Starting phenix.real_space_refine on Sat Feb 7 10:10:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o82_70215/02_2026/9o82_70215.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o82_70215/02_2026/9o82_70215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o82_70215/02_2026/9o82_70215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o82_70215/02_2026/9o82_70215.map" model { file = "/net/cci-nas-00/data/ceres_data/9o82_70215/02_2026/9o82_70215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o82_70215/02_2026/9o82_70215.cif" } resolution = 4.46 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 223 5.16 5 C 20291 2.51 5 N 5311 2.21 5 O 5486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31311 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7843 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 989} Chain breaks: 8 Unresolved non-hydrogen bonds: 545 Unresolved non-hydrogen angles: 672 Unresolved non-hydrogen dihedrals: 465 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 15, 'ARG:plan': 13, 'ASP:plan': 11, 'HIS:plan': 5, 'GLN:plan1': 14, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 315 Chain: "C" Number of atoms: 7888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7888 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 988} Chain breaks: 8 Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 421 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 16, 'ARG:plan': 12, 'ASP:plan': 8, 'HIS:plan': 5, 'GLN:plan1': 12, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 290 Chain: "D" Number of atoms: 7771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1033, 7761 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 991} Chain breaks: 6 Unresolved non-hydrogen bonds: 622 Unresolved non-hydrogen angles: 761 Unresolved non-hydrogen dihedrals: 512 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 19, 'ASP:plan': 13, 'HIS:plan': 5, 'GLN:plan1': 14, 'TRP:plan': 1, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 382 Conformer: "B" Number of residues, atoms: 1033, 7761 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 991} Chain breaks: 6 Unresolved non-hydrogen bonds: 622 Unresolved non-hydrogen angles: 761 Unresolved non-hydrogen dihedrals: 512 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 19, 'ASP:plan': 13, 'HIS:plan': 5, 'GLN:plan1': 14, 'TRP:plan': 1, 'ASN:plan1': 6, 'PHE:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 382 bond proxies already assigned to first conformer: 7930 Chain: "B" Number of atoms: 7809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1036, 7799 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 995} Chain breaks: 6 Unresolved non-hydrogen bonds: 623 Unresolved non-hydrogen angles: 765 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 19, 'ASP:plan': 12, 'HIS:plan': 5, 'GLN:plan1': 15, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 388 Conformer: "B" Number of residues, atoms: 1036, 7799 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 995} Chain breaks: 6 Unresolved non-hydrogen bonds: 623 Unresolved non-hydrogen angles: 765 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 19, 'ASP:plan': 12, 'HIS:plan': 5, 'GLN:plan1': 15, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 388 bond proxies already assigned to first conformer: 7967 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS D 674 " occ=0.27 ... (18 atoms not shown) pdb=" NE2BHIS D 674 " occ=0.73 residue: pdb=" N AHIS B 674 " occ=0.27 ... (18 atoms not shown) pdb=" NE2BHIS B 674 " occ=0.73 Time building chain proxies: 10.21, per 1000 atoms: 0.33 Number of scatterers: 31311 At special positions: 0 Unit cell: (147.028, 159.418, 156.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 223 16.00 O 5486 8.00 N 5311 7.00 C 20291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1061 " distance=2.03 Simple disulfide: pdb=" SG CYS C1044 " - pdb=" SG CYS C1061 " distance=2.03 Simple disulfide: pdb=" SG CYS D1044 " - pdb=" SG CYS D1061 " distance=2.03 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1061 " distance=2.04 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: 2.94 Conformation dependent library (CDL) restraints added in 2.2 seconds 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7796 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 11 sheets defined 67.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 59 through 63 removed outlier: 4.237A pdb=" N HIS A 63 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.845A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.736A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 206 removed outlier: 3.598A pdb=" N HIS A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.645A pdb=" N GLN A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 4.052A pdb=" N SER A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 404 through 418 removed outlier: 4.335A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 440 removed outlier: 4.096A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 465 through 475 removed outlier: 4.033A pdb=" N ASN A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 501 through 514 Processing helix chain 'A' and resid 533 through 544 Processing helix chain 'A' and resid 555 through 564 removed outlier: 3.902A pdb=" N LEU A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 625 removed outlier: 3.821A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.510A pdb=" N HIS A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 663 Processing helix chain 'A' and resid 665 through 694 removed outlier: 3.702A pdb=" N SER A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 704 Processing helix chain 'A' and resid 713 through 722 removed outlier: 3.582A pdb=" N LEU A 717 " --> pdb=" O THR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 729 removed outlier: 3.793A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.506A pdb=" N GLN A 733 " --> pdb=" O HIS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 4.037A pdb=" N LEU A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 767 Processing helix chain 'A' and resid 836 through 847 Processing helix chain 'A' and resid 847 through 871 Processing helix chain 'A' and resid 879 through 902 removed outlier: 3.655A pdb=" N MET A 897 " --> pdb=" O GLY A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 916 Processing helix chain 'A' and resid 918 through 939 removed outlier: 3.664A pdb=" N LEU A 925 " --> pdb=" O ASN A 921 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 967 removed outlier: 3.847A pdb=" N VAL A 950 " --> pdb=" O SER A 946 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 957 " --> pdb=" O CYS A 953 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR A 958 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 964 " --> pdb=" O TYR A 960 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 970 No H-bonds generated for 'chain 'A' and resid 968 through 970' Processing helix chain 'A' and resid 972 through 1010 removed outlier: 3.756A pdb=" N TYR A 976 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1024 removed outlier: 3.755A pdb=" N LYS A1021 " --> pdb=" O TRP A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 removed outlier: 3.514A pdb=" N TRP A1029 " --> pdb=" O TYR A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1033 No H-bonds generated for 'chain 'A' and resid 1031 through 1033' Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1067 through 1081 Processing helix chain 'A' and resid 1081 through 1103 removed outlier: 3.742A pdb=" N GLU A1097 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A1103 " --> pdb=" O LYS A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1117 removed outlier: 4.861A pdb=" N TYR A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1127 Processing helix chain 'A' and resid 1128 through 1140 removed outlier: 4.254A pdb=" N LEU A1140 " --> pdb=" O ILE A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'A' and resid 1163 through 1191 Processing helix chain 'A' and resid 1192 through 1231 removed outlier: 3.658A pdb=" N GLU A1202 " --> pdb=" O ARG A1198 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A1223 " --> pdb=" O HIS A1219 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 59 through 63 removed outlier: 4.286A pdb=" N HIS C 63 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.775A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 182 removed outlier: 3.761A pdb=" N LEU C 174 " --> pdb=" O PHE C 170 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 206 removed outlier: 3.908A pdb=" N HIS C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 308 through 319 removed outlier: 4.110A pdb=" N SER C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 353 through 368 Processing helix chain 'C' and resid 371 through 387 Processing helix chain 'C' and resid 404 through 418 removed outlier: 4.438A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 removed outlier: 4.168A pdb=" N ALA C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.736A pdb=" N ALA C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 465 through 475 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 501 through 514 removed outlier: 3.598A pdb=" N LEU C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR C 514 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 546 Processing helix chain 'C' and resid 555 through 564 removed outlier: 4.242A pdb=" N LEU C 561 " --> pdb=" O ARG C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 625 removed outlier: 4.165A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 637 Processing helix chain 'C' and resid 640 through 663 Processing helix chain 'C' and resid 666 through 694 Processing helix chain 'C' and resid 694 through 703 removed outlier: 3.574A pdb=" N ALA C 698 " --> pdb=" O ASP C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 722 removed outlier: 3.532A pdb=" N LEU C 717 " --> pdb=" O THR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 729 Processing helix chain 'C' and resid 729 through 741 Processing helix chain 'C' and resid 749 through 759 removed outlier: 3.507A pdb=" N LEU C 759 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 767 removed outlier: 3.712A pdb=" N SER C 766 " --> pdb=" O SER C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 845 Processing helix chain 'C' and resid 847 through 871 Processing helix chain 'C' and resid 879 through 902 Processing helix chain 'C' and resid 907 through 918 removed outlier: 3.859A pdb=" N GLU C 918 " --> pdb=" O VAL C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 940 removed outlier: 4.090A pdb=" N ILE C 926 " --> pdb=" O VAL C 922 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 927 " --> pdb=" O THR C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 967 removed outlier: 3.929A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE C 957 " --> pdb=" O CYS C 953 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR C 958 " --> pdb=" O VAL C 954 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 964 " --> pdb=" O TYR C 960 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 965 " --> pdb=" O ILE C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 970 No H-bonds generated for 'chain 'C' and resid 968 through 970' Processing helix chain 'C' and resid 972 through 1009 removed outlier: 4.183A pdb=" N TYR C 976 " --> pdb=" O TYR C 972 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 996 " --> pdb=" O ILE C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1025 removed outlier: 3.684A pdb=" N LYS C1021 " --> pdb=" O TRP C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1030 removed outlier: 3.689A pdb=" N TRP C1029 " --> pdb=" O TYR C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1063 through 1065 No H-bonds generated for 'chain 'C' and resid 1063 through 1065' Processing helix chain 'C' and resid 1066 through 1081 removed outlier: 4.469A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1102 removed outlier: 3.727A pdb=" N GLU C1097 " --> pdb=" O ASN C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1119 removed outlier: 4.016A pdb=" N TRP C1106 " --> pdb=" O SER C1102 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR C1111 " --> pdb=" O LYS C1107 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN C1112 " --> pdb=" O PHE C1108 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C1119 " --> pdb=" O MET C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1139 removed outlier: 3.986A pdb=" N SER C1131 " --> pdb=" O LEU C1127 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1192 removed outlier: 4.145A pdb=" N LYS C1168 " --> pdb=" O ASP C1164 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1232 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 130 through 141 Processing helix chain 'D' and resid 163 through 181 removed outlier: 3.764A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 209 Processing helix chain 'D' and resid 227 through 231 removed outlier: 3.860A pdb=" N ILE D 231 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 308 through 319 removed outlier: 4.089A pdb=" N SER D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 Processing helix chain 'D' and resid 353 through 368 removed outlier: 3.648A pdb=" N ASP D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 404 through 418 removed outlier: 3.762A pdb=" N ALA D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D 411 " --> pdb=" O LEU D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 removed outlier: 3.620A pdb=" N LEU D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 439 removed outlier: 3.698A pdb=" N ALA D 437 " --> pdb=" O ARG D 433 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER D 439 " --> pdb=" O ASP D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 465 through 476 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 484 through 494 removed outlier: 3.970A pdb=" N ASN D 493 " --> pdb=" O GLU D 489 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 510 Processing helix chain 'D' and resid 533 through 546 removed outlier: 3.577A pdb=" N TYR D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU D 544 " --> pdb=" O VAL D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 554 Processing helix chain 'D' and resid 555 through 564 removed outlier: 4.036A pdb=" N HIS D 563 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN D 564 " --> pdb=" O THR D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 624 removed outlier: 4.094A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.634A pdb=" N PHE D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 662 Processing helix chain 'D' and resid 665 through 692 removed outlier: 4.133A pdb=" N SER D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN D 670 " --> pdb=" O ASP D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 702 Processing helix chain 'D' and resid 714 through 721 Processing helix chain 'D' and resid 723 through 729 removed outlier: 4.088A pdb=" N ILE