Starting phenix.real_space_refine on Mon Aug 25 11:07:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srk_40734/08_2025/8srk_40734.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srk_40734/08_2025/8srk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8srk_40734/08_2025/8srk_40734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srk_40734/08_2025/8srk_40734.map" model { file = "/net/cci-nas-00/data/ceres_data/8srk_40734/08_2025/8srk_40734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srk_40734/08_2025/8srk_40734.cif" } 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-2.0-5787/lib/python3.9/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, 122 Unusual residues: {' CA': 2, 'APR': 1, 'CLR': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {' CA': 2, 'APR': 1, 'CLR': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Restraints were copied for chains: B, C Time building chain proxies: 6.85, per 1000 atoms: 0.25 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: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.03 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: 4.47 Time building geometry restraints manager: 2.97 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: 0.06 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: 1.570 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.500 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 aren 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 covalent geometry : bond 0.00815 (27904) covalent geometry : angle 1.22806 (38612) SS BOND : bond 0.00211 ( 3) SS BOND : angle 0.25836 ( 11) hydrogen bonds : bond 0.14245 ( 2033) hydrogen bonds : angle 7.96058 ( 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 : 0.777 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: 0.1379 time to fit residues: 76.3056 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 : 0.871 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 592 GLN A1078 HIS B 592 GLN B1078 HIS C 592 GLN C1078 HIS D 592 GLN D1078 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.059466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.041874 restraints weight = 182425.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.042942 restraints weight = 95924.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.043689 restraints weight = 61077.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.044187 restraints weight = 44343.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.044470 restraints weight = 35538.004| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27907 Z= 0.220 Angle : 0.621 6.236 38623 Z= 0.333 Chirality : 0.040 0.148 4784 Planarity : 0.005 0.038 5048 Dihedral : 8.482 85.783 5416 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.25 % Allowed : 3.37 % Favored : 96.38 % 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 aren not related in a simple way. whole: -1.59 (0.11), residues: 4260 helix: -0.91 (0.08), residues: 2836 sheet: -0.49 (0.39), residues: 232 loop : -1.06 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1135 TYR 0.017 0.002 TYR C 917 PHE 0.018 0.002 PHE D 905 TRP 0.020 0.001 TRP A 842 HIS 0.004 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00452 (27904) covalent geometry : angle 0.62125 (38612) SS BOND : bond 0.00141 ( 3) SS BOND : angle 0.30853 ( 11) hydrogen bonds : bond 0.03915 ( 2033) hydrogen bonds : angle 4.33418 ( 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 277 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 273 time to evaluate : 0.896 Fit side-chains REVERT: A 76 MET cc_start: 0.8953 (mmm) cc_final: 0.8527 (ppp) REVERT: A 602 MET cc_start: 0.9147 (mmm) cc_final: 0.8848 (mmp) REVERT: A 683 MET cc_start: 0.9295 (mmm) cc_final: 0.8872 (tpp) REVERT: A 1058 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8770 (mm-30) REVERT: A 1138 MET cc_start: 0.8767 (ppp) cc_final: 0.8501 (ppp) REVERT: A 1150 MET cc_start: 0.9227 (tpp) cc_final: 0.8669 (tmm) REVERT: B 76 MET cc_start: 0.8961 (mmm) cc_final: 0.8524 (ppp) REVERT: B 602 MET cc_start: 0.9150 (mmm) cc_final: 0.8851 (mmp) REVERT: B 683 MET cc_start: 0.9288 (mmm) cc_final: 0.8868 (tpp) REVERT: B 915 MET cc_start: 0.9240 (mmt) cc_final: 0.8960 (mmp) REVERT: B 1058 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8766 (mm-30) REVERT: B 1138 MET cc_start: 0.8763 (ppp) cc_final: 0.8493 (ppp) REVERT: B 1150 MET cc_start: 0.9232 (tpp) cc_final: 0.8670 (tmm) REVERT: C 76 MET cc_start: 0.8966 (mmm) cc_final: 0.8520 (ppp) REVERT: C 602 MET cc_start: 0.9152 (mmm) cc_final: 0.8855 (mmp) REVERT: C 683 MET cc_start: 0.9291 (mmm) cc_final: 0.8871 (tpp) REVERT: C 915 MET cc_start: 0.9235 (mmt) cc_final: 0.8960 (mmp) REVERT: C 1058 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8765 (mm-30) REVERT: C 1138 MET cc_start: 0.8762 (ppp) cc_final: 0.8491 (ppp) REVERT: C 1150 MET cc_start: 0.9239 (tpp) cc_final: 0.8671 (tmm) REVERT: D 76 MET cc_start: 0.8961 (mmm) cc_final: 0.8522 (ppp) REVERT: D 602 MET cc_start: 0.9148 (mmm) cc_final: 0.8853 (mmp) REVERT: D 683 MET cc_start: 0.9301 (mmm) cc_final: 0.8876 (tpp) REVERT: D 915 MET cc_start: 0.9231 (mmt) cc_final: 0.8956 (mmp) REVERT: D 1036 MET cc_start: 0.9469 (mmm) cc_final: 0.9178 (mmm) REVERT: D 1058 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8764 (mm-30) REVERT: D 1138 MET cc_start: 0.8766 (ppp) cc_final: 0.8501 (ppp) REVERT: D 1150 MET cc_start: 0.9238 (tpp) cc_final: 0.8671 (tmm) outliers start: 4 outliers final: 0 residues processed: 277 average time/residue: 0.1381 time to fit residues: 64.7694 Evaluate side-chains 226 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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: 6.9990 chunk 24 optimal weight: 50.0000 chunk 99 optimal weight: 50.0000 chunk 184 optimal weight: 2.9990 chunk 230 optimal weight: 30.0000 chunk 74 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 371 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.039841 restraints weight = 185475.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.040883 restraints weight = 95442.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.041624 restraints weight = 60111.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.042089 restraints weight = 43579.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.042320 restraints weight = 35155.060| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 27907 Z= 0.256 Angle : 0.612 7.078 38623 Z= 0.329 Chirality : 0.040 0.135 4784 Planarity : 0.004 0.036 5048 Dihedral : 7.500 87.718 5416 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % 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 aren not related in a simple way. whole: 0.96 (0.13), residues: 4260 helix: 1.26 (0.10), residues: 2848 sheet: -0.40 (0.39), residues: 232 loop : -0.51 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1135 TYR 0.024 0.002 TYR A 917 PHE 0.016 0.002 PHE C 905 TRP 0.021 0.002 TRP A 842 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00522 (27904) covalent geometry : angle 0.61235 (38612) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.40975 ( 11) hydrogen bonds : bond 0.03984 ( 2033) hydrogen bonds : angle 4.02201 ( 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 253 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.937 Fit side-chains REVERT: A 676 CYS cc_start: 0.9329 (m) cc_final: 0.9046 (t) REVERT: A 683 MET cc_start: 0.9401 (mmm) cc_final: 0.9062 (tpp) REVERT: A 933 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8914 (tm-30) REVERT: A 1036 MET cc_start: 0.9396 (mmt) cc_final: 0.8882 (mmt) REVERT: A 1058 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8767 (mm-30) REVERT: A 1138 MET cc_start: 0.8883 (ppp) cc_final: 0.8438 (ppp) REVERT: A 1150 MET cc_start: 0.9156 (tpp) cc_final: 0.8680 (tmm) REVERT: B 676 CYS cc_start: 0.9328 (m) cc_final: 0.9044 (t) REVERT: B 683 MET cc_start: 0.9393 (mmm) cc_final: 0.9059 (tpp) REVERT: B 933 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8934 (tm-30) REVERT: B 1036 MET cc_start: 0.9396 (mmt) cc_final: 0.8900 (mmt) REVERT: B 1058 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8758 (mm-30) REVERT: B 1138 MET cc_start: 0.8894 (ppp) cc_final: 0.8460 (ppp) REVERT: B 1150 MET cc_start: 0.9153 (tpp) cc_final: 0.8681 (tmm) REVERT: C 676 CYS cc_start: 0.9323 (m) cc_final: 0.9056 (t) REVERT: C 683 MET cc_start: 0.9396 (mmm) cc_final: 0.9061 (tpp) REVERT: C 933 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8930 (tm-30) REVERT: C 1036 MET cc_start: 0.9400 (mmt) cc_final: 0.8905 (mmt) REVERT: C 1058 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8763 (mm-30) REVERT: C 1138 MET cc_start: 0.8885 (ppp) cc_final: 0.8441 (ppp) REVERT: C 1150 MET cc_start: 0.9079 (tpp) cc_final: 0.8672 (tmm) REVERT: D 676 CYS cc_start: 0.9331 (m) cc_final: 0.9051 (t) REVERT: D 683 MET cc_start: 0.9404 (mmm) cc_final: 0.9064 (tpp) REVERT: D 1058 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8764 (mm-30) REVERT: D 1138 MET cc_start: 0.8895 (ppp) cc_final: 0.8461 (ppp) REVERT: D 1150 MET cc_start: 0.9080 (tpp) cc_final: 0.8671 (tmm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1429 time to fit residues: 60.8437 Evaluate side-chains 217 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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: 4.9990 chunk 78 optimal weight: 0.3980 chunk 309 optimal weight: 1.9990 chunk 352 optimal weight: 50.0000 chunk 62 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 14 optimal weight: 40.0000 chunk 250 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.059364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.041488 restraints weight = 181043.