Starting phenix.real_space_refine on Tue Sep 15 08:39:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v22_21025/09_2026/6v22_21025.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v22_21025/09_2026/6v22_21025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v22_21025/09_2026/6v22_21025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v22_21025/09_2026/6v22_21025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v22_21025/09_2026/6v22_21025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v22_21025/09_2026/6v22_21025.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6v22_21025/09_2026/6v22_21025.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v22_21025/09_2026/6v22_21025.cif" } resolution = 3.2 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= -0.319 sd= 0.838 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: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 P 40 5.49 5 Mg 4 5.21 5 S 244 5.16 5 C 24256 2.51 5 N 5748 2.21 5 O 6700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.23s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37004 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7137 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 27, 'TRANS': 868} Chain breaks: 4 Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain: "B" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7137 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 27, 'TRANS': 868} Chain breaks: 4 Chain: "A" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 419 Unusual residues: {' K': 4, ' CA': 2, ' MG': 1, 'CLR': 4, 'POV': 11} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 3, 'POV:plan-3': 4} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 112 Unusual residues: {'NAG': 2, 'POV': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 415 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 4, 'POV': 11} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-1': 6, 'POV:plan-2': 3} Unresolved non-hydrogen planarities: 46 Restraints were copied for chains: C, D, F, G, H Time building chain proxies: 13.46, per 1000 atoms: 0.36 Number of scatterers: 37004 At special positions: 0 Unit cell: (144.56, 144.56, 160.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 244 16.00 P 40 15.00 Mg 4 11.99 O 6700 8.00 N 5748 7.00 C 24256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS E2054 " - pdb=" SG CYS E2148 " distance=2.03 Simple disulfide: pdb=" SG CYS E2068 " - pdb=" SG CYS E2119 " distance=2.03 Simple disulfide: pdb=" SG CYS E2072 " - pdb=" SG CYS E2076 " distance=2.02 Simple disulfide: pdb=" SG CYS E2084 " - pdb=" SG CYS E2113 " distance=2.03 Simple disulfide: pdb=" SG CYS F2054 " - pdb=" SG CYS F2148 " distance=2.03 Simple disulfide: pdb=" SG CYS G2054 " - pdb=" SG CYS G2148 " distance=2.03 Simple disulfide: pdb=" SG CYS H2054 " - pdb=" SG CYS H2148 " distance=2.03 Simple disulfide: pdb=" SG CYS F2068 " - pdb=" SG CYS F2119 " distance=2.03 Simple disulfide: pdb=" SG CYS G2068 " - pdb=" SG CYS G2119 " distance=2.03 Simple disulfide: pdb=" SG CYS H2068 " - pdb=" SG CYS H2119 " distance=2.03 Simple disulfide: pdb=" SG CYS F2072 " - pdb=" SG CYS F2076 " distance=2.02 Simple disulfide: pdb=" SG CYS G2072 " - pdb=" SG CYS G2076 " distance=2.02 Simple disulfide: pdb=" SG CYS H2072 " - pdb=" SG CYS H2076 " distance=2.02 Simple disulfide: pdb=" SG CYS F2084 " - pdb=" SG CYS F2113 " distance=2.03 Simple disulfide: pdb=" SG CYS G2084 " - pdb=" SG CYS G2113 " distance=2.03 Simple disulfide: pdb=" SG CYS H2084 " - pdb=" SG CYS H2113 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Links applied NAG-ASN " NAG E2305 " - " ASN E2053 " " NAG E2306 " - " ASN E2090 " " NAG F2305 " - " ASN F2053 " " NAG F2306 " - " ASN F2090 " " NAG G2305 " - " ASN G2053 " " NAG G2306 " - " ASN G2090 " " NAG H2305 " - " ASN H2053 " " NAG H2306 " - " ASN H2090 " Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.5 seconds 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8312 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 36 sheets defined 53.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 21 through 47 removed outlier: 4.401A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 26 " --> pdb=" O TRP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 106 removed outlier: 3.539A pdb=" N SER A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 147 through 171 removed outlier: 3.626A pdb=" N GLN A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 200 removed outlier: 3.801A pdb=" N ASP A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Proline residue: A 191 - end of helix removed outlier: 3.883A pdb=" N PHE A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.657A pdb=" N LEU A 209 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 229 through 259 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.597A pdb=" N GLU A 264 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.595A pdb=" N CYS A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 326 removed outlier: 4.986A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.718A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.585A pdb=" N MET A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 4.164A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.515A pdb=" N PHE A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 604 through 609 removed outlier: 3.909A pdb=" N PHE A 609 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.554A pdb=" N VAL A 703 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 743 removed outlier: 4.042A pdb=" N ALA A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 759 through 771 removed outlier: 5.022A pdb=" N GLU A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.549A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 829 Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.917A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 