D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 Processing helix chain 'D' and resid 751 through 760 Processing helix chain 'D' and resid 761 through 767 removed outlier: 3.778A pdb=" N ILE D 764 " --> pdb=" O PRO D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 845 removed outlier: 3.507A pdb=" N GLU D 843 " --> pdb=" O ARG D 839 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR D 845 " --> pdb=" O ILE D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 872 removed outlier: 3.802A pdb=" N TYR D 868 " --> pdb=" O MET D 864 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 870 " --> pdb=" O PHE D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 902 Processing helix chain 'D' and resid 907 through 917 Processing helix chain 'D' and resid 918 through 940 removed outlier: 3.603A pdb=" N ILE D 936 " --> pdb=" O SER D 932 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 937 " --> pdb=" O VAL D 933 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN D 940 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 968 removed outlier: 3.999A pdb=" N VAL D 950 " --> pdb=" O SER D 946 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR D 952 " --> pdb=" O GLY D 948 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE D 957 " --> pdb=" O CYS D 953 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 958 " --> pdb=" O VAL D 954 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 961 " --> pdb=" O ILE D 957 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 963 " --> pdb=" O TRP D 959 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D 964 " --> pdb=" O TYR D 960 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP D 965 " --> pdb=" O ILE D 961 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 1007 removed outlier: 4.352A pdb=" N TYR D 976 " --> pdb=" O TYR D 972 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET D 978 " --> pdb=" O GLY D 974 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE D 990 " --> pdb=" O ASP D 986 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 992 " --> pdb=" O MET D 988 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 993 " --> pdb=" O TYR D 989 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN D1006 " --> pdb=" O GLY D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1024 removed outlier: 3.891A pdb=" N LYS D1021 " --> pdb=" O TRP D1017 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1025 through 1031 removed outlier: 4.107A pdb=" N TRP D1029 " --> pdb=" O TYR D1025 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1040 Processing helix chain 'D' and resid 1067 through 1081 Processing helix chain 'D' and resid 1082 through 1119 removed outlier: 3.719A pdb=" N ALA D1089 " --> pdb=" O ASN D1085 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE D1091 " --> pdb=" O LEU D1087 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR D1094 " --> pdb=" O VAL D1090 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE D1096 " --> pdb=" O ASN D1092 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU D1097 " --> pdb=" O ASN D1093 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN D1103 " --> pdb=" O LYS D1099 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLN D1104 " --> pdb=" O SER D1100 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP D1106 " --> pdb=" O SER D1102 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET D1115 " --> pdb=" O TYR D1111 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR D1116 " --> pdb=" O GLN D1112 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS D1118 " --> pdb=" O ILE D1114 " (cutoff:3.500A) Processing helix chain 'D' and resid 1127 through 1142 Processing helix chain 'D' and resid 1163 through 1191 removed outlier: 3.632A pdb=" N GLU D1179 " --> pdb=" O GLU D1175 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D1184 " --> pdb=" O GLU D1180 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP D1186 " --> pdb=" O PHE D1182 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1232 removed outlier: 3.575A pdb=" N GLU D1202 " --> pdb=" O ARG D1198 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET D1209 " --> pdb=" O GLU D1205 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D1216 " --> pdb=" O GLU D1212 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG D1231 " --> pdb=" O THR D1227 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 130 through 140 removed outlier: 3.789A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 182 Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.716A pdb=" N ILE B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.555A pdb=" N GLN B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 4.028A pdb=" N SER B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 353 through 368 removed outlier: 3.720A pdb=" N ASP B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 386 Processing helix chain 'B' and resid 387 through 390 removed outlier: 5.515A pdb=" N GLU B 390 " --> pdb=" O LYS B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 405 through 418 removed outlier: 4.293A pdb=" N THR B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 432 removed outlier: 3.614A pdb=" N SER B 426 " --> pdb=" O PRO B 422 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 451 through 462 removed outlier: 3.651A pdb=" N VAL B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 removed outlier: 3.583A pdb=" N LEU B 471 " --> pdb=" O ASP B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.650A pdb=" N LEU B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 546 Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 613 through 625 removed outlier: 4.232A pdb=" N GLU B 617 " --> pdb=" O PHE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.597A pdb=" N PHE B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 662 removed outlier: 3.522A pdb=" N LYS B 653 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 693 removed outlier: 4.005A pdb=" N SER B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 684 " --> pdb=" O GLY B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 702 removed outlier: 3.605A pdb=" N LYS B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 721 removed outlier: 3.538A pdb=" N ALA B 720 " --> pdb=" O GLN B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 729 removed outlier: 3.896A pdb=" N ILE B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 741 removed outlier: 3.762A pdb=" N GLN B 733 " --> pdb=" O HIS B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 759 removed outlier: 4.109A pdb=" N LEU B 759 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 767 Processing helix chain 'B' and resid 835 through 846 removed outlier: 3.659A pdb=" N TYR B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 872 removed outlier: 3.683A pdb=" N ALA B 858 " --> pdb=" O PHE B 854 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 868 " --> pdb=" O MET B 864 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 871 " --> pdb=" O ASN B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 902 removed outlier: 3.503A pdb=" N ILE B 884 " --> pdb=" O THR B 880 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 889 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU B 899 " --> pdb=" O GLU B 895 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 918 removed outlier: 3.685A pdb=" N GLN B 917 " --> pdb=" O LYS B 913 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU B 918 " --> pdb=" O VAL B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 940 removed outlier: 3.694A pdb=" N LEU B 925 " --> pdb=" O ASN B 921 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 929 " --> pdb=" O LEU B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 962 removed outlier: 3.592A pdb=" N VAL B 950 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE B 957 " --> pdb=" O CYS B 953 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 958 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TRP B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 967 removed outlier: 4.114A pdb=" N ILE B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 1006 removed outlier: 4.137A pdb=" N TYR B 976 " --> pdb=" O TYR B 972 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET B 978 " --> pdb=" O GLY B 974 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 992 " --> pdb=" O MET B 988 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B1000 " --> pdb=" O VAL B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1024 removed outlier: 4.208A pdb=" N ALA B1020 " --> pdb=" O SER B1016 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1030 removed outlier: 4.078A pdb=" N TRP B1029 " --> pdb=" O TYR B1025 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B1030 " --> pdb=" O MET B1026 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1025 through 1030' Processing helix chain 'B' and resid 1036 through 1041 removed outlier: 4.292A pdb=" N ASP B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1080 Processing helix chain 'B' and resid 1082 through 1094 Processing helix chain 'B' and resid 1094 through 1107 removed outlier: 3.575A pdb=" N VAL B1098 " --> pdb=" O THR B1094 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B1103 " --> pdb=" O LYS B1099 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN B1104 " --> pdb=" O SER B1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1120 removed outlier: 4.045A pdb=" N TYR B1111 " --> pdb=" O LYS B1107 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN B1112 " --> pdb=" O PHE B1108 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1139 removed outlier: 3.509A pdb=" N MET B1133 " --> pdb=" O ILE B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1191 removed outlier: 3.989A pdb=" N LYS B1169 " --> pdb=" O ASP B1165 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B1179 " --> pdb=" O GLU B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1232 removed outlier: 4.037A pdb=" N ALA B1223 " --> pdb=" O HIS B1219 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B1232 " --> pdb=" O VAL B1228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.678A pdb=" N GLN A 99 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 240 removed outlier: 5.818A pdb=" N THR A 108 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 236 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU A 110 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN A 112 " --> pdb=" O PRO A 238 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLN A 240 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ALA A 105 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N PHE A 259 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N MET A 121 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU A 261 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 123 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP A 263 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 125 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR A 215 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE A 260 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY A 217 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA A 262 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA A 219 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE A 216 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE A 185 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 218 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR A 187 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N VAL A 327 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA A 301 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N CYS A 329 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE A 303 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 326 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE A 395 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL A 328 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.702A pdb=" N GLN C 99 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 232 through 240 removed outlier: 6.804A pdb=" N PHE C 106 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR C 239 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU C 110 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA C 105 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 123 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR C 215 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE C 260 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY C 217 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA C 262 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 219 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE C 216 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE C 185 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 218 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N THR C 187 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N VAL C 327 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA C 301 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N CYS C 329 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE C 303 " --> pdb=" O CYS C 329 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE C 395 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL C 328 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.626A pdb=" N GLN D 99 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 232 through 240 removed outlier: 6.095A pdb=" N THR D 108 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL D 236 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU D 110 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN D 112 " --> pdb=" O PRO D 238 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLN D 240 " --> pdb=" O GLN D 112 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA D 105 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N PHE D 259 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N MET D 121 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU D 261 " --> pdb=" O MET D 121 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL D 123 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP D 263 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL D 125 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 184 through 186 removed outlier: 6.398A pdb=" N LEU D 150 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU D 302 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER D 152 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL D 304 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS D 154 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL D 326 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE D 395 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D 328 " --> pdb=" O PHE D 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 705 through 706 Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.668A pdb=" N GLN B 99 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 240 removed outlier: 7.190A pdb=" N PHE B 106 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B 108 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA B 105 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N PHE B 259 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET B 121 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU B 261 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 123 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ASP B 263 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 125 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 186 removed outlier: 6.913A pdb=" N ILE B 151 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL B 326 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE B 395 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL B 328 " --> pdb=" O PHE B 395 " (cutoff:3.500A) 1883 hydrogen bonds defined for protein. 