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.042609 restraints weight = 91317.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.043384 restraints weight = 56726.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.043750 restraints weight = 40352.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.044153 restraints weight = 33507.754| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27907 Z= 0.119 Angle : 0.503 7.575 38623 Z= 0.260 Chirality : 0.038 0.125 4784 Planarity : 0.003 0.034 5048 Dihedral : 7.117 87.386 5416 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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 aren not related in a simple way. whole: 1.70 (0.13), residues: 4260 helix: 1.89 (0.10), residues: 2832 sheet: -0.40 (0.39), residues: 232 loop : -0.35 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.027 0.001 TYR B1041 PHE 0.021 0.001 PHE C 665 TRP 0.029 0.002 TRP C 842 HIS 0.002 0.000 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00260 (27904) covalent geometry : angle 0.50257 (38612) SS BOND : bond 0.00008 ( 3) SS BOND : angle 0.15622 ( 11) hydrogen bonds : bond 0.03484 ( 2033) hydrogen bonds : angle 3.61881 ( 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 265 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.676 Fit side-chains REVERT: A 602 MET cc_start: 0.9180 (mmm) cc_final: 0.8899 (mmt) REVERT: A 615 MET cc_start: 0.9465 (mmp) cc_final: 0.8965 (mmm) REVERT: A 676 CYS cc_start: 0.9313 (m) cc_final: 0.9012 (t) REVERT: A 683 MET cc_start: 0.9315 (mmm) cc_final: 0.8814 (tpp) REVERT: A 1036 MET cc_start: 0.9331 (mmt) cc_final: 0.9042 (mmt) REVERT: A 1058 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8785 (mm-30) REVERT: A 1150 MET cc_start: 0.8912 (tpp) cc_final: 0.8541 (tmm) REVERT: B 602 MET cc_start: 0.9189 (mmm) cc_final: 0.8898 (mmt) REVERT: B 676 CYS cc_start: 0.9309 (m) cc_final: 0.9010 (t) REVERT: B 683 MET cc_start: 0.9310 (mmm) cc_final: 0.8811 (tpp) REVERT: B 927 LYS cc_start: 0.9574 (mmtm) cc_final: 0.9136 (mmtp) REVERT: B 1036 MET cc_start: 0.9328 (mmt) cc_final: 0.9048 (mmt) REVERT: B 1058 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8779 (mm-30) REVERT: B 1138 MET cc_start: 0.8798 (ppp) cc_final: 0.8522 (ppp) REVERT: B 1150 MET cc_start: 0.8907 (tpp) cc_final: 0.8543 (tmm) REVERT: C 602 MET cc_start: 0.9193 (mmm) cc_final: 0.8901 (mmt) REVERT: C 676 CYS cc_start: 0.9316 (m) cc_final: 0.9006 (t) REVERT: C 683 MET cc_start: 0.9310 (mmm) cc_final: 0.8813 (tpp) REVERT: C 927 LYS cc_start: 0.9575 (mmtm) cc_final: 0.9151 (mmtp) REVERT: C 1058 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8780 (mm-30) REVERT: C 1150 MET cc_start: 0.8921 (tpp) cc_final: 0.8544 (tmm) REVERT: D 602 MET cc_start: 0.9192 (mmm) cc_final: 0.8903 (mmt) REVERT: D 676 CYS cc_start: 0.9315 (m) cc_final: 0.9018 (t) REVERT: D 683 MET cc_start: 0.9314 (mmm) cc_final: 0.8815 (tpp) REVERT: D 927 LYS cc_start: 0.9583 (mmtm) cc_final: 0.9340 (mmtm) REVERT: D 1036 MET cc_start: 0.9490 (mmt) cc_final: 0.8909 (mmt) REVERT: D 1058 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8783 (mm-30) REVERT: D 1150 MET cc_start: 0.8926 (tpp) cc_final: 0.8548 (tmm) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1313 time to fit residues: 59.7511 Evaluate side-chains 234 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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: 40.0000 chunk 14 optimal weight: 40.0000 chunk 407 optimal weight: 9.9990 chunk 79 optimal weight: 0.0670 chunk 379 optimal weight: 5.9990 chunk 42 optimal weight: 0.0370 chunk 254 optimal weight: 10.0000 chunk 221 optimal weight: 50.0000 chunk 422 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 292 optimal weight: 0.6980 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.063133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.044518 restraints weight = 195079.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.045659 restraints weight = 96927.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.046430 restraints weight = 59822.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.046957 restraints weight = 42488.