817 (tpp) REVERT: B 1043 LYS cc_start: 0.9359 (mmtm) cc_final: 0.9147 (mmtp) REVERT: B 1058 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8777 (mm-30) REVERT: B 1150 MET cc_start: 0.9022 (tpp) cc_final: 0.8552 (tmm) REVERT: C 76 MET cc_start: 0.8963 (mmm) cc_final: 0.8582 (mmm) REVERT: C 683 MET cc_start: 0.9343 (mmm) cc_final: 0.8819 (tpp) REVERT: C 1036 MET cc_start: 0.9455 (mmt) cc_final: 0.9249 (mmt) REVERT: C 1043 LYS cc_start: 0.9359 (mmtm) cc_final: 0.9056 (mmtp) REVERT: C 1058 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8775 (mm-30) REVERT: C 1150 MET cc_start: 0.9020 (tpp) cc_final: 0.8555 (tmm) REVERT: D 76 MET cc_start: 0.8902 (mmm) cc_final: 0.8490 (mmm) REVERT: D 683 MET cc_start: 0.9342 (mmm) cc_final: 0.8834 (tpp) REVERT: D 1058 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8773 (mm-30) REVERT: D 1150 MET cc_start: 0.9028 (tpp) cc_final: 0.8553 (tmm) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1584 time to fit residues: 67.0573 Evaluate side-chains 228 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 194 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 413 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 424 optimal weight: 10.0000 chunk 263 optimal weight: 0.4980 chunk 91 optimal weight: 7.9990 chunk 380 optimal weight: 0.9980 chunk 339 optimal weight: 5.9990 chunk 346 optimal weight: 50.0000 chunk 153 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.059695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.042096 restraints weight = 176936.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.043265 restraints weight = 90110.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.044064 restraints weight = 56449.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.044595 restraints weight = 40189.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.044914 restraints weight = 31508.398| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27907 Z= 0.094 Angle : 0.486 6.693 38623 Z= 0.245 Chirality : 0.037 0.120 4784 Planarity : 0.003 0.029 5048 Dihedral : 6.352 88.889 5416 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.14), residues: 4260 helix: 2.63 (0.10), residues: 2832 sheet: -0.19 (0.39), residues: 236 loop : -0.02 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 576 TYR 0.023 0.001 TYR A1041 PHE 0.011 0.001 PHE C1037 TRP 0.016 0.001 TRP B 868 HIS 0.002 0.000 HIS D 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (27904) covalent geometry : angle 0.48653 / 0.25 (38612) SS BOND : bond 0.00003 / 0.00 ( 3) SS BOND : angle 0.18216 / 0.12 ( 11) hydrogen bonds : bond 0.02994 / 2.16 ( 2033) hydrogen bonds : angle 3.25801 / 2.32 ( 6036) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8858 (mmm) cc_final: 0.8395 (mmm) REVERT: A 683 MET cc_start: 0.9258 (mmm) cc_final: 0.8698 (tpp) REVERT: A 687 MET cc_start: 0.9649 (ppp) cc_final: 0.9395 (ppp) REVERT: A 985 GLU cc_start: 0.8524 (tp30) cc_final: 0.8319 (tp30) REVERT: A 1043 LYS cc_start: 0.9418 (mmtp) cc_final: 0.9120 (mmtp) REVERT: A 1058 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8741 (mm-30) REVERT: A 1150 MET cc_start: 0.9000 (tpp) cc_final: 0.8455 (tmm) REVERT: B 76 MET cc_start: 0.8854 (mmm) cc_final: 0.8370 (mmm) REVERT: B 683 MET cc_start: 0.9267 (mmm) cc_final: 0.8707 (tpp) REVERT: B 687 MET cc_start: 0.9649 (ppp) cc_final: 0.9396 (ppp) REVERT: B 985 GLU cc_start: 0.8527 (tp30) cc_final: 0.8309 (tp30) REVERT: B 1036 MET cc_start: 0.9348 (mmt) cc_final: 0.9128 (mmt) REVERT: B 1043 LYS cc_start: 0.9359 (mmtm) cc_final: 0.9153 (mmtp) REVERT: B 1058 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8768 (mm-30) REVERT: B 1150 MET cc_start: 0.9003 (tpp) cc_final: 0.8459 (tmm) REVERT: C 76 MET cc_start: 0.8849 (mmm) cc_final: 0.8369 (mmm) REVERT: C 683 MET cc_start: 0.9267 (mmm) cc_final: 0.8709 (tpp) REVERT: C 687 MET cc_start: 0.9649 (ppp) cc_final: 0.9398 (ppp) REVERT: C 985 GLU cc_start: 0.8516 (tp30) cc_final: 0.8310 (tp30) REVERT: C 1058 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8767 (mm-30) REVERT: C 1150 MET cc_start: 0.8990 (tpp) cc_final: 0.8459 (tmm) REVERT: D 76 MET cc_start: 0.8834 (mmm) cc_final: 0.8371 (mmm) REVERT: D 683 MET cc_start: 0.9268 (mmm) cc_final: 0.8704 (tpp) REVERT: D 687 MET cc_start: 0.9649 (ppp) cc_final: 0.9397 (ppp) REVERT: D 985 GLU cc_start: 0.8515 (tp30) cc_final: 0.8285 (tp30) REVERT: D 1036 MET cc_start: 0.9566 (mmm) cc_final: 0.9320 (mmm) REVERT: D 1058 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8766 (mm-30) REVERT: D 1150 MET cc_start: 0.8993 (tpp) cc_final: 0.8459 (tmm) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1595 time to fit residues: 73.8600 Evaluate side-chains 237 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 294 optimal weight: 2.9990 chunk 289 optimal weight: 9.9990 chunk 341 optimal weight: 50.0000 chunk 169 optimal weight: 9.9990 chunk 231 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 0 optimal weight: 60.0000 chunk 353 optimal weight: 3.9990 chunk 349 optimal weight: 40.0000 chunk 270 optimal weight: 3.9990 chunk 358 optimal weight: 0.0870 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 601 HIS D 601 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.063118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.044468 restraints weight = 196562.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.045605 restraints weight = 98766.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.046366 restraints weight = 61107.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.046870 restraints weight = 43797.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.047143 restraints weight = 34776.220| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27907 Z= 0.154 Angle : 0.521 6.418 38623 Z= 0.268 Chirality : 0.038 0.124 4784 Planarity : 0.003 0.028 5048 Dihedral : 6.209 89.980 5416 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.14), residues: 4260 helix: 2.77 (0.10), residues: 2836 sheet: -0.14 (0.39), residues: 236 loop : 0.11 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.019 0.001 TYR A1041 PHE 0.022 0.001 PHE D 883 TRP 0.023 0.001 TRP D 842 HIS 0.002 0.001 HIS D 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (27904) covalent geometry : angle 0.52105 / 0.27 (38612) SS BOND : bond 0.00078 / 0.04 ( 3) SS BOND : angle 0.17521 / 0.11 ( 11) hydrogen bonds : bond 0.03160 / 2.28 ( 2033) hydrogen bonds : angle 3.40466 / 2.43 ( 6036) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8863 (mmm) cc_final: 0.8465 (mmm) REVERT: A 560 MET cc_start: 0.9676 (mmt) cc_final: 0.9456 (mmp) REVERT: A 683 MET cc_start: 0.9335 (mmm) cc_final: 0.8799 (tpp) REVERT: A 687 MET cc_start: 0.9665 (ppp) cc_final: 0.9408 (ppp) REVERT: A 1058 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8733 (mm-30) REVERT: A 1150 MET cc_start: 0.8997 (tpp) cc_final: 0.8520 (tmm) REVERT: B 76 MET cc_start: 0.8861 (mmm) cc_final: 0.8464 (mmm) REVERT: B 560 MET cc_start: 0.9674 (mmt) cc_final: 0.9455 (mmp) REVERT: B 683 MET cc_start: 0.9334 (mmm) cc_final: 0.8800 (tpp) REVERT: B 687 MET cc_start: 0.9668 (ppp) cc_final: 0.9410 (ppp) REVERT: B 985 GLU cc_start: 0.8703 (tp30) cc_final: 0.8374 (tp30) REVERT: B 1036 MET cc_start: 0.9322 (mmt) cc_final: 0.9049 (mmt) REVERT: B 1045 GLN cc_start: 0.8863 (pt0) cc_final: 0.8634 (pm20) REVERT: B 1058 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8761 (mm-30) REVERT: B 1150 MET cc_start: 0.8988 (tpp) cc_final: 0.8521 (tmm) REVERT: C 76 MET cc_start: 0.8856 (mmm) cc_final: 0.8459 (mmm) REVERT: C 560 MET cc_start: 0.9668 (mmt) cc_final: 0.9453 (mmp) REVERT: C 683 MET cc_start: 0.9332 (mmm) cc_final: 0.8797 (tpp) REVERT: C 687 MET cc_start: 0.9666 (ppp) cc_final: 0.9408 (ppp) REVERT: C 985 GLU cc_start: 0.8695 (tp30) cc_final: 0.8351 (tp30) REVERT: C 1036 MET cc_start: 0.9406 (mmt) cc_final: 0.9074 (mpp) REVERT: C 1058 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8753 (mm-30) REVERT: C 1150 MET cc_start: 0.8973 (tpp) cc_final: 0.8520 (tmm) REVERT: D 76 MET cc_start: 0.8856 (mmm) cc_final: 0.8461 (mmm) REVERT: D 560 MET cc_start: 0.9670 (mmt) cc_final: 0.9452 (mmp) REVERT: D 683 MET cc_start: 0.9331 (mmm) cc_final: 0.8794 (tpp) REVERT: D 687 MET cc_start: 0.9665 (ppp) cc_final: 0.9409 (ppp) REVERT: D 985 GLU cc_start: 0.8692 (tp30) cc_final: 0.8349 (tp30) REVERT: D 1036 MET cc_start: 0.9458 (mmm) cc_final: 0.9194 (mmm) REVERT: D 1058 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8759 (mm-30) REVERT: D 1150 MET cc_start: 0.8991 (tpp) cc_final: 0.8523 (tmm) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1491 time to fit residues: 63.9385 Evaluate side-chains 225 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 379 optimal weight: 10.0000 chunk 24 optimal weight: 50.0000 chunk 242 optimal weight: 40.0000 chunk 134 optimal weight: 30.0000 chunk 354 optimal weight: 0.0270 chunk 388 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 overall best weight: 5.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 601 HIS D 601 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.057848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.039661 restraints weight = 179410.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.040721 restraints weight = 93310.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.041442 restraints weight = 60190.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.041854 restraints weight = 44346.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.042205 restraints weight = 36345.165| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 27907 Z= 0.262 Angle : 0.626 7.018 38623 Z= 0.328 Chirality : 0.041 0.134 4784 Planarity : 0.004 0.031 5048 Dihedral : 6.284 87.452 5416 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.14), residues: 4260 helix: 2.57 (0.10), residues: 2840 sheet: -0.14 (0.40), residues: 232 loop : 0.09 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B1135 TYR 0.021 0.002 TYR B 917 PHE 0.027 0.002 PHE B 948 TRP 0.038 0.002 TRP B 842 HIS 0.004 0.001 HIS D 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.26 (27904) covalent geometry : angle 0.62587 / 0.33 (38612) SS BOND : bond 0.00158 / 0.07 ( 3) SS BOND : angle 0.46572 / 0.30 ( 11) hydrogen bonds : bond 0.03690 / 2.68 ( 2033) hydrogen bonds : angle 3.79031 / 2.71 ( 6036) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.9016 (mmm) cc_final: 0.8664 (mmm) REVERT: A 659 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8916 (mm110) REVERT: A 683 MET cc_start: 0.9383 (mmm) cc_final: 0.8900 (tpp) REVERT: A 985 GLU cc_start: 0.8845 (tp30) cc_final: 0.8537 (tp30) REVERT: A 1058 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8739 (mm-30) REVERT: A 1150 MET cc_start: 0.8964 (tpp) cc_final: 0.8454 (tmm) REVERT: B 76 MET cc_start: 0.9016 (mmm) cc_final: 0.8662 (mmm) REVERT: B 659 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8921 (mm110) REVERT: B 683 MET cc_start: 0.9381 (mmm) cc_final: 0.8901 (tpp) REVERT: B 1058 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8767 (mm-30) REVERT: B 1150 MET cc_start: 0.8985 (tpp) cc_final: 0.8459 (tmm) REVERT: C 76 MET cc_start: 0.9010 (mmm) cc_final: 0.8658 (mmm) REVERT: C 659 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8921 (mm110) REVERT: C 683 MET cc_start: 0.9373 (mmm) cc_final: 0.8893 (tpp) REVERT: C 1036 MET cc_start: 0.9408 (mmt) cc_final: 0.9075 (mpp) REVERT: C 1058 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8759 (mm-30) REVERT: C 1150 MET cc_start: 0.8978 (tpp) cc_final: 0.8460 (tmm) REVERT: D 76 MET cc_start: 0.9011 (mmm) cc_final: 0.8656 (mmm) REVERT: D 659 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8918 (mm110) REVERT: D 683 MET cc_start: 0.9379 (mmm) cc_final: 0.8896 (tpp) REVERT: D 1036 MET cc_start: 0.9470 (mmm) cc_final: 0.9152 (mmm) REVERT: D 1058 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8762 (mm-30) REVERT: D 1150 MET cc_start: 0.8973 (tpp) cc_final: 0.8457 (tmm) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1405 time to fit residues: 59.1215 Evaluate side-chains 220 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 386 optimal weight: 2.9990 chunk 116 optimal weight: 40.0000 chunk 385 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 303 optimal weight: 0.6980 chunk 154 optimal weight: 20.0000 chunk 209 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 702 ASN B 702 ASN C 601 HIS C 702 ASN D 601 HIS D 702 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.063435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.044576 restraints weight = 194526.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.045743 restraints weight = 97206.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.046523 restraints weight = 60248.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.047032 restraints weight = 43201.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.047366 restraints weight = 34340.398| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27907 Z= 0.119 Angle : 0.517 7.424 38623 Z= 0.262 Chirality : 0.038 0.130 4784 Planarity : 0.003 0.027 5048 Dihedral : 6.130 88.048 5416 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.14), residues: 4260 helix: 2.78 (0.10), residues: 2836 sheet: -0.15 (0.39), residues: 236 loop : 0.15 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1135 TYR 0.017 0.001 TYR A1041 PHE 0.020 0.001 PHE B 883 TRP 0.035 0.002 TRP D 842 HIS 0.002 0.001 HIS C 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (27904) covalent geometry : angle 0.51718 / 0.26 (38612) SS BOND : bond 0.00006 / 0.00 ( 3) SS BOND : angle 0.18133 / 0.12 ( 11) hydrogen bonds : bond 0.03243 / 2.35 ( 2033) hydrogen bonds : angle 3.34638 / 2.38 ( 6036) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8986 (mmm) cc_final: 0.8634 (mmm) REVERT: A 659 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8850 (mm110) REVERT: A 683 MET cc_start: 0.9226 (mmm) cc_final: 0.8743 (tpp) REVERT: A 687 MET cc_start: 0.9661 (ppp) cc_final: 0.9412 (ppp) REVERT: A 1058 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8750 (mm-30) REVERT: A 1150 MET cc_start: 