5579 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.26 Time building geometry restraints manager: 3.99 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: 5114 1.32 - 1.45: 8852 1.45 - 1.58: 17693 1.58 - 1.72: 0 1.72 - 1.85: 370 Bond restraints: 32029 Sorted by residual: bond pdb=" C GLU A 904 " pdb=" N PRO A 905 " ideal model delta sigma weight residual 1.332 1.405 -0.073 1.12e-02 7.97e+03 4.29e+01 bond pdb=" C VAL A1068 " pdb=" N PRO A1069 " ideal model delta sigma weight residual 1.336 1.415 -0.079 1.23e-02 6.61e+03 4.16e+01 bond pdb=" C MET C1026 " pdb=" N PRO C1027 " ideal model delta sigma weight residual 1.335 1.408 -0.073 1.19e-02 7.06e+03 3.78e+01 bond pdb=" C MET B1026 " pdb=" N PRO B1027 " ideal model delta sigma weight residual 1.335 1.412 -0.078 1.28e-02 6.10e+03 3.68e+01 bond pdb=" C MET A1026 " pdb=" N PRO A1027 " ideal model delta sigma weight residual 1.336 1.407 -0.071 1.25e-02 6.40e+03 3.21e+01 ... (remaining 32024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 41555 3.02 - 6.04: 1704 6.04 - 9.06: 277 9.06 - 12.08: 39 12.08 - 15.10: 3 Bond angle restraints: 43578 Sorted by residual: angle pdb=" C ILE B1067 " pdb=" N VAL B1068 " pdb=" CA VAL B1068 " ideal model delta sigma weight residual 120.24 125.82 -5.58 6.30e-01 2.52e+00 7.84e+01 angle pdb=" N ILE D1128 " pdb=" CA ILE D1128 " pdb=" C ILE D1128 " ideal model delta sigma weight residual 113.07 101.88 11.19 1.37e+00 5.33e-01 6.67e+01 angle pdb=" N VAL A1098 " pdb=" CA VAL A1098 " pdb=" CB VAL A1098 " ideal model delta sigma weight residual 110.55 119.61 -9.06 1.17e+00 7.31e-01 5.99e+01 angle pdb=" C TYR A 868 " pdb=" N ILE A 869 " pdb=" CA ILE A 869 " ideal model delta sigma weight residual 121.85 113.02 8.83 1.19e+00 7.06e-01 5.50e+01 angle pdb=" N ILE D1129 " pdb=" CA ILE D1129 " pdb=" C ILE D1129 " ideal model delta sigma weight residual 111.00 102.96 8.04 1.09e+00 8.42e-01 5.44e+01 ... (remaining 43573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17386 17.95 - 35.91: 1254 35.91 - 53.86: 212 53.86 - 71.81: 54 71.81 - 89.76: 24 Dihedral angle restraints: 18930 sinusoidal: 6892 harmonic: 12038 Sorted by residual: dihedral pdb=" CB CYS C1044 " pdb=" SG CYS C1044 " pdb=" SG CYS C1061 " pdb=" CB CYS C1061 " ideal model delta sinusoidal sigma weight residual -86.00 -147.53 61.53 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" CA ALA A 721 " pdb=" C ALA A 721 " pdb=" N LYS A 722 " pdb=" CA LYS A 722 " ideal model delta harmonic sigma weight residual -180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ILE B 956 " pdb=" C ILE B 956 " pdb=" N ILE B 957 " pdb=" CA ILE B 957 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 18927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4231 0.091 - 0.182: 729 0.182 - 0.273: 68 0.273 - 0.364: 17 0.364 - 0.454: 5 Chirality restraints: 5050 Sorted by residual: chirality pdb=" CB VAL B 870 " pdb=" CA VAL B 870 " pdb=" CG1 VAL B 870 " pdb=" CG2 VAL B 870 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CB ILE A 849 " pdb=" CA ILE A 849 " pdb=" CG1 ILE A 849 " pdb=" CG2 ILE A 849 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB VAL D 872 " pdb=" CA VAL D 872 " pdb=" CG1 VAL D 872 " pdb=" CG2 VAL D 872 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 5047 not shown) Planarity restraints: 5485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 431 " 0.037 2.00e-02 2.50e+03 4.37e-02 4.77e+01 pdb=" CG TRP B 431 " -0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP B 431 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP B 431 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 431 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP B 431 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 431 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 431 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 431 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 431 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1091 " -0.031 2.00e-02 2.50e+03 3.86e-02 2.61e+01 pdb=" CG PHE A1091 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A1091 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 PHE A1091 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A1091 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE A1091 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A1091 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 673 " 0.025 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" CG ASN C 673 " -0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN C 673 " 0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN C 673 " 0.029 2.00e-02 2.50e+03 ... (remaining 5482 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 9523 2.84 - 3.36: 32812 3.36 - 3.87: 52224 3.87 - 4.39: 60479 4.39 - 4.90: 96709 Nonbonded interactions: 251747 Sorted by model distance: nonbonded pdb=" O VAL B1090 " pdb=" OG1 THR B1094 " model vdw 2.328 3.040 nonbonded pdb=" CG2 THR D 891 " pdb=" CD1 ILE D1129 " model vdw 2.333 3.880 nonbonded pdb=" O ILE B 436 " pdb=" N GLN B 440 " model vdw 2.367 3.120 nonbonded pdb=" N ILE D1128 " pdb=" N ILE D1129 " model vdw 2.467 2.560 nonbonded pdb=" O MET D 545 " pdb=" NZ LYS D 650 " model vdw 2.488 3.120 ... (remaining 251742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 203 or (resid 204 and (name N or name CA or nam \ e C or name O or name CB )) or resid 205 through 254 or (resid 255 and (name N o \ r name CA or name C or name O or name CB )) or resid 256 through 343 or (resid 3 \ 44 through 345 and (name N or name CA or name C or name O or name CB )) or resid \ 346 through 351 or (resid 352 through 354 and (name N or name CA or name C or n \ ame O or name CB )) or resid 355 through 356 or (resid 357 through 360 and (name \ N or name CA or name C or name O or name CB )) or resid 361 through 409 or (res \ id 410 and (name N or name CA or name C or name O or name CB )) or resid 411 thr \ ough 434 or (resid 435 and (name N or name CA or name C or name O or name CB )) \ or resid 436 through 437 or (resid 438 and (name N or name CA or name C or name \ O or name CB )) or resid 439 through 443 or (resid 444 and (name N or name CA or \ name C or name O or name CB )) or resid 445 through 467 or (resid 468 and (name \ N or name CA or name C or name O or name CB )) or resid 469 through 473 or (res \ id 474 and (name N or name CA or name C or name O or name CB )) or resid 475 thr \ ough 480 or (resid 481 and (name N or name CA or name C or name O or name CB )) \ or resid 482 through 489 or (resid 490 and (name N or name CA or name C or name \ O or name CB )) or resid 491 through 494 or (resid 495 and (name N or name CA or \ name C or name O or name CB )) or resid 496 through 499 or (resid 500 and (name \ N or name CA or name C or name O or name CB )) or resid 501 through 511 or (res \ id 512 through 513 and (name N or name CA or name C or name O or name CB )) or r \ esid 528 through 530 or (resid 531 and (name N or name CA or name C or name O or \ name CB )) or resid 532 through 535 or (resid 536 and (name N or name CA or nam \ e C or name O or name CB )) or resid 537 through 562 or (resid 563 through 608 a \ nd (name N or name CA or name C or name O or name CB )) or resid 609 through 626 \ or (resid 627 and (name N or name CA or name C or name O or name CB )) or resid \ 628 or (resid 629 and (name N or name CA or name C or name O or name CB )) or r \ esid 630 through 660 or (resid 661 and (name N or name CA or name C or name O or \ name CB )) or resid 662 or (resid 663 through 668 and (name N or name CA or nam \ e C or name O or name CB )) or resid 669 through 673 or resid 675 through 676 or \ (resid 677 and (name N or name CA or name C or name O or name CB )) or resid 67 \ 8 through 721 or (resid 722 and (name N or name CA or name C or name O or name C \ B )) or resid 723 through 744 or (resid 745 through 748 and (name N or name CA o \ r name C or name O or name CB )) or resid 749 through 757 or (resid 758 through \ 760 and (name N or name CA or name C or name O or name CB )) or resid 761 throug \ h 767 or (resid 768 and (name N or name CA or name C or name O or name CB )) or \ resid 769 or (resid 834 through 835 and (name N or name CA or name C or name O o \ r name CB )) or resid 836 or (resid 837 and (name N or name CA or name C or name \ O or name CB )) or resid 838 or (resid 839 and (name N or name CA or name C or \ name O or name CB )) or resid 840 through 842 or (resid 843 and (name N or name \ CA or name C or name O or name CB )) or resid 844 through 873 or (resid 874 and \ (name N or name CA or name C or name O or name CB )) or resid 875 through 896 or \ (resid 897 and (name N or name CA or name C or name O or name CB )) or resid 89 \ 8 through 899 or (resid 900 through 901 and (name N or name CA or name C or name \ O or name CB )) or resid 902 through 903 or (resid 904 and (name N or name CA o \ r name C or name O or name CB )) or resid 905 through 917 or (resid 918 and (nam \ e N or name CA or name C or name O or name CB )) or resid 919 through 944 or (re \ sid 945 and (name N or name CA or name C or name O or name CB )) or resid 946 th \ rough 948 or (resid 949 and (name N or name CA or name C or name O or name CB )) \ or resid 950 through 977 or (resid 978 through 979 and (name N or name CA or na \ me C or name O or name CB )) or resid 980 through 997 or (resid 998 and (name N \ or name CA or name C or name O or name CB )) or resid 999 through 1017 or (resid \ 1018 and (name N or name CA or name C or name O or name CB )) or resid 1019 thr \ ough 1040 or (resid 1041 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1042 through 1046 or resid 1059 through 1080 or (resid 1081 and (name \ N or name CA or name C or name O or name CB )) or resid 1082 through 1086 or (r \ esid 1087 and (name N or name CA or name C or name O or name CB )) or resid 1088 \ through 1111 or (resid 1112 through 1113 and (name N or name CA or name C or na \ me O or name CB )) or resid 1114 through 1118 or (resid 1119 through 1120 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1121 through 1127 or \ (resid 1128 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 129 through 1142 or resid 1159 through 1163 or (resid 1164 through 1165 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1166 or (resid 1167 th \ rough 1168 and (name N or name CA or name C or name O or name CB )) or resid 116 \ 9 through 1194 or (resid 1195 and (name N or name CA or name C or name O or name \ CB )) or resid 1196 through 1206 or (resid 1207 and (name N or name CA or name \ C or name O or name CB )) or resid 1208 through 1211 or (resid 1212 through 1213 \ and (name N or name CA or name C or name O or name CB )) or resid 1214 through \ 1217 or (resid 1218 through 1232 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'B' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 137 or (resid 138 and (name N or name CA or n \ ame C or name O or name CB )) or resid 139 through 207 or resid 213 through 229 \ or (resid 230 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 259 or (resid 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 342 or (resid 343 through 345 and (name N or name CA \ or name C or name O or name CB )) or resid 346 through 351 or (resid 352 throug \ h 354 and (name N or name CA or name C or name O or name CB )) or resid 355 thro \ ugh 356 or (resid 357 through 360 and (name N or name CA or name C or name O or \ name CB )) or resid 361 through 369 or (resid 370 and (name N or name CA or name \ C or name O or name CB )) or resid 371 through 385 or (resid 386 through 387 an \ d (name N or name CA or name C or name O or name CB )) or resid 388 through 398 \ or resid 403 or (resid 404 and (name N or name CA or name C or name O or name CB \ )) or resid 405 through 409 or (resid 410 and (name N or name CA or name C or n \ ame O or name CB )) or resid 411 through 413 or (resid 414 and (name N or name C \ A or name C or name O or name CB )) or resid 415 through 419 or (resid 420 throu \ gh 421 and (name N or name CA or name C or name O or name CB )) or resid 422 or \ (resid 423 and (name N or name CA or name C or name O or name CB )) or resid 424 \ through 451 or (resid 452 and (name N or name CA or name C or name O or name CB \ )) or resid 453 through 457 or (resid 458 and (name N or name CA or name C or n \ ame O or name CB )) or resid 459 through 466 or (resid 467 through 468 and (name \ N or name CA or name C or name O or name CB )) or resid 469 through 488 or (res \ id 489 through 490 and (name N or name CA or name C or name O or name CB )) or r \ esid 491 through 498 or (resid 499 through 500 and (name N or name CA or name C \ or name O or name CB )) or resid 501 through 502 or (resid 503 and (name N or na \ me CA or name C or name O or name CB )) or resid 504 or (resid 505 and (name N o \ r name CA or name C or name O or name CB )) or resid 506 or (resid 507 and (name \ N or name CA or name C or name O or name CB )) or resid 508 through 509 or (res \ id 510 through 513 and (name N or name CA or name C or name O or name CB )) or r \ esid 528 through 529 or (resid 530 through 531 and (name N or name CA or name C \ or name O or name CB )) or resid 532 through 667 or (resid 668 and (name N or na \ me CA or name C or name O or name CB )) or resid 669 through 673 or resid 675 th \ rough 676 or (resid 677 and (name N or name CA or name C or name O or name CB )) \ or resid 678 through 698 or (resid 699 and (name N or name CA or name C or name \ O or name CB )) or resid 700 through 705 or (resid 706 and (name N or name CA o \ r name C or name O or name CB )) or resid 707 through 721 or (resid 722 and (nam \ e N or name CA or name C or name O or name CB )) or resid 723 or (resid 724 and \ (name N or name CA or name C or name O or name CB )) or resid 725 through 733 or \ (resid 734 and (name N or name CA or name C or name O or name CB )) or resid 73 \ 5 through 737 or (resid 738 and (name N or name CA or name C or name O or name C \ B )) or resid 739 through 740 or (resid 741 and (name N or name CA or name C or \ name O or name CB )) or resid 742 through 745 or (resid 746 through 748 and (nam \ e N or