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.047198 restraints weight = 33492.604| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27907 Z= 0.133 Angle : 0.498 6.540 38623 Z= 0.259 Chirality : 0.038 0.143 4784 Planarity : 0.003 0.032 5048 Dihedral : 6.875 87.479 5416 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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 aren not related in a simple way. whole: 2.16 (0.14), residues: 4260 helix: 2.29 (0.10), residues: 2832 sheet: -0.48 (0.40), residues: 208 loop : -0.25 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.032 0.001 TYR A1041 PHE 0.017 0.001 PHE A 665 TRP 0.020 0.001 TRP B 842 HIS 0.003 0.001 HIS A 813 Details of bonding type rmsd covalent geometry : bond 0.00289 (27904) covalent geometry : angle 0.49840 (38612) SS BOND : bond 0.00069 ( 3) SS BOND : angle 0.06544 ( 11) hydrogen bonds : bond 0.03339 ( 2033) hydrogen bonds : angle 3.55372 ( 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 259 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 602 MET cc_start: 0.9178 (mmm) cc_final: 0.8937 (mmt) REVERT: A 615 MET cc_start: 0.9562 (mmp) cc_final: 0.9289 (tpp) REVERT: A 676 CYS cc_start: 0.9312 (m) cc_final: 0.9001 (t) REVERT: A 683 MET cc_start: 0.9341 (mmm) cc_final: 0.8791 (tpp) REVERT: A 1058 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8778 (mm-30) REVERT: A 1138 MET cc_start: 0.8719 (ppp) cc_final: 0.8429 (ppp) REVERT: A 1150 MET cc_start: 0.9003 (tpp) cc_final: 0.8548 (tmm) REVERT: B 602 MET cc_start: 0.9276 (mmt) cc_final: 0.9059 (mmp) REVERT: B 615 MET cc_start: 0.9485 (mmp) cc_final: 0.8921 (mmm) REVERT: B 676 CYS cc_start: 0.9318 (m) cc_final: 0.9000 (t) REVERT: B 683 MET cc_start: 0.9338 (mmm) cc_final: 0.8789 (tpp) REVERT: B 1058 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8779 (mm-30) REVERT: B 1150 MET cc_start: 0.9005 (tpp) cc_final: 0.8545 (tmm) REVERT: C 602 MET cc_start: 0.9184 (mmm) cc_final: 0.8945 (mmt) REVERT: C 615 MET cc_start: 0.9482 (mmp) cc_final: 0.8941 (mmm) REVERT: C 676 CYS cc_start: 0.9315 (m) cc_final: 0.9000 (t) REVERT: C 683 MET cc_start: 0.9352 (mmm) cc_final: 0.8829 (tpp) REVERT: C 1036 MET cc_start: 0.9472 (mmt) cc_final: 0.9139 (mpp) REVERT: C 1042 MET cc_start: 0.9157 (mmm) cc_final: 0.8913 (mmm) REVERT: C 1058 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8774 (mm-30) REVERT: C 1138 MET cc_start: 0.8720 (ppp) cc_final: 0.8433 (ppp) REVERT: C 1150 MET cc_start: 0.9011 (tpp) cc_final: 0.8547 (tmm) REVERT: D 602 MET cc_start: 0.9182 (mmm) cc_final: 0.8938 (mmt) REVERT: D 615 MET cc_start: 0.9477 (mmp) cc_final: 0.8936 (mmm) REVERT: D 676 CYS cc_start: 0.9315 (m) cc_final: 0.9006 (t) REVERT: D 683 MET cc_start: 0.9339 (mmm) cc_final: 0.8790 (tpp) REVERT: D 1036 MET cc_start: 0.9457 (mmt) cc_final: 0.9219 (mmp) REVERT: D 1058 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8777 (mm-30) REVERT: D 1150 MET cc_start: 0.9002 (tpp) cc_final: 0.8548 (tmm) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1536 time to fit residues: 66.6509 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 : 0.849 ------------------------------------------------------------------------------- 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: 50.0000 chunk 244 optimal weight: 10.0000 chunk 128 optimal weight: 50.0000 chunk 340 optimal weight: 5.9990 chunk 170 optimal weight: 0.0870 chunk 317 optimal weight: 9.9990 chunk 344 optimal weight: 9.9990 chunk 366 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 403 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.063300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.044685 restraints weight = 195209.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.045826 restraints weight = 96175.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.046596 restraints weight = 59215.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.047087 restraints weight = 42202.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.047319 restraints weight = 33454.909| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27907 Z= 0.133 Angle : 0.493 5.809 38623 Z= 0.256 Chirality : 0.037 0.118 4784 Planarity : 0.003 0.029 5048 Dihedral : 6.690 88.335 5416 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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 aren not related in a simple way. whole: 2.42 (0.14), residues: 4260 helix: 2.48 (0.10), residues: 2832 sheet: -0.38 (0.41), residues: 208 loop : -0.13 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1135 TYR 0.017 0.001 TYR D1041 PHE 0.016 0.001 PHE A 665 TRP 0.018 0.001 TRP C 842 HIS 0.002 0.001 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00292 (27904) covalent geometry : angle 0.49297 (38612) SS BOND : bond 0.00043 ( 3) SS BOND : angle 0.05155 ( 11) hydrogen bonds : bond 0.03246 ( 2033) hydrogen bonds : angle 3.47686 ( 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 253 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 615 MET cc_start: 0.9420 (mmp) cc_final: 0.9201 (tpp) REVERT: A 676 CYS cc_start: 0.9269 (m) cc_final: 0.8965 (t) REVERT: A 683 MET cc_start: 0.9249 (mmm) cc_final: 0.8710 (tpp) REVERT: A 687 MET