0.8893 (tpp) cc_final: 0.8400 (tmm) REVERT: B 76 MET cc_start: 0.8980 (mmm) cc_final: 0.8630 (mmm) REVERT: B 659 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8830 (mm110) REVERT: B 683 MET cc_start: 0.9227 (mmm) cc_final: 0.8725 (tpp) REVERT: B 687 MET cc_start: 0.9663 (ppp) cc_final: 0.9419 (ppp) REVERT: B 1058 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8762 (mm-30) REVERT: B 1150 MET cc_start: 0.8921 (tpp) cc_final: 0.8401 (tmm) REVERT: C 76 MET cc_start: 0.8980 (mmm) cc_final: 0.8627 (mmm) REVERT: C 659 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8831 (mm110) REVERT: C 683 MET cc_start: 0.9221 (mmm) cc_final: 0.8740 (tpp) REVERT: C 687 MET cc_start: 0.9660 (ppp) cc_final: 0.9415 (ppp) REVERT: C 1036 MET cc_start: 0.9369 (mmt) cc_final: 0.9088 (mmt) REVERT: C 1058 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8778 (mm-30) REVERT: C 1150 MET cc_start: 0.8912 (tpp) cc_final: 0.8406 (tmm) REVERT: D 76 MET cc_start: 0.8980 (mmm) cc_final: 0.8630 (mmm) REVERT: D 659 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8832 (mm110) REVERT: D 683 MET cc_start: 0.9224 (mmm) cc_final: 0.8719 (tpp) REVERT: D 687 MET cc_start: 0.9661 (ppp) cc_final: 0.9419 (ppp) REVERT: D 935 MET cc_start: 0.9098 (tpp) cc_final: 0.8683 (tpp) REVERT: D 1036 MET cc_start: 0.9457 (mmm) cc_final: 0.9124 (mmm) REVERT: D 1058 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8757 (mm-30) REVERT: D 1150 MET cc_start: 0.8881 (tpp) cc_final: 0.8402 (tmm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1414 time to fit residues: 61.3671 Evaluate side-chains 223 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 339 optimal weight: 30.0000 chunk 277 optimal weight: 3.9990 chunk 224 optimal weight: 50.0000 chunk 175 optimal weight: 0.0050 chunk 83 optimal weight: 0.9990 chunk 226 optimal weight: 30.0000 chunk 53 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 173 optimal weight: 0.0870 chunk 419 optimal weight: 30.0000 chunk 206 optimal weight: 50.0000 overall best weight: 1.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 HIS B 601 HIS C 601 HIS D 601 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.059435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.041292 restraints weight = 177949.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.042410 restraints weight = 91072.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.043183 restraints weight = 57893.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.043707 restraints weight = 41635.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.044052 restraints weight = 33150.531| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27907 Z= 0.115 Angle : 0.504 7.370 38623 Z= 0.255 Chirality : 0.037 0.125 4784 Planarity : 0.003 0.026 5048 Dihedral : 6.048 87.779 5416 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.14), residues: 4260 helix: 2.88 (0.10), residues: 2836 sheet: -0.16 (0.39), residues: 236 loop : 0.20 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1135 TYR 0.016 0.001 TYR A1041 PHE 0.026 0.001 PHE D 883 TRP 0.033 0.001 TRP D 842 HIS 0.003 0.001 HIS B 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (27904) covalent geometry : angle 0.50392 / 0.26 (38612) SS BOND : bond 0.00054 / 0.02 ( 3) SS BOND : angle 0.07114 / 0.05 ( 11) hydrogen bonds : bond 0.03073 / 2.22 ( 2033) hydrogen bonds : angle 3.27834 / 2.34 ( 6036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4244.49 seconds wall clock time: 73 minutes 47.70 seconds (4427.70 seconds total)