name CA or name C or name O or name CB )) or resid 749 through 873 or (re \ sid 874 and (name N or name CA or name C or name O or name CB )) or resid 875 th \ rough 934 or (resid 935 and (name N or name CA or name C or name O or name CB )) \ or resid 936 through 944 or (resid 945 and (name N or name CA or name C or name \ O or name CB )) or resid 946 through 948 or (resid 949 and (name N or name CA o \ r name C or name O or name CB )) or resid 950 through 955 or (resid 956 and (nam \ e N or name CA or name C or name O or name CB )) or resid 957 through 963 or (re \ sid 964 and (name N or name CA or name C or name O or name CB )) or resid 965 th \ rough 977 or (resid 978 through 979 and (name N or name CA or name C or name O o \ r name CB )) or resid 980 through 1040 or (resid 1041 and (name N or name CA or \ name C or name O or name CB )) or resid 1042 through 1046 or resid 1059 through \ 1061 or (resid 1062 and (name N or name CA or name C or name O or name CB )) or \ resid 1063 through 1080 or (resid 1081 and (name N or name CA or name C or name \ O or name CB )) or resid 1082 through 1086 or (resid 1087 and (name N or name CA \ or name C or name O or name CB )) or resid 1088 through 1098 or (resid 1099 and \ (name N or name CA or name C or name O or name CB )) or resid 1100 through 1108 \ or (resid 1109 and (name N or name CA or name C or name O or name CB )) or resi \ d 1110 through 1112 or (resid 1113 and (name N or name CA or name C or name O or \ name CB )) or resid 1114 through 1119 or (resid 1120 and (name N or name CA or \ name C or name O or name CB )) or resid 1121 through 1127 or (resid 1128 and (na \ me N or name CA or name C or name O or name CB )) or resid 1129 through 1132 or \ (resid 1133 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 34 through 1138 or (resid 1139 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1140 through 1142 or resid 1159 through 1163 or (resid 1164 thr \ ough 1165 and (name N or name CA or name C or name O or name CB )) or resid 1166 \ or (resid 1167 through 1168 and (name N or name CA or name C or name O or name \ CB )) or resid 1169 through 1201 or (resid 1202 and (name N or name CA or name C \ or name O or name CB )) or resid 1203 through 1232)) selection = (chain 'C' and (resid 30 through 203 or (resid 204 and (name N or name CA or nam \ e C or name O or name CB )) or resid 205 through 254 or (resid 255 and (name N o \ r name CA or name C or name O or name CB )) or resid 256 through 343 or (resid 3 \ 44 through 345 and (name N or name CA or name C or name O or name CB )) or resid \ 346 through 351 or (resid 352 through 354 and (name N or name CA or name C or n \ ame O or name CB )) or resid 355 through 356 or (resid 357 through 360 and (name \ N or name CA or name C or name O or name CB )) or resid 361 through 422 or (res \ id 423 and (name N or name CA or name C or name O or name CB )) or resid 424 thr \ ough 434 or (resid 435 and (name N or name CA or name C or name O or name CB )) \ or resid 436 through 437 or (resid 438 and (name N or name CA or name C or name \ O or name CB )) or resid 439 through 443 or (resid 444 and (name N or name CA or \ name C or name O or name CB )) or resid 445 through 446 or (resid 447 and (name \ N or name CA or name C or name O or name CB )) or resid 448 through 457 or (res \ id 458 and (name N or name CA or name C or name O or name CB )) or resid 459 thr \ ough 464 or (resid 465 and (name N or name CA or name C or name O or name CB )) \ or resid 466 or (resid 467 through 468 and (name N or name CA or name C or name \ O or name CB )) or resid 469 through 473 or (resid 474 and (name N or name CA or \ name C or name O or name CB )) or resid 475 through 480 or (resid 481 and (name \ N or name CA or name C or name O or name CB )) or resid 482 or (resid 483 and ( \ name N or name CA or name C or name O or name CB )) or resid 484 through 489 or \ (resid 490 and (name N or name CA or name C or name O or name CB )) or resid 491 \ through 494 or (resid 495 and (name N or name CA or name C or name O or name CB \ )) or resid 496 through 499 or (resid 500 and (name N or name CA or name C or n \ ame O or name CB )) or resid 501 through 502 or (resid 503 and (name N or name C \ A or name C or name O or name CB )) or resid 504 or (resid 505 and (name N or na \ me CA or name C or name O or name CB )) or resid 506 or (resid 507 and (name N o \ r name CA or name C or name O or name CB )) or resid 508 through 511 or (resid 5 \ 12 through 513 and (name N or name CA or name C or name O or name CB )) or resid \ 528 through 530 or (resid 531 and (name N or name CA or name C or name O or nam \ e CB )) or resid 532 through 535 or (resid 536 and (name N or name CA or name C \ or name O or name CB )) or resid 537 through 562 or (resid 563 through 608 and ( \ name N or name CA or name C or name O or name CB )) or resid 609 through 626 or \ (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 628 \ or (resid 629 and (name N or name CA or name C or name O or name CB )) or resid \ 630 through 660 or (resid 661 and (name N or name CA or name C or name O or nam \ e CB )) or resid 662 or (resid 663 through 668 and (name N or name CA or name C \ or name O or name CB )) or resid 669 through 673 or resid 675 through 698 or (re \ sid 699 and (name N or name CA or name C or name O or name CB )) or resid 700 th \ rough 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) \ or resid 707 through 733 or (resid 734 and (name N or name CA or name C or name \ O or name CB )) or resid 735 through 737 or (resid 738 and (name N or name CA o \ r name C or name O or name CB )) or resid 739 through 740 or (resid 741 and (nam \ e N or name CA or name C or name O or name CB )) or resid 742 through 744 or (re \ sid 745 through 748 and (name N or name CA or name C or name O or name CB )) or \ resid 749 through 757 or (resid 758 through 760 and (name N or name CA or name C \ or name O or name CB )) or resid 761 through 767 or (resid 768 and (name N or n \ ame CA or name C or name O or name CB )) or resid 769 or (resid 834 through 835 \ and (name N or name CA or name C or name O or name CB )) or resid 836 or (resid \ 837 and (name N or name CA or name C or name O or name CB )) or resid 838 or (re \ sid 839 and (name N or name CA or name C or name O or name CB )) or resid 840 th \ rough 842 or (resid 843 and (name N or name CA or name C or name O or name CB )) \ or resid 844 through 873 or (resid 874 and (name N or name CA or name C or name \ O or name CB )) or resid 875 through 896 or (resid 897 and (name N or name CA o \ r name C or name O or name CB )) or resid 898 through 899 or (resid 900 through \ 901 and (name N or name CA or name C or name O or name CB )) or resid 902 throug \ h 903 or (resid 904 and (name N or name CA or name C or name O or name CB )) or \ resid 905 through 917 or (resid 918 and (name N or name CA or name C or name O o \ r name CB )) or resid 919 through 944 or (resid 945 and (name N or name CA or na \ me C or name O or name CB )) or resid 946 through 948 or (resid 949 and (name N \ or name CA or name C or name O or name CB )) or resid 950 through 963 or (resid \ 964 and (name N or name CA or name C or name O or name CB )) or resid 965 throug \ h 977 or (resid 978 through 979 and (name N or name CA or name C or name O or na \ me CB )) or resid 980 through 997 or (resid 998 and (name N or name CA or name C \ or name O or name CB )) or resid 999 through 1017 or (resid 1018 and (name N or \ name CA or name C or name O or name CB )) or resid 1019 through 1075 or (resid \ 1076 and (name N or name CA or name C or name O or name CB )) or resid 1077 thro \ ugh 1080 or (resid 1081 and (name N or name CA or name C or name O or name CB )) \ or resid 1082 through 1086 or (resid 1087 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1088 through 1098 or (resid 1099 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1100 through 1108 or (resid 1109 \ and (name N or name CA or name C or name O or name CB )) or resid 1110 through \ 1111 or (resid 1112 through 1113 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1114 through 1118 or (resid 1119 through 1120 and (name N or \ name CA or name C or name O or name CB )) or resid 1121 through 1127 or (resid 1 \ 128 and (name N or name CA or name C or name O or name CB )) or resid 1129 throu \ gh 1142 or resid 1159 through 1163 or (resid 1164 through 1165 and (name N or na \ me CA or name C or name O or name CB )) or resid 1166 or (resid 1167 through 116 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 1169 through \ 1194 or (resid 1195 and (name N or name CA or name C or name O or name CB )) or \ resid 1196 through 1206 or (resid 1207 and (name N or name CA or name C or name \ O or name CB )) or resid 1208 through 1212 or (resid 1213 and (name N or name C \ A or name C or name O or name CB )) or resid 1214 through 1217 or (resid 1218 th \ rough 1232 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 137 or (resid 138 and (name N or name CA or n \ ame C or name O or name CB )) or resid 139 through 207 or resid 213 through 229 \ or (resid 230 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 259 or (resid 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 342 or (resid 343 through 345 and (name N or name CA \ or name C or name O or name CB )) or resid 346 through 369 or (resid 370 and (n \ ame N or name CA or name C or name O or name CB )) or resid 371 through 385 or ( \ resid 386 through 387 and (name N or name CA or name C or name O or name CB )) o \ r resid 388 through 398 or resid 403 or (resid 404 and (name N or name CA or nam \ e C or name O or name CB )) or resid 405 through 409 or (resid 410 and (name N o \ r name CA or name C or name O or name CB )) or resid 411 through 413 or (resid 4 \ 14 and (name N or name CA or name C or name O or name CB )) or resid 415 through \ 419 or (resid 420 through 421 and (name N or name CA or name C or name O or nam \ e CB )) or resid 422 or (resid 423 and (name N or name CA or name C or name O or \ name CB )) or resid 424 through 437 or (resid 438 and (name N or name CA or nam \ e C or name O or name CB )) or resid 439 through 451 or (resid 452 and (name N o \ r name CA or name C or name O or name CB )) or resid 453 through 457 or (resid 4 \ 58 and (name N or name CA or name C or name O or name CB )) or resid 459 through \ 464 or (resid 465 and (name N or name CA or name C or name O or name CB )) or r \ esid 466 or (resid 467 through 468 and (name N or name CA or name C or name O or \ name CB )) or resid 469 through 482 or (resid 483 and (name N or name CA or nam \ e C or name O or name CB )) or resid 484 through 488 or (resid 489 through 490 a \ nd (name N or name CA or name C or name O or name CB )) or resid 491 through 498 \ or (resid 499 through 500 and (name N or name CA or name C or name O or name CB \ )) or resid 501 through 502 or (resid 503 and (name N or name CA or name C or n \ ame O or name CB )) or resid 504 through 506 or (resid 507 and (name N or name C \ A or name C or name O or name CB )) or resid 508 through 509 or (resid 510 throu \ gh 513 and (name N or name CA or name C or name O or name CB )) or resid 528 thr \ ough 529 or (resid 530 through 531 and (name N or name CA or name C or name O or \ name CB )) or resid 532 through 662 or (resid 663 through 668 and (name N or na \ me CA or name C or name O or name CB )) or resid 669 through 673 or resid 675 th \ rough 676 or (resid 677 and (name N or name CA or name C or name O or name CB )) \ or resid 678 through 698 or (resid 699 and (name N or name CA or name C or name \ O or name CB )) or resid 700 through 705 or (resid 706 and (name N or name CA o \ r name C or name O or name CB )) or resid 707 through 721 or (resid 722 and (nam \ e N or name CA or name C or name O or name CB )) or resid 723 or (resid 724 and \ (name N or name CA or name C or name O or name CB )) or resid 725 through 733 or \ (resid 734 and (name N or name CA or name C or name O or name CB )) or resid 73 \ 5 through 737 or (resid 738 and (name N or name CA or name C or name O or name C \ B )) or resid 739 through 740 or (resid 741 and (name N or name CA or name C or \ name O or name CB )) or resid 742 through 744 or (resid 745 through 748 and (nam \ e N or name CA or name C or name O or name CB )) or resid 749 through 757 or (re \ sid 758 through 760 and (name N or name CA or name C or name O or name CB )) or \ resid 761 through 769 or resid 834 through 896 or (resid 897 and (name N or name \ CA or name C or name O or name CB )) or resid 898 through 899 or (resid 900 thr \ ough 901 and (name N or name CA or name C or name O or name CB )) or resid 902 t \ hrough 934 or (resid 935 and (name N or name CA or name C or name O or name CB ) \ ) or resid 936 through 955 or (resid 956 and (name N or name CA or name C or nam \ e O or name CB )) or resid 957 through 963 or (resid 964 and (name N or name CA \ or name C or name O or name CB )) or resid 965 through 978 or (resid 979 and (na \ me N or name CA or name C or name O or name CB )) or resid 980 through 997 or (r \ esid 998 and (name N or name CA or name C or name O or name CB )) or resid 999 t \ hrough 1040 or (resid 1041 and (name N or name CA or name C or name O or name CB \ )) or resid 1042 through 1046 or resid 1059 through 1061 or (resid 1062 and (na \ me N or name CA or name C or name O or name CB )) or resid 1063 through 1075 or \ (resid 1076 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 77 through 1098 or (resid 1099 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1100 through 1108 or (resid 1109 and (name N or name CA or name \ C or name O or name CB )) or resid 1110 through 1132 or (resid 1133 and (name N \ or name CA or name C or name O or name CB )) or resid 1134 through 1138 or (res \ id 1139 and (name N or name CA or name C or name O or name CB )) or resid 1140 t \ hrough 1164 or (resid 1165 and (name N or name CA or name C or name O or name CB \ )) or resid 1166 through 1201 or (resid 1202 and (name N or name CA or name C o \ r name O or name CB )) or resid 1203 through 1206 or (resid 1207 and (name N or \ name CA or name C or name O or name CB )) or resid 1208 through 1232)) } 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=0.27 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.180 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: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 36.410 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 0.105 32033 Z= 0.412 Angle : 1.386 15.103 43586 Z= 0.791 Chirality : 0.068 0.454 5050 Planarity : 0.010 0.123 5485 Dihedral : 13.491 89.762 11122 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 1.51 % Allowed : 0.87 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.11), residues: 4072 helix: -2.32 (0.08), residues: 2535 sheet: -0.76 (0.34), residues: 237 loop : -1.90 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG A 938 TYR 0.075 0.005 TYR A 960 PHE 0.078 0.005 PHE C 854 TRP 0.113 0.005 TRP B 