cc_start: 0.9629 (ppp) cc_final: 0.9400 (ppp) REVERT: A 1058 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8719 (mm-30) REVERT: A 1138 MET cc_start: 0.8772 (ppp) cc_final: 0.8496 (ppp) REVERT: A 1150 MET cc_start: 0.8841 (tpp) cc_final: 0.8435 (tmm) REVERT: B 602 MET cc_start: 0.9193 (mmt) cc_final: 0.8984 (mmp) REVERT: B 615 MET cc_start: 0.9339 (mmp) cc_final: 0.8775 (mmm) REVERT: B 676 CYS cc_start: 0.9272 (m) cc_final: 0.8967 (t) REVERT: B 683 MET cc_start: 0.9242 (mmm) cc_final: 0.8709 (tpp) REVERT: B 687 MET cc_start: 0.9632 (ppp) cc_final: 0.9402 (ppp) REVERT: B 1058 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8724 (mm-30) REVERT: B 1138 MET cc_start: 0.8708 (ppp) cc_final: 0.8432 (ppp) REVERT: B 1150 MET cc_start: 0.8841 (tpp) cc_final: 0.8438 (tmm) REVERT: C 615 MET cc_start: 0.9282 (mmp) cc_final: 0.8758 (mmm) REVERT: C 676 CYS cc_start: 0.9270 (m) cc_final: 0.8964 (t) REVERT: C 683 MET cc_start: 0.9249 (mmm) cc_final: 0.8717 (tpp) REVERT: C 687 MET cc_start: 0.9630 (ppp) cc_final: 0.9402 (ppp) REVERT: C 1058 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8722 (mm-30) REVERT: C 1138 MET cc_start: 0.8780 (ppp) cc_final: 0.8491 (ppp) REVERT: C 1150 MET cc_start: 0.8855 (tpp) cc_final: 0.8440 (tmm) REVERT: D 615 MET cc_start: 0.9284 (mmp) cc_final: 0.8759 (mmm) REVERT: D 676 CYS cc_start: 0.9277 (m) cc_final: 0.8973 (t) REVERT: D 683 MET cc_start: 0.9248 (mmm) cc_final: 0.8711 (tpp) REVERT: D 687 MET cc_start: 0.9623 (ppp) cc_final: 0.9397 (ppp) REVERT: D 1036 MET cc_start: 0.9431 (mmt) cc_final: 0.9057 (mmp) REVERT: D 1043 LYS cc_start: 0.9344 (mmtm) cc_final: 0.9058 (mmtp) REVERT: D 1058 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8718 (mm-30) REVERT: D 1138 MET cc_start: 0.8712 (ppp) cc_final: 0.8434 (ppp) REVERT: D 1150 MET cc_start: 0.8841 (tpp) cc_final: 0.8438 (tmm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1380 time to fit residues: 60.2170 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 : 1.174 ------------------------------------------------------------------------------- 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: 1.9990 chunk 89 optimal weight: 3.9990 chunk 413 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 424 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 380 optimal weight: 7.9990 chunk 339 optimal weight: 30.0000 chunk 346 optimal weight: 50.0000 chunk 153 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS C 601 HIS D 601 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.044185 restraints weight = 193643.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.045313 restraints weight = 97158.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.046091 restraints weight = 60422.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.046584 restraints weight = 43124.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.046876 restraints weight = 34224.440| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27907 Z= 0.164 Angle : 0.534 6.600 38623 Z= 0.276 Chirality : 0.038 0.148 4784 Planarity : 0.003 0.029 5048 Dihedral : 6.623 89.264 5416 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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 aren not related in a simple way. whole: 2.56 (0.14), residues: 4260 helix: 2.55 (0.10), residues: 2836 sheet: -0.23 (0.41), residues: 208 loop : -0.00 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 614 TYR 0.014 0.001 TYR D1041 PHE 0.013 0.001 PHE D 948 TRP 0.019 0.001 TRP D 842 HIS 0.002 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00359 (27904) covalent geometry : angle 0.53430 (38612) SS BOND : bond 0.00093 ( 3) SS BOND : angle 0.15653 ( 11) hydrogen bonds : bond 0.03299 ( 2033) hydrogen bonds : angle 3.52563 ( 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 248 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 615 MET cc_start: 0.9380 (mmp) cc_final: 0.9178 (tpp) REVERT: A 676 CYS cc_start: 0.9267 (m) cc_final: 0.8978 (t) REVERT: A 683 MET cc_start: 0.9250 (mmm) cc_final: 0.8728 (tpp) REVERT: A 1058 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8710 (mm-30) REVERT: A 1138 MET cc_start: 0.8833 (ppp) cc_final: 0.8492 (ppp) REVERT: A 1150 MET cc_start: 0.8824 (tpp) cc_final: 0.8382 (tmm) REVERT: B 602 MET cc_start: 0.9183 (mmt) cc_final: 0.8970 (mmm) REVERT: B 676 CYS cc_start: 0.9268 (m) cc_final: 0.8976 (t) REVERT: B 683 MET cc_start: 0.9245 (mmm) cc_final: 0.8721 (tpp) REVERT: B 1036 MET cc_start: 0.9314 (mmm) cc_final: 0.8447 (mpp) REVERT: B 1058 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8709 (mm-30) REVERT: B 1150 MET cc_start: 0.8821 (tpp) cc_final: 0.8380 (tmm) REVERT: C 676 CYS cc_start: 0.9277 (m) cc_final: 0.8977 (t) REVERT: C 683 MET cc_start: 0.9250 (mmm) cc_final: 0.8732 (tpp) REVERT: C 1036 MET cc_start: 0.9442 (mmt) cc_final: 0.9128 (mpp) REVERT: C 1058 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8710 (mm-30) REVERT: C 1138 MET cc_start: 0.8826 (ppp) cc_final: 0.8485 (ppp) REVERT: C 1150 MET cc_start: 0.8837 (tpp) cc_final: 0.8385 (tmm) REVERT: D 676 CYS cc_start: 0.9272 (m) cc_final: 0.8981 (t) REVERT: D 683 MET cc_start: 0.9243 (mmm) cc_final: 0.8718 (tpp) REVERT: D 1058 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8712 (mm-30) REVERT: D 1150 MET cc_start: 0.8812 (tpp) cc_final: 0.8382 (tmm) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1267 time to fit residues: 54.3253 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 : 1.017 ------------------------------------------------------------------------------- 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: 0.9990 chunk 341 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 231 optimal weight: 30.0000 chunk 190 optimal weight: 0.9990 chunk 0 optimal weight: 70.0000 chunk 353 optimal weight: 0.3980 chunk 349 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 358 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS C 601 HIS D 601 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.063730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.044977 restraints weight = 194326.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.046149 restraints weight = 97305.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.046944 restraints weight = 59846.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.047461 restraints weight = 42490.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.047839 restraints weight = 33492.243| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27907 Z= 0.116 Angle : 0.496 6.750 38623 Z= 0.255 Chirality : 0.038 0.182 4784 Planarity : 0.003 0.028 5048 Dihedral : 6.486 89.575 5416 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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 aren not related in a simple way. whole: 2.69 (0.14), residues: 4260 helix: 2.65 (0.10), residues: 2832 sheet: -0.15 (0.41), residues: 208 loop : 0.04 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1135 TYR 0.012 0.001 TYR D1041 PHE 0.012 0.001 PHE A 948 TRP 0.021 0.001 TRP B 842 HIS 0.002 0.000 HIS D 813 Details of bonding type rmsd covalent geometry : bond 0.00256 (27904) covalent geometry : angle 0.49583 (38612) SS BOND : bond 0.00049 ( 3) SS BOND : angle 0.10895 ( 11) hydrogen bonds : bond 0.03119 ( 2033) hydrogen bonds : angle 3.38384 ( 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 254 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 676 CYS cc_start: 0.9269 (m) cc_final: 0.8958 (t) REVERT: A 683 MET cc_start: 0.9219 (mmm) cc_final: 0.8697 (tpp) REVERT: A 687 MET cc_start: 0.9610 (ppp) cc_final: 0.9401 (ppp) REVERT: A 1036 MET cc_start: 0.9254 (mmm) cc_final: 0.8302 (mpp) REVERT: A 1058 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8730 (mm-30) REVERT: A 1138 MET cc_start: 0.8817 (ppp) cc_final: 0.8432 (ppp) REVERT: A 1150 MET cc_start: 0.8767 (tpp) cc_final: 0.8342 (tmm) REVERT: B 602 MET cc_start: 0.9170 (mmt) cc_final: 0.8957 (mmm) REVERT: B 676 CYS cc_start: 0.9270 (m) cc_final: 0.8959 (t) REVERT: B 683 MET cc_start: 0.9207 (mmm) cc_final: 0.8683 (tpp) REVERT: B 687 MET cc_start: 0.9611 (ppp) cc_final: 0.9403 (ppp) REVERT: B 816 LEU cc_start: 0.9543 (tt) cc_final: 0.9343 (tp) REVERT: B 1036 MET cc_start: 0.9255 (mmm) cc_final: 0.8460 (mpp) REVERT: B 1058 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8754 (mm-30) REVERT: B 1138 MET cc_start: 0.8704 (ppp) cc_final: 0.8500 (ppp) REVERT: B 1150 MET cc_start: 0.8778 (tpp) cc_final: 0.8346 (tmm) REVERT: C 676 CYS cc_start: 0.9271 (m) cc_final: 0.8960 (t) REVERT: C 683 MET cc_start: 0.9214 (mmm) cc_final: 0.8694 (tpp) REVERT: C 687 MET cc_start: 0.9610 (ppp) cc_final: 0.9401 (ppp) REVERT: C 1058 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8758 (mm-30) REVERT: C 1138 MET cc_start: 0.8817 (ppp) cc_final: 0.8442 (ppp) REVERT: C 1150 MET cc_start: 0.8785 (tpp) cc_final: 0.8348 (tmm) REVERT: D 676 CYS cc_start: 0.9270 (m) cc_final: 0.8967 (t) REVERT: D 683 MET cc_start: 0.9202 (mmm) cc_final: 0.8679 (tpp) REVERT: D 687 MET cc_start: 0.9612 (ppp) cc_final: 0.9405 (ppp) REVERT: D 1046 GLU cc_start: 0.8446 (pp20) cc_final: 0.8073 (pp20) REVERT: D 1058 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8737 (mm-30) REVERT: D 1150 MET cc_start: 0.8768 (tpp) cc_final: 0.8345 (tmm) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1457 time to fit residues: 63.2281 Evaluate side-chains 232 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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: 0.0570 chunk 24 optimal weight: 50.0000 chunk 242 optimal weight: 50.0000 chunk 134 optimal weight: 30.0000 chunk 354 optimal weight: 50.0000 chunk 388 optimal weight: 9.9990 chunk 14 optimal weight: 30.0000 chunk 17 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 238 optimal weight: 50.0000 chunk 32 optimal weight: 8.9990 overall best weight: 4.