891 " --> pdb=" O VAL A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 918 through 921 Processing helix chain 'A' and resid 922 through 930 Processing helix chain 'A' and resid 931 through 942 removed outlier: 4.460A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 956 removed outlier: 3.629A pdb=" N GLU A 950 " --> pdb=" O THR A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 971 Processing helix chain 'A' and resid 972 through 974 No H-bonds generated for 'chain 'A' and resid 972 through 974' Processing helix chain 'A' and resid 987 through 992 removed outlier: 3.620A pdb=" N GLY A 991 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 992 " --> pdb=" O ASP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'E' and resid 2011 through 2039 removed outlier: 3.950A pdb=" N PHE E2037 " --> pdb=" O PHE E2033 " (cutoff:3.500A) Processing helix chain 'E' and resid 2039 through 2049 removed outlier: 3.681A pdb=" N ALA E2049 " --> pdb=" O GLN E2045 " (cutoff:3.500A) Processing helix chain 'E' and resid 2103 through 2110 Processing helix chain 'E' and resid 2122 through 2140 removed outlier: 3.680A pdb=" N GLU E2140 " --> pdb=" O TYR E2136 " (cutoff:3.500A) Processing helix chain 'E' and resid 2168 through 2204 removed outlier: 3.817A pdb=" N PHE E2174 " --> pdb=" O LEU E2170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TRP E2176 " --> pdb=" O HIS E2172 " (cutoff:3.500A) Proline residue: E2177 - end of helix Processing helix chain 'B' and resid 21 through 47 removed outlier: 4.401A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 26 " --> pdb=" O TRP B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 106 removed outlier: 3.540A pdb=" N SER B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 134 Processing helix chain 'B' and resid 147 through 171 removed outlier: 3.626A pdb=" N GLN B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 180 through 200 removed outlier: 3.801A pdb=" N ASP B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Proline residue: B 191 - end of helix removed outlier: 3.883A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.657A pdb=" N LEU B 209 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 214 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'B' and resid 229 through 259 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.597A pdb=" N GLU B 264 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 265' Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.595A pdb=" N CYS B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 326 removed outlier: 4.986A pdb=" N ALA B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.718A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 500 Processing helix chain 'B' and resid 502 through 510 removed outlier: 3.585A pdb=" N MET B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 533 removed outlier: 4.163A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.515A pdb=" N PHE B 545 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 604 through 609 removed outlier: 3.908A pdb=" N PHE B 609 " --> pdb=" O LYS B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.553A pdb=" N VAL B 703 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 743 removed outlier: 4.041A pdb=" N ALA B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 743' Processing helix chain 'B' and resid 759 through 771 removed outlier: 5.022A pdb=" N GLU B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU B 770 " --> pdb=" O GLU B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 792 removed outlier: 3.549A pdb=" N LEU B 789 " --> pdb=" O SER B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 884 through 891 removed outlier: 3.917A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 891 " --> pdb=" O VAL B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 918 through 921 Processing helix chain 'B' and resid 922 through 930 Processing helix chain 'B' and resid 931 through 942 removed outlier: 4.461A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 956 removed outlier: 3.629A pdb=" N GLU B 950 " --> pdb=" O THR B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 971 Processing helix chain 'B' and resid 972 through 974 No H-bonds generated for 'chain 'B' and resid 972 through 974' Processing helix chain 'B' and resid 987 through 992 removed outlier: 3.620A pdb=" N GLY B 991 " --> pdb=" O ALA B 988 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 992 " --> pdb=" O ASP B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'F' and resid 2011 through 2039 removed outlier: 3.950A pdb=" N PHE F2037 " --> pdb=" O PHE F2033 " (cutoff:3.500A) Processing helix chain 'F' and resid 2039 through 2049 removed outlier: 3.681A pdb=" N ALA F2049 " --> pdb=" O GLN F2045 " (cutoff:3.500A) Processing helix chain 'F' and resid 2103 through 2110 Processing helix chain 'F' and resid 2122 through 2140 removed outlier: 3.679A pdb=" N GLU F2140 " --> pdb=" O TYR F2136 " (cutoff:3.500A) Processing helix chain 'F' and resid 2168 through 2204 removed outlier: 3.817A pdb=" N PHE F2174 " --> pdb=" O LEU F2170 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TRP F2176 " --> pdb=" O HIS F2172 " (cutoff:3.500A) Proline residue: F2177 - end of helix Processing helix chain 'C' and resid 21 through 47 removed outlier: 4.401A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 106 removed outlier: 3.538A pdb=" N SER C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 147 through 171 removed outlier: 3.625A pdb=" N GLN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 180 through 200 removed outlier: 3.801A pdb=" N ASP C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Proline residue: C 191 - end of helix removed outlier: 3.883A pdb=" N PHE C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.656A