431 HIS 0.035 0.003 HIS A 563 Details of bonding type rmsd covalent geometry : bond 0.00790 (32029) covalent geometry : angle 1.38541 (43578) SS BOND : bond 0.00379 ( 4) SS BOND : angle 3.04683 ( 8) hydrogen bonds : bond 0.20263 ( 1883) hydrogen bonds : angle 8.40758 ( 5579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 780 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASN cc_start: 0.8843 (m-40) cc_final: 0.8521 (t0) REVERT: A 259 PHE cc_start: 0.8372 (m-80) cc_final: 0.7553 (m-80) REVERT: A 286 LEU cc_start: 0.9080 (mt) cc_final: 0.8788 (pp) REVERT: A 552 ASN cc_start: 0.8931 (t0) cc_final: 0.8571 (m-40) REVERT: A 630 MET cc_start: 0.8267 (mtt) cc_final: 0.7798 (mtt) REVERT: A 894 ILE cc_start: 0.9336 (mm) cc_final: 0.9093 (tt) REVERT: A 902 MET cc_start: 0.7454 (mmt) cc_final: 0.7116 (mmt) REVERT: A 962 ARG cc_start: 0.8308 (tpt170) cc_final: 0.7713 (tpt170) REVERT: A 978 MET cc_start: 0.8967 (mpp) cc_final: 0.8477 (tpp) REVERT: A 984 MET cc_start: 0.8495 (mmm) cc_final: 0.8243 (mmm) REVERT: A 987 MET cc_start: 0.8838 (mmm) cc_final: 0.8464 (tmm) REVERT: A 1012 ASN cc_start: 0.8553 (m-40) cc_final: 0.8344 (p0) REVERT: A 1160 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7914 (pp) REVERT: A 1182 PHE cc_start: 0.7953 (m-80) cc_final: 0.7143 (m-80) REVERT: C 242 MET cc_start: 0.4034 (tpt) cc_final: 0.2645 (tmm) REVERT: C 619 MET cc_start: 0.9473 (tpt) cc_final: 0.9270 (tpp) REVERT: C 621 TRP cc_start: 0.8208 (t60) cc_final: 0.7496 (t60) REVERT: C 634 PHE cc_start: 0.9332 (m-80) cc_final: 0.8867 (m-80) REVERT: C 642 MET cc_start: 0.9300 (tpp) cc_final: 0.8716 (mmt) REVERT: C 664 MET cc_start: 0.2548 (mtt) cc_final: 0.2332 (mpp) REVERT: C 681 GLN cc_start: 0.9177 (tp40) cc_final: 0.8786 (tp-100) REVERT: C 685 GLU cc_start: 0.9054 (mp0) cc_final: 0.8737 (mp0) REVERT: C 687 LEU cc_start: 0.9544 (tp) cc_final: 0.9286 (mt) REVERT: C 703 THR cc_start: 0.9173 (p) cc_final: 0.8885 (t) REVERT: C 704 TYR cc_start: 0.7981 (p90) cc_final: 0.7403 (p90) REVERT: C 924 ASP cc_start: 0.7163 (m-30) cc_final: 0.6245 (m-30) REVERT: C 971 LYS cc_start: 0.9254 (ptpp) cc_final: 0.8946 (pttm) REVERT: C 984 MET cc_start: 0.8683 (tpt) cc_final: 0.7724 (tmm) REVERT: C 988 MET cc_start: 0.8717 (ttp) cc_final: 0.8511 (tmm) REVERT: C 990 PHE cc_start: 0.8893 (t80) cc_final: 0.8445 (t80) REVERT: C 1024 PHE cc_start: 0.8555 (m-10) cc_final: 0.8122 (t80) REVERT: C 1030 MET cc_start: 0.8546 (mmt) cc_final: 0.8315 (mmt) REVERT: C 1130 PHE cc_start: 0.9291 (m-10) cc_final: 0.8954 (t80) REVERT: C 1209 MET cc_start: 0.9292 (mmt) cc_final: 0.8838 (mmm) REVERT: D 138 MET cc_start: 0.9198 (mtp) cc_final: 0.8971 (mmt) REVERT: D 159 ASN cc_start: 0.8374 (m-40) cc_final: 0.7581 (t0) REVERT: D 386 MET cc_start: 0.2110 (mmt) cc_final: 0.1289 (tpp) REVERT: D 397 MET cc_start: 0.7197 (mmm) cc_final: 0.6963 (mmm) REVERT: D 630 MET cc_start: 0.9176 (ttm) cc_final: 0.8801 (ttm) REVERT: D 634 PHE cc_start: 0.8712 (m-80) cc_final: 0.8425 (m-80) REVERT: D 699 MET cc_start: 0.9386 (mtt) cc_final: 0.8717 (mtt) REVERT: D 707 LYS cc_start: 0.9257 (mtmm) cc_final: 0.9003 (mptt) REVERT: D 711 ASN cc_start: 0.9564 (m-40) cc_final: 0.9357 (m-40) REVERT: D 739 MET cc_start: 0.9166 (tpt) cc_final: 0.8709 (tpp) REVERT: D 740 TRP cc_start: 0.8966 (t-100) cc_final: 0.8620 (t-100) REVERT: D 979 MET cc_start: 0.8690 (ttm) cc_final: 0.8292 (mtm) REVERT: D 982 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8645 (mmtm) REVERT: D 984 MET cc_start: 0.8726 (tpp) cc_final: 0.8511 (tpp) REVERT: D 987 MET cc_start: 0.9283 (tpt) cc_final: 0.8970 (tpp) REVERT: D 998 LEU cc_start: 0.8713 (tp) cc_final: 0.8508 (tp) REVERT: D 999 MET cc_start: 0.8326 (tmm) cc_final: 0.7871 (tmm) REVERT: D 1082 LEU cc_start: 0.8846 (tp) cc_final: 0.8644 (mp) REVERT: D 1115 MET cc_start: 0.8837 (tpp) cc_final: 0.8486 (tmm) REVERT: D 1133 MET cc_start: 0.8848 (mmm) cc_final: 0.8421 (tmm) REVERT: D 1141 CYS cc_start: 0.6030 (OUTLIER) cc_final: 0.5524 (p) REVERT: B 174 LEU cc_start: 0.8986 (tp) cc_final: 0.8669 (pp) REVERT: B 184 TRP cc_start: 0.8043 (m-10) cc_final: 0.7718 (m-10) REVERT: B 403 GLN cc_start: 0.7189 (mm-40) cc_final: 0.6623 (mm-40) REVERT: B 436 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8902 (pt) REVERT: B 457 MET cc_start: 0.9082 (tpt) cc_final: 0.8722 (ttm) REVERT: B 505 LEU cc_start: 0.9352 (mm) cc_final: 0.9117 (tt) REVERT: B 625 MET cc_start: 0.8723 (mmt) cc_final: 0.8325 (mmt) REVERT: B 626 LYS cc_start: 0.9267 (tttt) cc_final: 0.9044 (ttpt) REVERT: B 634 PHE cc_start: 0.8830 (m-10) cc_final: 0.8518 (m-80) REVERT: B 673 ASN cc_start: 0.9379 (t0) cc_final: 0.9176 (t0) REVERT: B 699 MET cc_start: 0.8997 (mmt) cc_final: 0.8683 (mmt) REVERT: B 704 TYR cc_start: 0.8248 (p90) cc_final: 0.8044 (p90) REVERT: B 716 GLN cc_start: 0.9056 (mt0) cc_final: 0.8602 (mt0) REVERT: B 722 LYS cc_start: 0.9312 (mmtm) cc_final: 0.9072 (mmmm) REVERT: B 734 MET cc_start: 0.9051 (mtp) cc_final: 0.8570 (mmp) REVERT: B 739 MET cc_start: 0.8683 (tpp) cc_final: 0.8351 (tpp) REVERT: B 935 MET cc_start: 0.9061 (tmm) cc_final: 0.8745 (tpp) REVERT: B 956 ILE cc_start: 0.9207 (mt) cc_final: 0.8960 (mt) REVERT: B 960 TYR cc_start: 0.8403 (t80) cc_final: 0.7978 (t80) REVERT: B 988 MET cc_start: 0.8957 (tpt) cc_final: 0.8485 (tpt) REVERT: B 992 ILE cc_start: 0.9184 (mm) cc_final: 0.8949 (mm) REVERT: B 996 VAL cc_start: 0.9207 (t) cc_final: 0.8909 (t) REVERT: B 999 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6914 (ppp) REVERT: B 1023 ILE cc_start: 0.7987 (mm) cc_final: 0.7749 (mt) REVERT: B 1046 GLN cc_start: 0.8538 (tp-100) cc_final: 0.7952 (mp10) REVERT: B 1108 PHE cc_start: 0.8914 (t80) cc_final: 0.8703 (t80) REVERT: B 1133 MET cc_start: 0.9092 (ttp) cc_final: 0.8759 (ptp) outliers start: 47 outliers final: 8 residues processed: 814 average time/residue: 0.1800 time to fit residues: 238.4287 Evaluate side-chains 548 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 536 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 overall best weight: 6.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 ASN A1215 ASN C 480 HIS C 716 GLN ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1022 ASN C1085 ASN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 636 GLN D 637 HIS ** D 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN D1176 GLN B 227 GLN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 HIS B1103 ASN B1215 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.063270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.046526 restraints weight = 329146.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048713 restraints weight = 167939.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.050229 restraints weight = 105728.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.051269 restraints weight = 75456.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.052017 restraints weight = 58679.726| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 32033 Z= 0.263 Angle : 0.820 13.407 43586 Z= 0.435 Chirality : 0.045 0.253 5050 Planarity : 0.006 0.051 5485 Dihedral : 5.202 23.473 4399 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.18 % Rotamer: Outliers : 0.26 % Allowed : 4.11 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.12), residues: 4072 helix: -0.66 (0.09), residues: 2565 sheet: -0.88 (0.30), residues: 285 loop : -1.57 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 210 TYR 0.034 0.003 TYR B 960 PHE 0.054 0.003 PHE C 854 TRP 0.048 0.003 TRP B 431 HIS 0.010 0.002 HIS A 563 Details of bonding type rmsd covalent geometry : bond 0.00552 (32029) covalent geometry : angle 0.81946 (43578) SS BOND : bond 0.01194 ( 4) SS BOND : angle 1.47282 ( 8) hydrogen bonds : bond 0.05796 ( 1883) hydrogen bonds : angle 5.62338 ( 5579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 589 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LEU cc_start: 0.8353 (mt) cc_final: 0.8132 (mt) REVERT: A 259 PHE cc_start: 0.8271 (m-80) cc_final: 0.7450 (m-80) REVERT: A 459 ASP cc_start: 0.9200 (m-30) cc_final: 0.8987 (m-30) REVERT: A 552 ASN cc_start: 0.8940 (t0) cc_final: 0.8601 (m-40) REVERT: A 630 MET cc_start: 0.8416 (mtt) cc_final: 0.8115 (mtt) REVERT: A 733 GLN cc_start: 0.8894 (tt0) cc_final: 0.8303 (tm-30) REVERT: A 894 ILE cc_start: 0.9292 (mm) cc_final: 0.9076 (tt) REVERT: A 971 LYS cc_start: 0.9345 (ptpp) cc_final: 0.9142 (ptpp) REVERT: A 998 LEU cc_start: 0.8085 (tp) cc_final: 0.7745 (tp) REVERT: A 1012 ASN cc_start: 0.8745 (m-40) cc_final: 0.8097 (p0) REVERT: A 1095 PHE cc_start: 0.8399 (t80) cc_final: 0.8000 (t80) REVERT: A 1182 PHE cc_start: 0.7996 (m-80) cc_final: 0.7399 (m-80) REVERT: C 242 MET cc_start: 0.4338 (tpt) cc_final: 0.2620 (tmm) REVERT: C 467 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8309 (p0) REVERT: C 482 PHE cc_start: 0.8834 (t80) cc_final: 0.8237 (t80) REVERT: C 545 MET cc_start: 0.7997 (tpp) cc_final: 0.7656 (tpp) REVERT: C 621 TRP cc_start: 0.8108 (t60) cc_final: 0.7906 (t60) REVERT: C 634 PHE cc_start: 0.9471 (m-80) cc_final: 0.9040 (m-80) REVERT: C 664 MET cc_start: 0.2562 (mtt) cc_final: 0.1578 (mpp) REVERT: C 681 GLN cc_start: 0.8920 (tp40) cc_final: 0.8445 (tp40) REVERT: C 704 TYR cc_start: 0.8263 (p90) cc_final: 0.7500 (p90) REVERT: C 707 LYS cc_start: 0.9127 (mppt) cc_final: 0.8875 (mmtm) REVERT: C 738 ASP cc_start: 0.8837 (m-30) cc_final: 0.8609 (m-30) REVERT: C 984 MET cc_start: 0.8185 (tpt) cc_final: 0.7741 (tmm) REVERT: C 988 MET cc_start: 0.8656 (ttp) cc_final: 0.8395 (tmm) REVERT: C 1024 PHE cc_start: 0.8687 (m-10) cc_final: 0.8125 (t80) REVERT: C 1076 LEU cc_start: 0.9071 (tp) cc_final: 0.8737 (tp) REVERT: C 1130 PHE cc_start: 0.9289 (m-10) cc_final: 0.8974 (t80) REVERT: D 159 ASN cc_start: 0.8307 (m-40) cc_final: 0.7439 (t0) REVERT: D 179 MET cc_start: 0.9122 (mmp) cc_final: 0.8889 (mmm) REVERT: D 386 MET cc_start: 0.2266 (mmt) cc_final: 0.1280 (tpp) REVERT: D 457 MET cc_start: 0.8911 (mtp) cc_final: 0.8654 (mtp) REVERT: D 545 MET cc_start: 0.8295 (tpp) cc_final: 0.7971 (tpp) REVERT: D 625 MET cc_start: 0.8753 (mmp) cc_final: 0.8538 (mmm) REVERT: D 699 MET cc_start: 0.9496 (mtt) cc_final: 0.9014 (mtt) REVERT: D 740 TRP cc_start: 0.8865 (t-100) cc_final: 0.8588 (t-100) REVERT: D 987 MET cc_start: 0.9437 (tpt) cc_final: 0.9111 (tpp) REVERT: D 998 LEU cc_start: 0.8800 (tp) cc_final: 0.8529 (tp) REVERT: D 1040 ILE cc_start: 0.8766 (mm) cc_final: 0.8515 (mm) REVERT: D 1133 MET cc_start: 0.8812 (mmp) cc_final: 0.8319 (tmm) REVERT: B 150 LEU cc_start: 0.8786 (tp) cc_final: 0.8113 (mt) REVERT: B 170 PHE cc_start: 0.8096 (t80) cc_final: 0.7789 (t80) REVERT: B 403 GLN cc_start: 0.6975 (mm-40) cc_final: 0.6195 (mm-40) REVERT: B 457 MET cc_start: 0.9143 (tpt) cc_final: 0.8875 (ttm) REVERT: B 630 MET cc_start: 0.8647 (tpp) cc_final: 0.8231 (tpp) REVERT: B 634 PHE cc_start: 0.8857 (m-10) cc_final: 0.8624 (m-80) REVERT: B 657 HIS cc_start: 0.9003 (t70) cc_final: 0.8622 (t70) REVERT: B 699 MET cc_start: 0.8996 (mmt) cc_final: 0.8784 (mmt) REVERT: B 722 LYS cc_start: 0.9322 (mmtm) cc_final: 0.9107 (mmmm) REVERT: B 734 MET cc_start: 0.8809 (mtp) cc_final: 0.8461 (mmm) REVERT: B 894 ILE cc_start: 0.9207 (mm) cc_final: 0.8990 (tt) REVERT: B 895 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8659 (tp30) REVERT: B 960 TYR cc_start: 0.8220 (t80) cc_final: 0.7910 (t80) REVERT: B 978 MET cc_start: 0.9081 (mmp) cc_final: 0.8793 (mpp) REVERT: B 988 MET cc_start: 0.9065 (tpt) cc_final: 0.8670 (tpt) REVERT: B 1108 PHE cc_start: 0.8999 (t80) cc_final: 0.8742 (t80) REVERT: B 1133 MET cc_start: 0.8929 (ttp) cc_final: 0.8589 (ptp) outliers start: 8 outliers final: 2 residues processed: 593 average time/residue: 0.1698 time to fit residues: 166.8800 Evaluate side-chains 471 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 468 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 114 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 365 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 328 optimal weight: 40.0000 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 242 optimal weight: 9.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN C 440 GLN ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 970 ASN D 279 GLN D 616 HIS ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 ASN D 955 ASN D1132 HIS ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.065038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.048073 restraints weight = 307306.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050291 restraints weight = 161619.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.051835 restraints weight = 103216.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.052915 restraints weight = 73920.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.053643 restraints weight = 57527.567| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32033 Z= 0.143 Angle : 0.664 10.097 43586 Z= 0.341 Chirality : 0.042 0.189 5050 Planarity : 0.005 0.058 5485 Dihedral : 4.785 25.873 4399 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 0.16 % Allowed : 2.99 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 4072 helix: 0.16 (0.10), residues: 2578 sheet: -0.64 (0.30), residues: 284 loop : -1.39 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1183 TYR 0.028 0.002 TYR C 958 PHE 0.034 0.002 PHE C 854 TRP 0.028 0.002 TRP B 431 HIS 0.010 0.001 HIS A 563 Details of bonding type rmsd covalent geometry : bond 0.00303 (32029) covalent geometry : angle 0.66354 (43578) SS BOND : bond 0.00062 ( 4) SS BOND : angle 0.87096 ( 8) hydrogen bonds : bond 0.04908 ( 1883) hydrogen bonds : angle 4.97225 ( 5579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 604 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LEU cc_start: 0.8219 (mt) cc_final: 0.7962 (mt) REVERT: A 259 PHE cc_start: 0.8296 (m-80) cc_final: 0.7378 (m-80) REVERT: A 459 ASP cc_start: 0.9046 (m-30) cc_final: 0.8828 (m-30) REVERT: A 552 ASN cc_start: 0.8960 (t0) cc_final: 0.8690 (m-40) REVERT: A 630 MET cc_start: 0.8431 (mtt) cc_final: 0.8186 (mtt) REVERT: A 733 GLN cc_start: 0.8860 (tt0) cc_final: 0.8605 (tm-30) REVERT: A 894 ILE cc_start: 0.9252 (mm) cc_final: 0.9023 (tt) REVERT: A 1012 ASN cc_start: 0.8580 (m-40) cc_final: 0.7893 (p0) REVERT: A 1182 PHE cc_start: 0.8154 (m-80) cc_final: 0.7535 (m-80) REVERT: C 242 MET cc_start: 0.4291 (tpt) cc_final: 0.3700 (tpp) REVERT: C 482 PHE cc_start: 0.8611 (t80) cc_final: 0.7848 (t80) REVERT: C 619 MET cc_start: 0.9333 (mmm) cc_final: 0.9037 (mmm) REVERT: C 664 MET cc_start: 0.2432 (mtt) cc_final: 0.1509 (mpp) REVERT: C 703 THR cc_start: 0.9172 (p) cc_final: 0.8861 (t) REVERT: C 704 TYR cc_start: 0.8086 (p90) cc_final: 0.7506 (p90) REVERT: C 738 ASP cc_start: 0.8881 (m-30) cc_final: 0.8440 (m-30) REVERT: C 924 ASP cc_start: 0.6947 (m-30) cc_final: 0.6457 (m-30) REVERT: C 984 MET cc_start: 0.8392 (tpt) cc_final: 0.8001 (tpp) REVERT: C 988 MET cc_start: 0.8675 (ttp) cc_final: 0.8419 (tmm) REVERT: C 999 MET cc_start: 0.8698 (ttt) cc_final: 0.8470 (ttt) REVERT: C 1024 PHE cc_start: 0.8622 (m-10) cc_final: 0.8133 (t80) REVERT: C 1130 