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 HIS ** C1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 HIS ** D1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.062629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.043744 restraints weight = 194677.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.044840 restraints weight = 96563.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.045614 restraints weight = 59945.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.046136 restraints weight = 42765.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.046475 restraints weight = 33627.373| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27907 Z= 0.194 Angle : 0.568 6.950 38623 Z= 0.294 Chirality : 0.039 0.154 4784 Planarity : 0.003 0.029 5048 Dihedral : 6.442 89.529 5416 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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 aren not related in a simple way. whole: 2.74 (0.14), residues: 4260 helix: 2.68 (0.10), residues: 2832 sheet: -0.05 (0.42), residues: 200 loop : 0.07 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 617 TYR 0.016 0.001 TYR C 917 PHE 0.023 0.002 PHE B 883 TRP 0.027 0.001 TRP B 842 HIS 0.003 0.001 HIS C 682 Details of bonding type rmsd covalent geometry : bond 0.00419 (27904) covalent geometry : angle 0.56799 (38612) SS BOND : bond 0.00125 ( 3) SS BOND : angle 0.20768 ( 11) hydrogen bonds : bond 0.03376 ( 2033) hydrogen bonds : angle 3.58647 ( 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 249 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 560 MET cc_start: 0.9729 (mmp) cc_final: 0.9365 (mmt) REVERT: A 676 CYS cc_start: 0.9273 (m) cc_final: 0.8992 (t) REVERT: A 683 MET cc_start: 0.9267 (mmm) cc_final: 0.8763 (tpp) REVERT: A 687 MET cc_start: 0.9629 (ppp) cc_final: 0.9414 (ppp) REVERT: A 1022 ILE cc_start: 0.9777 (tt) cc_final: 0.9575 (tt) REVERT: A 1058 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8674 (mm-30) REVERT: A 1150 MET cc_start: 0.8802 (tpp) cc_final: 0.8350 (tmm) REVERT: B 560 MET cc_start: 0.9726 (mmp) cc_final: 0.9343 (mmt) REVERT: B 602 MET cc_start: 0.9192 (mmt) cc_final: 0.8974 (mmm) REVERT: B 676 CYS cc_start: 0.9274 (m) cc_final: 0.8991 (t) REVERT: B 683 MET cc_start: 0.9255 (mmm) cc_final: 0.8750 (tpp) REVERT: B 687 MET cc_start: 0.9627 (ppp) cc_final: 0.9415 (ppp) REVERT: B 1036 MET cc_start: 0.9283 (mmm) cc_final: 0.8778 (mpp) REVERT: B 1058 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8697 (mm-30) REVERT: B 1138 MET cc_start: 0.8685 (ppp) cc_final: 0.8462 (ppp) REVERT: B 1150 MET cc_start: 0.8788 (tpp) cc_final: 0.8413 (tmm) REVERT: C 560 MET cc_start: 0.9724 (mmp) cc_final: 0.9353 (mmt) REVERT: C 676 CYS cc_start: 0.9293 (m) cc_final: 0.9012 (t) REVERT: C 683 MET cc_start: 0.9264 (mmm) cc_final: 0.8758 (tpp) REVERT: C 687 MET cc_start: 0.9626 (ppp) cc_final: 0.9409 (ppp) REVERT: C 1036 MET cc_start: 0.9454 (mmt) cc_final: 0.9200 (mpp) REVERT: C 1058 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8697 (mm-30) REVERT: C 1150 MET cc_start: 0.8820 (tpp) cc_final: 0.8355 (tmm) REVERT: D 560 MET cc_start: 0.9729 (mmp) cc_final: 0.9363 (mmt) REVERT: D 676 CYS cc_start: 0.9272 (m) cc_final: 0.8991 (t) REVERT: D 683 MET cc_start: 0.9256 (mmm) cc_final: 0.8748 (tpp) REVERT: D 687 MET cc_start: 0.9627 (ppp) cc_final: 0.9416 (ppp) REVERT: D 1058 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8737 (mm-30) REVERT: D 1150 MET cc_start: 0.8795 (tpp) cc_final: 0.8414 (tmm) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1427 time to fit residues: 61.1907 Evaluate side-chains 227 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 0.8980 chunk 116 optimal weight: 50.0000 chunk 385 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 303 optimal weight: 0.5980 chunk 154 optimal weight: 20.0000 chunk 209 optimal weight: 4.9990 chunk 366 optimal weight: 9.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS C 601 HIS D 601 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.044995 restraints weight = 193058.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.046147 restraints weight = 96863.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.046950 restraints weight = 60270.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.047489 restraints weight = 42799.