PHE cc_start: 0.9229 (m-10) cc_final: 0.8955 (t80) REVERT: C 1179 GLU cc_start: 0.8267 (tm-30) cc_final: 0.8020 (tm-30) REVERT: D 159 ASN cc_start: 0.8280 (m-40) cc_final: 0.7445 (t0) REVERT: D 179 MET cc_start: 0.9206 (mmp) cc_final: 0.8959 (mmm) REVERT: D 242 MET cc_start: 0.3462 (ppp) cc_final: 0.2778 (mmt) REVERT: D 386 MET cc_start: 0.2150 (mmt) cc_final: 0.1224 (tpp) REVERT: D 397 MET cc_start: 0.7341 (mmm) cc_final: 0.6948 (mmp) REVERT: D 457 MET cc_start: 0.8870 (mtp) cc_final: 0.8648 (mtp) REVERT: D 545 MET cc_start: 0.8078 (tpp) cc_final: 0.7756 (tpp) REVERT: D 699 MET cc_start: 0.9492 (mtt) cc_final: 0.8598 (mtt) REVERT: D 740 TRP cc_start: 0.8849 (t-100) cc_final: 0.8452 (t-100) REVERT: D 897 MET cc_start: 0.8251 (ppp) cc_final: 0.7953 (ppp) REVERT: D 984 MET cc_start: 0.8997 (tpp) cc_final: 0.8688 (mmm) REVERT: D 987 MET cc_start: 0.9346 (tpt) cc_final: 0.8872 (tmm) REVERT: D 998 LEU cc_start: 0.8742 (tp) cc_final: 0.8534 (tp) REVERT: D 999 MET cc_start: 0.8551 (tmm) cc_final: 0.7932 (tmm) REVERT: D 1109 GLN cc_start: 0.9168 (mm110) cc_final: 0.8954 (mm-40) REVERT: D 1115 MET cc_start: 0.9156 (tmm) cc_final: 0.8931 (tmm) REVERT: D 1133 MET cc_start: 0.8827 (mmp) cc_final: 0.8235 (tmm) REVERT: B 150 LEU cc_start: 0.8724 (tp) cc_final: 0.8152 (mt) REVERT: B 457 MET cc_start: 0.9052 (tpt) cc_final: 0.8755 (ttm) REVERT: B 545 MET cc_start: 0.8335 (tpt) cc_final: 0.8081 (tpp) REVERT: B 630 MET cc_start: 0.8595 (tpp) cc_final: 0.7877 (tpp) REVERT: B 634 PHE cc_start: 0.8731 (m-10) cc_final: 0.8411 (m-80) REVERT: B 640 GLU cc_start: 0.8034 (mp0) cc_final: 0.7714 (mp0) REVERT: B 657 HIS cc_start: 0.8992 (t70) cc_final: 0.8580 (t70) REVERT: B 699 MET cc_start: 0.8886 (mmt) cc_final: 0.8600 (mmt) REVERT: B 734 MET cc_start: 0.8727 (mtp) cc_final: 0.8406 (mmm) REVERT: B 888 TYR cc_start: 0.8510 (t80) cc_final: 0.7995 (t80) REVERT: B 895 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8413 (tp30) REVERT: B 960 TYR cc_start: 0.8385 (t80) cc_final: 0.8038 (t80) REVERT: B 978 MET cc_start: 0.9099 (mmp) cc_final: 0.8831 (mpp) REVERT: B 979 MET cc_start: 0.9422 (ttm) cc_final: 0.8692 (mtp) REVERT: B 1133 MET cc_start: 0.8894 (ttp) cc_final: 0.8164 (ptp) REVERT: B 1175 GLU cc_start: 0.9115 (mp0) cc_final: 0.8845 (mp0) REVERT: B 1186 ASP cc_start: 0.9381 (m-30) cc_final: 0.9107 (m-30) outliers start: 5 outliers final: 1 residues processed: 608 average time/residue: 0.1825 time to fit residues: 184.6327 Evaluate side-chains 485 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 484 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 192 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 278 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 318 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 50.0000 chunk 390 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 GLN C 693 GLN ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 674 HIS B ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.063486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.046660 restraints weight = 333282.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.048880 restraints weight = 170583.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.050407 restraints weight = 107386.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.051473 restraints weight = 76240.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.052239 restraints weight = 58894.401| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32033 Z= 0.183 Angle : 0.679 10.795 43586 Z= 0.353 Chirality : 0.042 0.213 5050 Planarity : 0.005 0.090 5485 Dihedral : 4.634 26.294 4399 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4072 helix: 0.46 (0.10), residues: 2584 sheet: -0.66 (0.31), residues: 282 loop : -1.27 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1203 TYR 0.025 0.002 TYR D1181 PHE 0.038 0.002 PHE C1091 TRP 0.023 0.002 TRP C 621 HIS 0.007 0.001 HIS A 563 Details of bonding type rmsd covalent geometry : bond 0.00396 (32029) covalent geometry : angle 0.67869 (43578) SS BOND : bond 0.00486 ( 4) SS BOND : angle 0.83037 ( 8) hydrogen bonds : bond 0.04685 ( 1883) hydrogen bonds : angle 4.89349 ( 5579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 566 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 ASP cc_start: 0.9080 (m-30) cc_final: 0.8851 (m-30) REVERT: A 552 ASN cc_start: 0.8951 (t0) cc_final: 0.8685 (m-40) REVERT: A 722 LYS cc_start: 0.9257 (tmtt) cc_final: 0.9047 (tptp) REVERT: A 733 GLN cc_start: 0.8888 (tt0) cc_final: 0.8620 (tm-30) REVERT: A 894 ILE cc_start: 0.9245 (mm) cc_final: 0.9020 (tt) REVERT: A 994 MET cc_start: 0.9058 (tpt) cc_final: 0.8842 (tpp) REVERT: A 1012 ASN cc_start: 0.8625 (m-40) cc_final: 0.7582 (p0) REVERT: A 1030 MET cc_start: 0.9285 (mtp) cc_final: 0.8552 (mmm) REVERT: A 1182 PHE cc_start: 0.8157 (m-80) cc_final: 0.7499 (m-80) REVERT: A 1209 MET cc_start: 0.8634 (tmm) cc_final: 0.8362 (tmm) REVERT: C 242 MET cc_start: 0.4240 (tpt) cc_final: 0.3516 (tpp) REVERT: C 634 PHE cc_start: 0.9465 (m-80) cc_final: 0.9054 (m-80) REVERT: C 664 MET cc_start: 0.2393 (mtt) cc_final: 0.1510 (mpp) REVERT: C 681 GLN cc_start: 0.9045 (tp40) cc_final: 0.8586 (tp-100) REVERT: C 703 THR cc_start: 0.9231 (p) cc_final: 0.8949 (t) REVERT: C 704 TYR cc_start: 0.8336 (p90) cc_final: 0.7769 (p90) REVERT: C 924 ASP cc_start: 0.7048 (m-30) cc_final: 0.6570 (m-30) REVERT: C 984 MET cc_start: 0.8463 (tpt) cc_final: 0.8045 (tmm) REVERT: C 988 MET cc_start: 0.8610 (ttp) cc_final: 0.8361 (tmm) REVERT: C 999 MET cc_start: 0.8728 (ttt) cc_final: 0.8429 (ttt) REVERT: C 1024 PHE cc_start: 0.8618 (m-10) cc_final: 0.8108 (t80) REVERT: C 1130 PHE cc_start: 0.9247 (m-10) cc_final: 0.8974 (t80) REVERT: C 1179 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8095 (tm-30) REVERT: D 159 ASN cc_start: 0.8318 (m-40) cc_final: 0.7551 (t0) REVERT: D 174 LEU cc_start: 0.9204 (pp) cc_final: 0.8891 (pp) REVERT: D 179 MET cc_start: 0.9273 (mmp) cc_final: 0.9017 (mmm) REVERT: D 386 MET cc_start: 0.2214 (mmt) cc_final: 0.1608 (tpp) REVERT: D 545 MET cc_start: 0.8281 (tpp) cc_final: 0.8016 (tpp) REVERT: D 655 MET cc_start: 0.9352 (ttp) cc_final: 0.9131 (tmm) REVERT: D 699 MET cc_start: 0.9501 (mtt) cc_final: 0.8599 (mtt) REVERT: D 707 LYS cc_start: 0.8885 (mppt) cc_final: 0.8635 (mptt) REVERT: D 740 TRP cc_start: 0.8851 (t-100) cc_final: 0.8468 (t-100) REVERT: D 862 TYR cc_start: 0.7971 (t80) cc_final: 0.7752 (t80) REVERT: D 979 MET cc_start: 0.9190 (ttm) cc_final: 0.8744 (ttp) REVERT: D 984 MET cc_start: 0.9035 (tpp) cc_final: 0.8637 (mmm) REVERT: D 987 MET cc_start: 0.9322 (tpt) cc_final: 0.8946 (tmm) REVERT: D 998 LEU cc_start: 0.8630 (tp) cc_final: 0.8319 (tp) REVERT: D 1109 GLN cc_start: 0.9178 (mm110) cc_final: 0.8868 (mm-40) REVERT: D 1115 MET cc_start: 0.9191 (tmm) cc_final: 0.8971 (tmm) REVERT: D 1133 MET cc_start: 0.8836 (mmp) cc_final: 0.8226 (tmm) REVERT: B 150 LEU cc_start: 0.8787 (tp) cc_final: 0.8192 (mt) REVERT: B 457 MET cc_start: 0.9089 (tpt) cc_final: 0.8888 (ttm) REVERT: B 545 MET cc_start: 0.8451 (tpt) cc_final: 0.8227 (tpp) REVERT: B 640 GLU cc_start: 0.8061 (mp0) cc_final: 0.7715 (mp0) REVERT: B 657 HIS cc_start: 0.9003 (t70) cc_final: 0.8600 (t70) REVERT: B 699 MET cc_start: 0.9077 (mmt) cc_final: 0.8857 (mmt) REVERT: B 734 MET cc_start: 0.8722 (mtp) cc_final: 0.8441 (mmm) REVERT: B 894 ILE cc_start: 0.9118 (mm) cc_final: 0.8880 (tt) REVERT: B 895 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8393 (tp30) REVERT: B 960 TYR cc_start: 0.8562 (t80) cc_final: 0.8069 (t80) REVERT: B 978 MET cc_start: 0.9118 (mmp) cc_final: 0.8849 (mpp) REVERT: B 983 MET cc_start: 0.9180 (mmp) cc_final: 0.8925 (mmt) REVERT: B 1133 MET cc_start: 0.8880 (ttp) cc_final: 0.8528 (ptp) outliers start: 0 outliers final: 0 residues processed: 566 average time/residue: 0.1767 time to fit residues: 166.7624 Evaluate side-chains 462 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 12 optimal weight: 8.9990 chunk 106 optimal weight: 40.0000 chunk 46 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 chunk 271 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 ASN C 480 HIS ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 674 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.062458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.045944 restraints weight = 313257.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048026 restraints weight = 165707.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049452 restraints weight = 106447.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.050456 restraints weight = 76817.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.051185 restraints weight = 60163.411| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32033 Z= 0.200 Angle : 0.695 9.761 43586 Z= 0.363 Chirality : 0.043 0.173 5050 Planarity : 0.005 0.101 5485 Dihedral : 4.653 25.915 4399 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4072 helix: 0.53 (0.10), residues: 2607 sheet: -0.66 (0.29), residues: 298 loop : -1.33 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 555 TYR 0.030 0.002 TYR A 960 PHE 0.042 0.002 PHE C 854 TRP 0.044 0.002 TRP B 142 HIS 0.007 0.001 HIS A 563 Details of bonding type rmsd covalent geometry : bond 0.00423 (32029) covalent geometry : angle 0.69544 (43578) SS BOND : bond 0.00128 ( 4) SS BOND : angle 0.79552 ( 8) hydrogen bonds : bond 0.04609 ( 1883) hydrogen bonds : angle 4.89219 ( 5579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 545 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 ASP cc_start: 0.9019 (m-30) cc_final: 0.8775 (m-30) REVERT: A 492 TYR cc_start: 0.9019 (m-80) cc_final: 0.8755 (m-80) REVERT: A 552 ASN cc_start: 0.8913 (t0) cc_final: 0.8681 (m-40) REVERT: A 702 LEU cc_start: 0.9221 (mm) cc_final: 0.9012 (mm) REVERT: A 722 LYS cc_start: 0.9196 (tmtt) cc_final: 0.8911 (tptp) REVERT: A 930 LEU cc_start: 0.8825 (tp) cc_final: 0.8562 (tp) REVERT: A 962 ARG cc_start: 0.7905 (tpt170) cc_final: 0.7298 (tpt170) REVERT: A 987 MET cc_start: 0.9048 (mmt) cc_final: 0.8299 (tmm) REVERT: A 990 PHE cc_start: 0.8658 (t80) cc_final: 0.8263 (t80) REVERT: A 994 MET cc_start: 0.9035 (tpt) cc_final: 0.8823 (tpp) REVERT: A 1012 ASN cc_start: 0.8771 (m-40) cc_final: 0.7671 (p0) REVERT: C 242 MET cc_start: 0.4504 (tpt) cc_final: 0.3785 (tpp) REVERT: C 457 MET cc_start: 0.9160 (mmt) cc_final: 0.8943 (mmm) REVERT: C 492 TYR cc_start: 0.8611 (m-10) cc_final: 0.8230 (m-80) REVERT: C 619 MET cc_start: 0.9313 (mmm) cc_final: 0.9068 (mmm) REVERT: C 634 PHE cc_start: 0.9489 (m-80) cc_final: 0.8991 (m-80) REVERT: C 664 MET cc_start: 0.2485 (mtt) cc_final: 0.1563 (mpp) REVERT: C 681 GLN cc_start: 0.9088 (tp40) cc_final: 0.8559 (tp-100) REVERT: C 685 GLU cc_start: 0.9078 (mp0) cc_final: 0.8682 (mp0) REVERT: C 704 TYR cc_start: 0.8511 (p90) cc_final: 0.7975 (p90) REVERT: C 978 MET cc_start: 0.8961 (mmm) cc_final: 0.8686 (mmt) REVERT: C 984 MET cc_start: 0.8442 (tpt) cc_final: 0.8231 (tpt) REVERT: C 988 MET cc_start: 0.8608 (ttp) cc_final: 0.8391 (tmm) REVERT: C 1024 PHE cc_start: 0.8645 (m-10) cc_final: 0.8024 (t80) REVERT: C 1097 GLU cc_start: 0.8069 (mp0) cc_final: 0.7760 (mp0) REVERT: C 1130 PHE cc_start: 0.9249 (m-10) cc_final: 0.8977 (t80) REVERT: C 1179 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8083 (tm-30) REVERT: D 138 MET cc_start: 0.8652 (tmm) cc_final: 0.8408 (tmm) REVERT: D 159 ASN cc_start: 0.8349 (m-40) cc_final: 0.7649 (t0) REVERT: D 174 LEU cc_start: 0.9211 (pp) cc_final: 0.8888 (pp) REVERT: D 179 MET cc_start: 0.9355 (mmp) cc_final: 0.9065 (mmm) REVERT: D 386 MET cc_start: 0.2269 (mmt) cc_final: 0.1717 (tpp) REVERT: D 457 MET cc_start: 0.8834 (mtp) cc_final: 0.8493 (mtt) REVERT: D 545 MET cc_start: 0.8420 (tpp) cc_final: 0.7934 (tpp) REVERT: D 699 MET cc_start: 0.9481 (mtt) cc_final: 0.8740 (mtt) REVERT: D 740 TRP cc_start: 0.8817 (t-100) cc_final: 0.8374 (t-100) REVERT: D 984 MET cc_start: 0.9002 (tpp) cc_final: 0.8647 (mmm) REVERT: D 987 MET cc_start: 0.9316 (tpt) cc_final: 0.8940 (tmm) REVERT: D 998 LEU cc_start: 0.8646 (tp) cc_final: 0.8395 (tp) REVERT: D 999 MET cc_start: 0.8560 (tmm) cc_final: 0.8139 (tmm) REVERT: D 1082 LEU cc_start: 0.8859 (tt) cc_final: 0.8567 (mp) REVERT: D 1109 GLN cc_start: 0.9159 (mm110) cc_final: 0.8846 (mm-40) REVERT: D 1115 MET cc_start: 0.9205 (tmm) cc_final: 0.8988 (tmm) REVERT: D 1133 MET cc_start: 0.8823 (mmp) cc_final: 0.8187 (tmm) REVERT: D 1205 GLU cc_start: 0.9249 (tp30) cc_final: 0.8889 (tp30) REVERT: B 121 MET cc_start: 0.9348 (mtp) cc_final: 0.8811 (mmp) REVERT: B 150 LEU cc_start: 0.8809 (tp) cc_final: 0.8210 (mt) REVERT: B 545 MET cc_start: 0.8531 (tpt) cc_final: 0.8298 (tpp) REVERT: B 630 MET cc_start: 0.8520 (tpp) cc_final: 0.7985 (tpt) REVERT: B 640 GLU cc_start: 0.8079 (mp0) cc_final: 0.7693 (mp0) REVERT: B 657 HIS cc_start: 0.9048 (t70) cc_final: 0.8640 (t70) REVERT: B 894 ILE cc_start: 0.9094 (mm) cc_final: 0.8848 (tt) REVERT: B 895 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8380 (tp30) REVERT: B 960 TYR cc_start: 0.8205 (t80) cc_final: 0.7832 (t80) REVERT: B 978 MET cc_start: 0.9070 (mmp) cc_final: 0.8837 (mpp) REVERT: B 983 MET cc_start: 0.9214 (mmp) cc_final: 0.8956 (mmt) REVERT: B 1109 GLN cc_start: 0.9016 (mp10) cc_final: 0.8809 (mp10) REVERT: B 1133 MET cc_start: 0.8874 (ttp) cc_final: 0.8126 (ptp) outliers start: 1 outliers final: 0 residues processed: 546 average time/residue: 0.1733 time to fit residues: 158.5059 Evaluate side-chains 450 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 275 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 352 optimal weight: 8.9990 chunk 235 optimal weight: 50.0000 chunk 182 optimal weight: 9.9990 chunk 49 optimal weight: 0.0670 chunk 16 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 383 optimal weight: 3.9990 chunk 394 optimal weight: 9.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1085 ASN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 674 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 ASN ** B1092 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 = 0.3453 r_free = 0.3453 target = 0.062358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.045912 restraints weight = 299940.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.047935 restraints weight = 160704.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049344 restraints weight = 103972.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.050309 restraints weight = 75450.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.051019 restraints weight = 59560.331| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32033 Z= 0.189 Angle : 0.687 10.553 43586 Z= 0.356 Chirality : 0.043 0.174 5050 Planarity : 0.005 0.147 5485 Dihedral : 4.625 24.420 4399 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.91 % Rotamer: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4072 helix: 0.62 (0.10), residues: 2598 sheet: -0.65 (0.30), residues: 290 loop : -1.32 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 487 TYR 0.025 0.002 TYR A 960 PHE 0.041 0.002 PHE A1091 TRP 0.029 0.002 TRP A 184 HIS 0.011 0.001 HIS D1139 Details of bonding type rmsd covalent geometry : bond 0.00403 (32029) covalent geometry : angle 0.68664 (43578) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.51097 ( 8) hydrogen bonds : bond 0.04525 ( 1883) hydrogen bonds : angle 4.84540 ( 5579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 546 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 ASP cc_start: 0.8985 (m-30) cc_final: 0.8764 (m-30) REVERT: A 492 TYR cc_start: 0.9076 (m-80) cc_final: 0.8795 (m-80) REVERT: A 552 ASN cc_start: 0.8966 (t0) cc_final: 0.8713 (m-40) REVERT: A 702 LEU cc_start: 0.9226 (mm) cc_final: 0.8996 (mm) REVERT: A 722 LYS cc_start: 0.9218 (tmtt) cc_final: 0.8875 (tptp) REVERT: A 894 ILE cc_start: 0.9270 (mm) cc_final: 0.9040 (tt) REVERT: A 930 LEU cc_start: 0.8823 (tp) cc_final: 0.8561 (tp) REVERT: A 962 ARG cc_start: 0.7897 (tpt170) cc_final: 0.7286 (tpt170) REVERT: A 999 MET cc_start: 0.7896 (ttt) cc_final: 0.7674 (ttt) REVERT: A 1012 ASN cc_start: 0.8697 (m-40) cc_final: 0.7608 (p0) REVERT: A 1175 GLU cc_start: 0.8943 (pp20) cc_final: 0.8626 (mm-30) REVERT: C 179 MET cc_start: 0.9333 (mmm) cc_final: 0.8992 (mmm) REVERT: C 242 MET cc_start: 0.4648 (tpt) cc_final: 0.3898 (tpp) REVERT: C 492 TYR cc_start: 0.8669 (m-10) cc_final: 0.8265 (m-80) REVERT: C 619 MET cc_start: 0.9290 (mmm) cc_final: 0.9032 (mmm) REVERT: C 634 PHE cc_start: 0.9462 (m-80) cc_final: 0.8983 (m-80) REVERT: C 664 MET cc_start: 0.2503 (mtt) cc_final: 0.1448 (mpp) REVERT: C 681 GLN cc_start: 0.9029 (tp40) cc_final: 0.8555 (tp-100) REVERT: C 704 TYR cc_start: 0.8488 (p90) cc_final: 0.7973 (p90) REVERT: C 978 MET cc_start: 0.8963 (mmm) cc_final: 0.8739 (mmt) REVERT: C 984 MET cc_start: 0.8397 (tpt) cc_final: 0.8061 (tmm) REVERT: C 988 MET cc_start: 0.8604 (ttp) cc_final: 0.8372 (tmm) REVERT: C 990 PHE cc_start: 0.8760 (t80) cc_final: 0.8461 (t80) REVERT: C 1024 PHE cc_start: 0.8697 (m-10) cc_final: 0.8020 (t80) REVERT: C 1097 GLU cc_start: 0.8091 (mp0) cc_final: 0.7875 (mp0) REVERT: C 1130 PHE cc_start: 0.9242 (m-10) cc_final: 0.8959 (t80) REVERT: C 1179 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8075 (tm-30) REVERT: D 174 LEU cc_start: 0.9222 (pp) cc_final: 0.8917 (pp) REVERT: D 179 MET cc_start: 0.9385 (mmp) cc_final: 0.9080 (mmm) REVERT: D 386 MET cc_start: 0.2351 (mmt) cc_final: 0.1763 (tpp) REVERT: D 457 MET cc_start: 0.8828 (mtp) cc_final: 0.8479 (mtp) REVERT: D 699 MET cc_start: 0.9437 (mtt) cc_final: 0.8672 (mtt) REVERT: D 740 TRP cc_start: 0.8729 (t-100) cc_final: 0.8272 (t-100) REVERT: D 979 MET cc_start: 0.9149 (ttm) cc_final: 0.8845 (ttm) REVERT: D 982 LYS cc_start: 0.9258 (tppt) cc_final: 0.8966 (tppt) REVERT: D 984 MET cc_start: 0.8987 (tpp) cc_final: 0.8566 (mmm) REVERT: D 987 MET cc_start: 0.9294 (tpt) cc_final: 0.8951 (tmm) REVERT: D 998 LEU cc_start: 0.8730 (tp) cc_final: 0.8513 (tp) REVERT: D 1109 GLN cc_start: 0.9116 (mm110) cc_final: 0.8792 (mm-40) REVERT: D 1115 MET cc_start: 0.9185 (tmm) cc_final: 0.8952 (tmm) REVERT: D 1133 MET cc_start: 0.8791 (mmp) cc_final: 0.8295 (tmm) REVERT: D 1205 GLU cc_start: 0.9267 (tp30) cc_final: 0.9019 (tp30) REVERT: B 121 MET cc_start: 0.9404 (mtp) cc_final: 0.8855 (mmp) REVERT: B 150 LEU cc_start: 0.8844 (tp) cc_final: 0.8235 (mt) REVERT: B 386 MET cc_start: 0.3487 (mmm) cc_final: 0.2579 (mmt) REVERT: B 640 GLU cc_start: 0.8152 (mp0) cc_final: 0.7746 (mp0) REVERT: B 642 MET cc_start: 0.9408 (mmt) cc_final: 0.9182 (mmm) REVERT: B 657 HIS cc_start: 0.9020 (t70) cc_final: 0.8616 (t-90) REVERT: B 734 MET cc_start: 0.8667 (mmp) cc_final: 0.8319 (mmm) REVERT: B 894 ILE cc_start: 0.9069 (mm) cc_final: 0.8816 (tt) REVERT: B 895 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8391 (tp30) REVERT: B 960 TYR cc_start: 0.8460 (t80) cc_final: 0.8022 (t80) REVERT: B 978 MET cc_start: 0.9040 (mmp) cc_final: 0.8793 (mpp) REVERT: B 979 MET cc_start: 0.9078 (mtm) cc_final: 0.8822 (mpp) REVERT: B 983 MET cc_start: 0.9170 (mmp) cc_final: 0.8901 (mmt) REVERT: B 1109 GLN cc_start: 0.9081 (mp10) cc_final: 0.8796 (mp10) REVERT: B 1133 MET cc_start: 0.8865 (ttp) cc_final: 0.8606 (ptp) outliers start: 1 outliers final: 0 residues processed: 547 average time/residue: 0.1797 time to fit residues: 164.4439 Evaluate side-chains 450 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 171 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 255 optimal weight: 30.0000 chunk 393 optimal weight: 8.9990 chunk 291 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 189 optimal weight: 40.0000 chunk 254 optimal weight: 1.9990 chunk 26 optimal weight: 40.0000 chunk 203 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 GLN A1193 ASN C 693 GLN C1104 GLN C1118 HIS D 279 GLN ** D 674 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.061984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.045471 restraints weight = 315566.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.047525 restraints weight = 168357.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.048962 restraints weight = 108453.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049959 restraints weight = 78528.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.050641 restraints weight = 61670.164| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32033 Z= 0.185 Angle : 0.693 9.728 43586 Z= 0.358 Chirality : 0.043 0.220 5050 Planarity : 0.005 0.114 5485 Dihedral : 4.656 30.522 4399 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.13), residues: 4072 helix: 0.62 (0.10), residues: 2611 sheet: -0.65 (0.30), residues: 294 loop : -1.31 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 747 TYR 0.025 0.002 TYR D1181 PHE 0.048 0.002 PHE D1091 TRP 0.036 0.002 TRP A 184 HIS 0.007 0.001 HIS A 563 Details of bonding type rmsd covalent geometry : bond 0.00401 (32029) covalent geometry : angle 0.69311 (43578) SS BOND : bond 0.00108 ( 4) SS BOND : angle 1.38197 ( 8) hydrogen bonds : bond 0.04478 ( 1883) hydrogen bonds : angle 4.87432 ( 5579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8608 (m-80) cc_final: 0.8392 (m-80) REVERT: A 459 ASP cc_start: 0.8965 (m-30) cc_final: 0.8745 (m-30) REVERT: A 545 MET cc_start: 0.8893 (ppp) cc_final: 0.8509 (ppp) REVERT: A 552 ASN cc_start: 0.8934 (t0) cc_final: 0.8710 (m-40) REVERT: A 722 LYS cc_start: 0.9152 (tmtt) cc_final: 0.8805 (tptp) REVERT: A 894 ILE cc_start: 0.9269 (mm) cc_final: 0.9046 (tt) REVERT: A 930 LEU cc_start: 0.8807 (tp) cc_final: 0.8542 (tp) REVERT: A 962 ARG cc_start: 0.7919 (tpt170) cc_final: 0.7324 (tpt170) REVERT: A 987 MET cc_start: 0.9028 (mmt) cc_final: 0.8367 (tmm) REVERT: A 1012 ASN cc_start: 0.8755 (m-40) cc_final: 0.7598 (p0) REVERT: A 1175 GLU cc_start: 0.8890 (pp20) cc_final: 0.8569 (mm-30) REVERT: C 179 MET cc_start: 0.9346 (mmm) cc_final: 0.8982 (mmm) REVERT: C 242 MET cc_start: 0.4699 (tpt) cc_final: 0.3927 (tpp) REVERT: C 492 TYR cc_start: 0.8747 (m-10) cc_final: 0.8332 (m-80) REVERT: C 619 MET cc_start: 0.9309 (mmm) cc_final: 0.9066 (mmm) REVERT: C 634 PHE cc_start: 0.9456 (m-80) cc_final: 0.8970 (m-80) REVERT: C 664 MET cc_start: 0.2649 (mtt) cc_final: 0.1594 (mpp) REVERT: C 681 GLN cc_start: 0.9124 (tp40) cc_final: 0.8788 (tp-100) REVERT: C 685 GLU cc_start: 0.9186 (mp0) cc_final: 0.8790 (mp0) REVERT: C 703 THR cc_start: 0.9324 (p) cc_final: 0.9030 (t) REVERT: C 704 TYR cc_start: 0.8524 (p90) cc_final: 0.7991 (p90) REVERT: C 741 MET cc_start: 0.8069 (ttp) cc_final: 0.7813 (ttp) REVERT: C 978 MET cc_start: 0.8987 (mmm) cc_final: 0.8782 (mmt) REVERT: C 984 MET cc_start: 0.8353 (tpt) cc_final: 0.8078 (tpt) REVERT: C 988 MET cc_start: 0.8580 (ttp) cc_final: 0.8359 (tmm) REVERT: C 1097 GLU cc_start: 0.8094 (mp0) cc_final: 0.7877 (mp0) REVERT: C 1130 PHE cc_start: 0.9235 (m-10) cc_final: 0.8971 (t80) REVERT: C 1179 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8075 (tm-30) REVERT: D 138 MET cc_start: 0.8770 (tmm) cc_final: 0.8450 (tmm) REVERT: D 174 LEU cc_start: 0.9219 (pp) cc_final: 0.8924 (pp) REVERT: D 179 MET cc_start: 0.9388 (mmp) cc_final: 0.9073 (mmm) REVERT: D 386 MET cc_start: 0.2671 (mmt) cc_final: 0.2100 (tpp) REVERT: D 457 MET cc_start: 0.8680 (mtp) cc_final: 0.8401 (mtt) REVERT: D 459 ASP cc_start: 0.8496 (m-30) cc_final: 0.8200 (m-30) REVERT: D 655 MET cc_start: 0.9341 (ttp) cc_final: 0.9112 (tmm) REVERT: D 699 MET cc_start: 0.9453 (mtt) cc_final: 0.8808 (mtt) REVERT: D 740 TRP cc_start: 0.8664 (t-100) cc_final: 0.8246 (t-100) REVERT: D 897 MET cc_start: 0.8099 (ppp) cc_final: 0.7714 (ppp) REVERT: D 982 LYS cc_start: 0.9260 (tppt) cc_final: 0.8938 (tppt) REVERT: D 984 MET cc_start: 0.9013 (tpp) cc_final: 0.8533 (mmm) REVERT: D 987 MET cc_start: 0.9295 (tpt) cc_final: 0.8962 (tmm) REVERT: D 1082 LEU cc_start: 0.8907 (tt) cc_final: 0.8624 (mp) REVERT: D 1109 GLN cc_start: 0.9106 (mm110) cc_final: 0.8786 (mm-40) REVERT: D 1115 MET cc_start: 0.9197 (tmm) cc_final: 0.8956 (tmm) REVERT: D 1123 LEU cc_start: 0.8015 (mt) cc_final: 0.7749 (mt) REVERT: D 1133 MET cc_start: 0.8763 (mmp) cc_final: 0.8283 (tmm) REVERT: D 1205 GLU cc_start: 0.9269 (tp30) cc_final: 0.8988 (tp30) REVERT: D 1206 ASN cc_start: 0.9088 (m-40) cc_final: 0.8674 (p0) REVERT: B 121 MET cc_start: 0.9421 (mtp) cc_final: 0.8857 (mmp) REVERT: B 150 LEU cc_start: 0.8820 (tp) cc_final: 0.8249 (mt) REVERT: B 386 MET cc_start: 0.3388 (mmm) cc_final: 0.2537 (mmt) REVERT: B 625 MET cc_start: 0.8630 (mmt) cc_final: 0.8308 (mmt) REVERT: B 640 GLU cc_start: 0.8132 (mp0) cc_final: 0.7727 (mp0) REVERT: B 657 HIS cc_start: 0.9026 (t70) cc_final: 0.8635 (t-90) REVERT: B 734 MET cc_start: 0.8662 (mmp) cc_final: 0.8236 (mmm) REVERT: B 894 ILE cc_start: 0.9064 (mm) cc_final: 0.8798 (tt) REVERT: B 895 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8473 (tp30) REVERT: B 960 TYR cc_start: 0.8460 (t80) cc_final: 0.8117 (t80) REVERT: B 978 MET cc_start: 0.9152 (mmp) cc_final: 0.8929 (mpp) REVERT: B 979 MET cc_start: 0.9002 (mtm) cc_final: 0.8739 (mpp) REVERT: B 983 MET cc_start: 0.9161 (mmp) cc_final: 0.8933 (mmt) REVERT: B 1109 GLN cc_start: 0.9106 (mp10) cc_final: 0.8784 (mp10) REVERT: B 1133 MET cc_start: 0.8781 (ttp) cc_final: 0.8200 (ptp) REVERT: B 1210 ARG cc_start: 0.8836 (ttm170) cc_final: 0.8541 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.1679 time to fit residues: 152.3306 Evaluate side-chains 450 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 72 optimal weight: 10.0000 chunk 293 optimal weight: 0.0670 chunk 232 optimal weight: 1.9990 chunk 403 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 266 optimal weight: 0.2980 chunk 317 optimal weight: 30.0000 chunk 336 optimal weight: 0.3980 chunk 77 optimal weight: 0.0980 chunk 250 optimal weight: 0.0870 chunk 236 optimal weight: 7.9990 overall best weight: 0.1896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 ASN C 205 HIS C 440 GLN C1085 ASN ** D 674 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 HIS B 675 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.047985 restraints weight = 273080.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.050029 restraints weight = 150102.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.051461 restraints weight = 97969.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.052463 restraints weight = 71529.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053135 restraints weight = 56468.075| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32033 Z= 0.134 Angle : 0.666 11.879 43586 Z= 0.337 Chirality : 0.042 0.262 5050 Planarity : 0.004 0.085 5485 Dihedral : 4.498 28.988 4399 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 4072 helix: 0.85 (0.10), residues: 2583 sheet: -0.42 (0.31), residues: 292 loop : -1.12 (0.19), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1188 TYR 0.027 0.002 TYR C 958 PHE 0.048 0.002 PHE D1091 TRP 0.046 0.002 TRP C 184 HIS 0.011 0.001 HIS A 563 Details of bonding type rmsd covalent geometry : bond 0.00279 (32029) covalent geometry : angle 0.66587 (43578) SS BOND : bond 0.00138 ( 4) SS BOND : angle 0.84816 ( 8) hydrogen bonds : bond 0.04165 ( 1883) hydrogen bonds : angle 4.59200 ( 5579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 MET cc_start: 0.8853 (ppp) cc_final: 0.8517 (ppp) REVERT: A 722 LYS cc_start: 0.9115 (tmtt) cc_final: 0.8751 (tptp) REVERT: A 894 ILE cc_start: 0.9291 (mm) cc_final: 0.9047 (tt) REVERT: A 930 LEU cc_start: 0.8822 (tp) cc_final: 0.8579 (tp) REVERT: A 962 ARG cc_start: 0.7877 (tpt170) cc_final: 0.7241 (tpt170) REVERT: A 1026 MET cc_start: 0.8581 (mpp) cc_final: 0.8333 (mpp) REVERT: A 1030 MET cc_start: 0.9109 (mtp) cc_final: 0.8732 (mmm) REVERT: A 1159 LYS cc_start: 0.8124 (mppt) cc_final: 0.7714 (mtmt) REVERT: C 179 MET cc_start: 0.9337 (mmm) cc_final: 0.8924 (mmm) REVERT: C 242 MET cc_start: 0.4576 (tpt) cc_final: 0.3820 (tpp) REVERT: C 492 TYR cc_start: 0.8692 (m-10) cc_final: 0.8287 (m-80) REVERT: C 619 MET cc_start: 0.9334 (mmm) cc_final: 0.9078 (mmm) REVERT: C 634 PHE cc_start: 0.9386 (m-80) cc_final: 0.8777 (m-80) REVERT: C 664 MET cc_start: 0.2099 (mtt) cc_final: 0.1213 (mpp) REVERT: C 703 THR cc_start: 0.9248 (p) cc_final: 0.9005 (t) REVERT: C 704 TYR cc_start: 0.8205 (p90) cc_final: 0.7693 (p90) REVERT: C 738 ASP cc_start: 0.8954 (m-30) cc_final: 0.8702 (m-30) REVERT: C 978 MET cc_start: 0.8981 (mmm) cc_final: 0.8727 (mmm) REVERT: C 984 MET cc_start: 0.8335 (tpt) cc_final: 0.8089 (tpt) REVERT: C 998 LEU cc_start: 0.8733 (tt) cc_final: 0.8462 (tt) REVERT: C 1097 GLU cc_start: 0.8193 (mp0) cc_final: 0.7954 (mp0) REVERT: C 1130 PHE cc_start: 0.9232 (m-10) cc_final: 0.8957 (t80) REVERT: C 1179 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8043 (tm-30) REVERT: D 179 MET cc_start: 0.9365 (mmm) cc_final: 0.9126 (mmm) REVERT: D 386 MET cc_start: 0.2573 (mmt) cc_final: 0.1788 (tpp) REVERT: D 457 MET cc_start: 0.8696 (mtp) cc_final: 0.8399 (mtp) REVERT: D 459 ASP cc_start: 0.8354 (m-30) cc_final: 0.8043 (m-30) REVERT: D 488 LEU cc_start: 0.9537 (tp) cc_final: 0.8185 (tp) REVERT: D 534 LEU cc_start: 0.9073 (mt) cc_final: 0.8797 (mt) REVERT: D 543 TYR cc_start: 0.8313 (t80) cc_final: 0.8055 (t80) REVERT: D 544 LEU cc_start: 0.8765 (mm) cc_final: 0.8464 (mm) REVERT: D 655 MET cc_start: 0.9268 (ttp) cc_final: 0.9063 (tmm) REVERT: D 699 MET cc_start: 0.9411 (mtt) cc_final: 0.8793 (mtt) REVERT: D 740 TRP cc_start: 0.8516 (t-100) cc_final: 0.8180 (t-100) REVERT: D 982 LYS cc_start: 0.9169 (tppt) cc_final: 0.8930 (tppt) REVERT: D 984 MET cc_start: 0.8836 (tpp) cc_final: 0.8298 (mmm) REVERT: D 987 MET cc_start: 0.9253 (tpt) cc_final: 0.8932 (tmm) REVERT: D 988 MET cc_start: 0.8642 (ttm) cc_final: 0.8359 (ttp) REVERT: D 1109 GLN cc_start: 0.9081 (mm110) cc_final: 0.8774 (mm-40) REVERT: D 1115 MET cc_start: 0.9145 (tmm) cc_final: 0.8868 (tmm) REVERT: D 1123 LEU cc_start: 0.7982 (mt) cc_final: 0.7724 (mt) REVERT: D 1133 MET cc_start: 0.8798 (mmp) cc_final: 0.8330 (tmm) REVERT: D 1180 GLU cc_start: 0.9177 (mp0) cc_final: 0.8896 (mp0) REVERT: B 121 MET cc_start: 0.9418 (mtp) cc_final: 0.8859 (mmp) REVERT: B 386 MET cc_start: 0.3453 (mmm) cc_final: 0.2578 (mmt) REVERT: B 545 MET cc_start: 0.8461 (tpt) cc_final: 0.8169 (tpp) REVERT: B 640 GLU cc_start: 0.7861 (mp0) cc_final: 0.7480 (mp0) REVERT: B 642 MET cc_start: 0.9360 (mmm) cc_final: 0.9006 (mmm) REVERT: B 657 HIS cc_start: 0.8978 (t70) cc_final: 0.8593 (t-90) REVERT: B 863 LEU cc_start: 0.8592 (tp) cc_final: 0.8306 (tp) REVERT: B 894 ILE cc_start: 0.9039 (mm) cc_final: 0.8797 (tt) REVERT: B 895 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8461 (tp30) REVERT: B 925 LEU cc_start: 0.9125 (tp) cc_final: 0.8844 (tp) REVERT: B 960 TYR cc_start: 0.8395 (t80) cc_final: 0.7785 (t80) REVERT: B 991 VAL cc_start: 0.9250 (t) cc_final: 0.8990 (t) REVERT: B 999 MET cc_start: 0.7787 (ppp) cc_final: 0.7528 (tmm) REVERT: B 1133 MET cc_start: 0.8844 (ttp) cc_final: 0.8143 (ptp) REVERT: B 1210 ARG cc_start: 0.8772 (ttm170) cc_final: 0.8507 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 595 average time/residue: 0.1758 time to fit residues: 173.6527 Evaluate side-chains 487 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 216 optimal weight: 50.0000 chunk 85 optimal weight: 6.9990 chunk 302 optimal weight: 0.8980 chunk 360 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 229 optimal weight: 0.1980 chunk 330 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 333 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN A 674 HIS ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 636 GLN ** D 674 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.062813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.046171 restraints weight = 327221.