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.047842 restraints weight = 33618.302| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27907 Z= 0.108 Angle : 0.520 7.637 38623 Z= 0.262 Chirality : 0.037 0.149 4784 Planarity : 0.003 0.029 5048 Dihedral : 6.311 89.466 5416 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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 aren not related in a simple way. whole: 2.89 (0.14), residues: 4260 helix: 2.80 (0.10), residues: 2832 sheet: -0.02 (0.42), residues: 200 loop : 0.11 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 614 TYR 0.009 0.001 TYR D1041 PHE 0.016 0.001 PHE C 883 TRP 0.026 0.002 TRP C 842 HIS 0.002 0.001 HIS B 813 Details of bonding type rmsd covalent geometry : bond 0.00241 (27904) covalent geometry : angle 0.51980 (38612) SS BOND : bond 0.00027 ( 3) SS BOND : angle 0.19672 ( 11) hydrogen bonds : bond 0.03099 ( 2033) hydrogen bonds : angle 3.32928 ( 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 253 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 560 MET cc_start: 0.9771 (mmp) cc_final: 0.9562 (mmt) REVERT: A 676 CYS cc_start: 0.9327 (m) cc_final: 0.8979 (t) REVERT: A 683 MET cc_start: 0.9319 (mmm) cc_final: 0.8801 (tpp) REVERT: A 687 MET cc_start: 0.9654 (ppp) cc_final: 0.9399 (ppp) REVERT: A 1036 MET cc_start: 0.9259 (mmm) cc_final: 0.8262 (mpp) REVERT: A 1058 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8768 (mm-30) REVERT: A 1150 MET cc_start: 0.8870 (tpp) cc_final: 0.8450 (tmm) REVERT: B 560 MET cc_start: 0.9774 (mmp) cc_final: 0.9553 (mmt) REVERT: B 676 CYS cc_start: 0.9330 (m) cc_final: 0.8982 (t) REVERT: B 683 MET cc_start: 0.9320 (mmm) cc_final: 0.8804 (tpp) REVERT: B 687 MET cc_start: 0.9654 (ppp) cc_final: 0.9401 (ppp) REVERT: B 1036 MET cc_start: 0.9301 (mmm) cc_final: 0.8481 (mpp) REVERT: B 1058 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8759 (mm-30) REVERT: B 1138 MET cc_start: 0.8690 (ppp) cc_final: 0.8452 (ppp) REVERT: C 560 MET cc_start: 0.9771 (mmp) cc_final: 0.9560 (mmt) REVERT: C 676 CYS cc_start: 0.9329 (m) cc_final: 0.8978 (t) REVERT: C 683 MET cc_start: 0.9320 (mmm) cc_final: 0.8800 (tpp) REVERT: C 687 MET cc_start: 0.9653 (ppp) cc_final: 0.9395 (ppp) REVERT: C 1045 GLN cc_start: 0.7611 (pm20) cc_final: 0.7335 (pm20) REVERT: C 1058 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8761 (mm-30) REVERT: D 560 MET cc_start: 0.9770 (mmp) cc_final: 0.9556 (mmt) REVERT: D 676 CYS cc_start: 0.9332 (m) cc_final: 0.8980 (t) REVERT: D 683 MET cc_start: 0.9313 (mmm) cc_final: 0.8794 (tpp) REVERT: D 687 MET cc_start: 0.9654 (ppp) cc_final: 0.9406 (ppp) REVERT: D 1058 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8771 (mm-30) REVERT: D 1150 MET cc_start: 0.8878 (tpp) cc_final: 0.8533 (tmm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1485 time to fit residues: 63.9843 Evaluate side-chains 229 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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: 40.0000 chunk 277 optimal weight: 3.9990 chunk 224 optimal weight: 40.0000 chunk 175 optimal weight: 0.0060 chunk 83 optimal weight: 0.9990 chunk 226 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 419 optimal weight: 20.0000 chunk 206 optimal weight: 50.0000 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS C 601 HIS D 601 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.063932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.045198 restraints weight = 191766.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.046376 restraints weight = 95855.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.047170 restraints weight = 58991.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.047696 restraints weight = 41881.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048069 restraints weight = 32910.895| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27907 Z= 0.109 Angle : 0.512 7.236 38623 Z= 0.259 Chirality : 0.037 0.143 4784 Planarity : 0.003 0.043 5048 Dihedral : 6.206 89.118 5416 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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 aren not related in a simple way. whole: 3.00 (0.14), residues: 4260 helix: 2.91 (0.10), residues: 2832 sheet: -0.03 (0.41), residues: 200 loop : 0.12 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 916 TYR 0.009 0.001 TYR A1041 PHE 0.020 0.001 PHE D 883 TRP 0.023 0.001 TRP C 842 HIS 0.002 0.000 HIS A 813 Details of bonding type rmsd covalent geometry : bond 0.00244 (27904) covalent geometry : angle 0.51257 (38612) SS BOND : bond 0.00052 ( 3) SS BOND : angle 0.08946 ( 11) hydrogen bonds : bond 0.02999 ( 2033) hydrogen bonds : angle 3.29637 ( 6036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3995.77 seconds wall clock time: 69 minutes 25.01 seconds (4165.01 seconds total)