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.048293 restraints weight = 170968.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049793 restraints weight = 109312.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.050826 restraints weight = 78425.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.051549 restraints weight = 61106.345| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32033 Z= 0.162 Angle : 0.675 9.915 43586 Z= 0.347 Chirality : 0.042 0.192 5050 Planarity : 0.005 0.103 5485 Dihedral : 4.459 27.376 4399 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.13), residues: 4072 helix: 0.83 (0.10), residues: 2607 sheet: -0.35 (0.31), residues: 289 loop : -1.13 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1203 TYR 0.028 0.002 TYR D1181 PHE 0.043 0.002 PHE D1091 TRP 0.025 0.002 TRP C 621 HIS 0.007 0.001 HIS A 563 Details of bonding type rmsd covalent geometry : bond 0.00354 (32029) covalent geometry : angle 0.67497 (43578) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.79597 ( 8) hydrogen bonds : bond 0.04230 ( 1883) hydrogen bonds : angle 4.67676 ( 5579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 553 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 LEU cc_start: 0.9122 (mt) cc_final: 0.8777 (pp) REVERT: A 545 MET cc_start: 0.8837 (ppp) cc_final: 0.8446 (ppp) REVERT: A 722 LYS cc_start: 0.9146 (tmtt) cc_final: 0.8742 (tptp) REVERT: A 894 ILE cc_start: 0.9261 (mm) cc_final: 0.9024 (tt) REVERT: A 930 LEU cc_start: 0.8807 (tp) cc_final: 0.8545 (tp) REVERT: A 962 ARG cc_start: 0.7856 (tpt170) cc_final: 0.7247 (tpt170) REVERT: A 999 MET cc_start: 0.7760 (ttt) cc_final: 0.7529 (ttt) REVERT: A 1012 ASN cc_start: 0.8620 (m110) cc_final: 0.7705 (p0) REVERT: A 1026 MET cc_start: 0.8656 (mpp) cc_final: 0.7831 (mpp) REVERT: A 1030 MET cc_start: 0.9216 (mtp) cc_final: 0.8727 (mmm) REVERT: A 1182 PHE cc_start: 0.7712 (m-80) cc_final: 0.7401 (m-80) REVERT: C 179 MET cc_start: 0.9349 (mmm) cc_final: 0.8971 (mmm) REVERT: C 242 MET cc_start: 0.4638 (tpt) cc_final: 0.3872 (tpp) REVERT: C 492 TYR cc_start: 0.8766 (m-10) cc_final: 0.8310 (m-80) REVERT: C 619 MET cc_start: 0.9342 (mmm) cc_final: 0.9060 (mmm) REVERT: C 634 PHE cc_start: 0.9428 (m-80) cc_final: 0.8933 (m-80) REVERT: C 664 MET cc_start: 0.2248 (mtt) cc_final: 0.1250 (mpp) REVERT: C 681 GLN cc_start: 0.9067 (tp40) cc_final: 0.8834 (tp-100) REVERT: C 685 GLU cc_start: 0.9244 (mp0) cc_final: 0.8891 (mp0) REVERT: C 703 THR cc_start: 0.9289 (p) cc_final: 0.9040 (t) REVERT: C 704 TYR cc_start: 0.8440 (p90) cc_final: 0.7868 (p90) REVERT: C 741 MET cc_start: 0.8047 (ttp) cc_final: 0.7737 (ttp) REVERT: C 978 MET cc_start: 0.9046 (mmm) cc_final: 0.8780 (mmm) REVERT: C 984 MET cc_start: 0.8250 (tpt) cc_final: 0.7996 (tpt) REVERT: C 998 LEU cc_start: 0.8764 (tt) cc_final: 0.8520 (tt) REVERT: C 999 MET cc_start: 0.9116 (ttm) cc_final: 0.8571 (ttp) REVERT: C 1097 GLU cc_start: 0.8170 (mp0) cc_final: 0.7957 (mp0) REVERT: C 1130 PHE cc_start: 0.9248 (m-10) cc_final: 0.8968 (t80) REVERT: C 1179 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8073 (tm-30) REVERT: D 138 MET cc_start: 0.8873 (tmm) cc_final: 0.8554 (tmm) REVERT: D 174 LEU cc_start: 0.9233 (pp) cc_final: 0.8881 (pp) REVERT: D 179 MET cc_start: 0.9335 (mmm) cc_final: 0.9059 (mmm) REVERT: D 386 MET cc_start: 0.2649 (mmt) cc_final: 0.1842 (tpp) REVERT: D 459 ASP cc_start: 0.8449 (m-30) cc_final: 0.8178 (m-30) REVERT: D 543 TYR cc_start: 0.8389 (t80) cc_final: 0.8051 (t80) REVERT: D 544 LEU cc_start: 0.8814 (mm) cc_final: 0.8492 (mm) REVERT: D 699 MET cc_start: 0.9437 (mtt) cc_final: 0.8973 (mtt) REVERT: D 740 TRP cc_start: 0.8599 (t-100) cc_final: 0.8215 (t-100) REVERT: D 960 TYR cc_start: 0.7986 (m-10) cc_final: 0.7782 (m-10) REVERT: D 982 LYS cc_start: 0.9214 (tppt) cc_final: 0.8956 (tppt) REVERT: D 984 MET cc_start: 0.8898 (tpp) cc_final: 0.8461 (mmm) REVERT: D 987 MET cc_start: 0.9292 (tpt) cc_final: 0.8962 (tmm) REVERT: D 988 MET cc_start: 0.8691 (ttm) cc_final: 0.8405 (ttp) REVERT: D 1109 GLN cc_start: 0.9066 (mm110) cc_final: 0.8746 (mm-40) REVERT: D 1123 LEU cc_start: 0.7946 (mt) cc_final: 0.7721 (mt) REVERT: D 1133 MET cc_start: 0.8804 (mmp) cc_final: 0.8342 (tmm) REVERT: D 1206 ASN cc_start: 0.9014 (m-40) cc_final: 0.8796 (p0) REVERT: B 121 MET cc_start: 0.9431 (mtp) cc_final: 0.8852 (mmp) REVERT: B 150 LEU cc_start: 0.8801 (tp) cc_final: 0.8239 (mt) REVERT: B 386 MET cc_start: 0.3376 (mmm) cc_final: 0.2534 (mmt) REVERT: B 640 GLU cc_start: 0.8004 (mp0) cc_final: 0.7618 (mp0) REVERT: B 657 HIS cc_start: 0.8987 (t70) cc_final: 0.8606 (t-90) REVERT: B 894 ILE cc_start: 0.9041 (mm) cc_final: 0.8799 (tt) REVERT: B 895 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8500 (tp30) REVERT: B 925 LEU cc_start: 0.9080 (tp) cc_final: 0.8859 (tp) REVERT: B 960 TYR cc_start: 0.8477 (t80) cc_final: 0.8069 (t80) REVERT: B 978 MET cc_start: 0.9092 (mmm) cc_final: 0.8830 (mmm) REVERT: B 1133 MET cc_start: 0.8835 (ttp) cc_final: 0.8114 (ptp) REVERT: B 1210 ARG cc_start: 0.8863 (ttm170) cc_final: 0.8552 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 553 average time/residue: 0.1592 time to fit residues: 147.5585 Evaluate side-chains 464 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 55 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 370 optimal weight: 8.9990 chunk 318 optimal weight: 20.0000 chunk 299 optimal weight: 0.0770 chunk 156 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 330 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 356 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1085 ASN D 279 GLN ** D 674 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** D1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** 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 = 0.3491 r_free = 0.3491 target = 0.063874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.046782 restraints weight = 343108.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049055 restraints weight = 175671.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.050625 restraints weight = 111115.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.051736 restraints weight = 79130.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052535 restraints weight = 61278.166| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 32033 Z= 0.135 Angle : 0.677 10.727 43586 Z= 0.340 Chirality : 0.042 0.267 5050 Planarity : 0.004 0.089 5485 Dihedral : 4.418 27.114 4399 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.94 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.13), residues: 4072 helix: 0.87 (0.10), residues: 2608 sheet: -0.32 (0.31), residues: 294 loop : -1.10 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1188 TYR 0.032 0.002 TYR B 845 PHE 0.048 0.002 PHE C1001 TRP 0.026 0.001 TRP C 621 HIS 0.008 0.001 HIS A 563 Details of bonding type rmsd covalent geometry : bond 0.00294 (32029) covalent geometry : angle 0.67740 (43578) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.63685 ( 8) hydrogen bonds : bond 0.04076 ( 1883) hydrogen bonds : angle 4.56885 ( 5579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 565 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 MET cc_start: 0.8422 (ttm) cc_final: 0.8126 (mtt) REVERT: A 457 MET cc_start: 0.9089 (tpp) cc_final: 0.8798 (ttp) REVERT: A 545 MET cc_start: 0.8840 (ppp) cc_final: 0.8397 (ppp) REVERT: A 722 LYS cc_start: 0.9173 (tmtt) cc_final: 0.8753 (tptp) REVERT: A 894 ILE cc_start: 0.9260 (mm) cc_final: 0.9029 (tt) REVERT: A 930 LEU cc_start: 0.8801 (tp) cc_final: 0.8555 (tp) REVERT: A 962 ARG cc_start: 0.7837 (tpt170) cc_final: 0.7195 (tpt170) REVERT: A 1026 MET cc_start: 0.8662 (mpp) cc_final: 0.7904 (mpp) REVERT: A 1030 MET cc_start: 0.9180 (mtp) cc_final: 0.8779 (mmm) REVERT: A 1159 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8234 (mtmt) REVERT: A 1175 GLU cc_start: 0.8896 (pp20) cc_final: 0.8534 (pp20) REVERT: A 1182 PHE cc_start: 0.7707 (m-80) cc_final: 0.7323 (m-80) REVERT: C 179 MET cc_start: 0.9354 (mmm) cc_final: 0.8960 (mmm) REVERT: C 242 MET cc_start: 0.4620 (tpt) cc_final: 0.3806 (tpp) REVERT: C 492 TYR cc_start: 0.8726 (m-10) cc_final: 0.8268 (m-80) REVERT: C 619 MET cc_start: 0.9356 (mmm) cc_final: 0.9112 (mmm) REVERT: C 634 PHE cc_start: 0.9424 (m-80) cc_final: 0.8958 (m-80) REVERT: C 664 MET cc_start: 0.2106 (mtt) cc_final: 0.1173 (mpp) REVERT: C 685 GLU cc_start: 0.9187 (mp0) cc_final: 0.8970 (mp0) REVERT: C 703 THR cc_start: 0.9277 (p) cc_final: 0.9062 (t) REVERT: C 704 TYR cc_start: 0.8372 (p90) cc_final: 0.7798 (p90) REVERT: C 741 MET cc_start: 0.8077 (ttp) cc_final: 0.7778 (ttp) REVERT: C 978 MET cc_start: 0.9063 (mmm) cc_final: 0.8799 (mmm) REVERT: C 984 MET cc_start: 0.8193 (tpt) cc_final: 0.7960 (tpt) REVERT: C 998 LEU cc_start: 0.8689 (tt) cc_final: 0.8419 (tt) REVERT: C 999 MET cc_start: 0.9036 (ttm) cc_final: 0.8487 (ttm) REVERT: C 1097 GLU cc_start: 0.8169 (mp0) cc_final: 0.7957 (mp0) REVERT: C 1130 PHE cc_start: 0.9252 (m-10) cc_final: 0.8962 (t80) REVERT: C 1179 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8105 (tm-30) REVERT: C 1188 ARG cc_start: 0.8900 (mmp80) cc_final: 0.8594 (mtm110) REVERT: D 179 MET cc_start: 0.9351 (mmm) cc_final: 0.9065 (mmm) REVERT: D 386 MET cc_start: 0.2584 (mmt) cc_final: 0.1810 (tpp) REVERT: D 457 MET cc_start: 0.8723 (mtp) cc_final: 0.8439 (mtt) REVERT: D 459 ASP cc_start: 0.8422 (m-30) cc_final: 0.8110 (m-30) REVERT: D 488 LEU cc_start: 0.9465 (tp) cc_final: 0.9000 (tp) REVERT: D 492 TYR cc_start: 0.8256 (m-80) cc_final: 0.7753 (m-80) REVERT: D 543 TYR cc_start: 0.8408 (t80) cc_final: 0.8108 (t80) REVERT: D 544 LEU cc_start: 0.8793 (mm) cc_final: 0.8282 (mm) REVERT: D 699 MET cc_start: 0.9401 (mtt) cc_final: 0.8961 (mtt) REVERT: D 722 LYS cc_start: 0.9248 (mmtp) cc_final: 0.9009 (mptt) REVERT: D 740 TRP cc_start: 0.8556 (t-100) cc_final: 0.8211 (t-100) REVERT: D 924 ASP cc_start: 0.7273 (m-30) cc_final: 0.7003 (m-30) REVERT: D 960 TYR cc_start: 0.8059 (m-10) cc_final: 0.7341 (m-10) REVERT: D 979 MET cc_start: 0.9239 (ttm) cc_final: 0.9033 (ttm) REVERT: D 982 LYS cc_start: 0.9195 (tppt) cc_final: 0.8961 (tppt) REVERT: D 984 MET cc_start: 0.8828 (tpp) cc_final: 0.8375 (mmm) REVERT: D 987 MET cc_start: 0.9266 (tpt) cc_final: 0.8944 (tmm) REVERT: D 988 MET cc_start: 0.8730 (ttm) cc_final: 0.8455 (ttp) REVERT: D 1109 GLN cc_start: 0.9094 (mm110) cc_final: 0.8763 (mm-40) REVERT: D 1123 LEU cc_start: 0.7913 (mt) cc_final: 0.7659 (mt) REVERT: D 1133 MET cc_start: 0.8828 (mmp) cc_final: 0.8490 (tmm) REVERT: B 121 MET cc_start: 0.9425 (mtp) cc_final: 0.8851 (mmp) REVERT: B 386 MET cc_start: 0.3447 (mmm) cc_final: 0.2559 (mmt) REVERT: B 545 MET cc_start: 0.8520 (tpt) cc_final: 0.8139 (tpp) REVERT: B 640 GLU cc_start: 0.7897 (mp0) cc_final: 0.7505 (mp0) REVERT: B 657 HIS cc_start: 0.9000 (t70) cc_final: 0.8608 (t-90) REVERT: B 888 TYR cc_start: 0.8384 (t80) cc_final: 0.8004 (t80) REVERT: B 894 ILE cc_start: 0.8988 (mm) cc_final: 0.8748 (tt) REVERT: B 895 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8470 (tp30) REVERT: B 925 LEU cc_start: 0.9053 (tp) cc_final: 0.8780 (tp) REVERT: B 960 TYR cc_start: 0.8431 (t80) cc_final: 0.7815 (t80) REVERT: B 978 MET cc_start: 0.9122 (mmm) cc_final: 0.8838 (mmm) REVERT: B 991 VAL cc_start: 0.9226 (t) cc_final: 0.9017 (t) REVERT: B 1072 MET cc_start: 0.8399 (ttm) cc_final: 0.8081 (tmm) REVERT: B 1133 MET cc_start: 0.8802 (ttp) cc_final: 0.8065 (ptp) REVERT: B 1210 ARG cc_start: 0.8850 (ttm170) cc_final: 0.8558 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 565 average time/residue: 0.1565 time to fit residues: 149.0309 Evaluate side-chains 473 residues out of total 3674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 198 optimal weight: 0.7980 chunk 219 optimal weight: 10.0000 chunk 309 optimal weight: 1.9990 chunk 357 optimal weight: 0.0010 chunk 395 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 18 optimal weight: 0.1980 chunk 90 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 318 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 674 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1085 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.063582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047396 restraints weight = 272563.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.049389 restraints weight = 151703.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.050751 restraints weight = 100089.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.051706 restraints weight = 73614.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.052400 restraints weight = 58591.081| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 32033 Z= 0.140 Angle : 0.669 10.823 43586 Z= 0.338 Chirality : 0.042 0.180 5050 Planarity : 0.004 0.090 5485 Dihedral : 4.390 25.818 4399 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4072 helix: 0.90 (0.10), residues: 2610 sheet: -0.31 (0.31), residues: 295 loop : -1.10 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C1188 TYR 0.028 0.002 TYR A 862 PHE 0.043 0.002 PHE C1001 TRP 0.025 0.002 TRP C 621 HIS 0.007 0.001 HIS A 563 Details of bonding type rmsd covalent geometry : bond 0.00310 (32029) covalent geometry : angle 0.66870 (43578) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.66257 ( 8) hydrogen bonds : bond 0.04044 ( 1883) hydrogen bonds : angle 4.59530 ( 5579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6071.32 seconds wall clock time: 105 minutes 43.04 seconds (6343.04 seconds total)