pdb=" N LEU C 209 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 214 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 229 through 259 Processing helix chain 'C' and resid 261 through 265 removed outlier: 3.597A pdb=" N GLU C 264 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN C 265 " --> pdb=" O PRO C 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 265' Processing helix chain 'C' and resid 273 through 286 removed outlier: 3.594A pdb=" N CYS C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 326 removed outlier: 4.987A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 463 through 471 removed outlier: 3.718A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 510 removed outlier: 3.585A pdb=" N MET C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.163A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.514A pdb=" N PHE C 545 " --> pdb=" O SER C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 604 through 609 removed outlier: 3.908A pdb=" N PHE C 609 " --> pdb=" O LYS C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 703 removed outlier: 3.554A pdb=" N VAL C 703 " --> pdb=" O ILE C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 743 removed outlier: 4.041A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 759 through 771 removed outlier: 5.022A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C 770 " --> pdb=" O GLU C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 removed outlier: 3.549A pdb=" N LEU C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 829 Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.917A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 891 " --> pdb=" O VAL C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 918 through 921 Processing helix chain 'C' and resid 922 through 930 Processing helix chain 'C' and resid 931 through 942 removed outlier: 4.461A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 956 removed outlier: 3.628A pdb=" N GLU C 950 " --> pdb=" O THR C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 971 Processing helix chain 'C' and resid 972 through 974 No H-bonds generated for 'chain 'C' and resid 972 through 974' Processing helix chain 'C' and resid 987 through 992 removed outlier: 3.619A pdb=" N GLY C 991 " --> pdb=" O ALA C 988 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 992 " --> pdb=" O ASP C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1007 Processing helix chain 'G' and resid 2011 through 2039 removed outlier: 3.951A pdb=" N PHE G2037 " --> pdb=" O PHE G2033 " (cutoff:3.500A) Processing helix chain 'G' and resid 2039 through 2049 removed outlier: 3.681A pdb=" N ALA G2049 " --> pdb=" O GLN G2045 " (cutoff:3.500A) Processing helix chain 'G' and resid 2103 through 2110 Processing helix chain 'G' and resid 2122 through 2140 removed outlier: 3.680A pdb=" N GLU G2140 " --> pdb=" O TYR G2136 " (cutoff:3.500A) Processing helix chain 'G' and resid 2168 through 2204 removed outlier: 3.817A pdb=" N PHE G2174 " --> pdb=" O LEU G2170 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TRP G2176 " --> pdb=" O HIS G2172 " (cutoff:3.500A) Proline residue: G2177 - end of helix Processing helix chain 'D' and resid 21 through 47 removed outlier: 4.401A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 26 " --> pdb=" O TRP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 106 removed outlier: 3.540A pdb=" N SER D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 134 Processing helix chain 'D' and resid 147 through 171 removed outlier: 3.626A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 200 removed outlier: 3.801A pdb=" N ASP D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Proline residue: D 191 - end of helix removed outlier: 3.883A pdb=" N PHE D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.657A pdb=" N LEU D 209 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 214 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 229 through 259 Processing helix chain 'D' and resid 261 through 265 removed outlier: 3.597A pdb=" N GLU D 264 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN D 265 " --> pdb=" O PRO D 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 261 through 265' Processing helix chain 'D' and resid 273 through 286 removed outlier: 3.595A pdb=" N CYS D 277 " --> pdb=" O THR D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 326 removed outlier: 4.986A pdb=" N ALA D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'D' and resid 463 through 471 removed outlier: 3.718A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 510 removed outlier: 3.585A pdb=" N MET D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.163A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU D 530 " --> pdb=" O LYS D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 removed outlier: 3.515A pdb=" N PHE D 545 " --> pdb=" O SER D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 604 through 609 removed outlier: 3.908A pdb=" N PHE D 609 " --> pdb=" O LYS D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 703 removed outlier: 3.553A pdb=" N VAL D 703 " --> pdb=" O ILE D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 740 through 743 removed outlier: 4.041A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 759 through 771 removed outlier: 5.022A pdb=" N GLU D 768 " --> pdb=" O LYS D 764 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR D 769 " --> pdb=" O ARG D 765 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU D 770 " --> pdb=" O GLU D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 removed outlier: 3.549A pdb=" N LEU D 789 " --> pdb=" O SER D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 829 Processing helix chain 'D' and resid 884 through 891 removed outlier: 3.917A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 891 " --> pdb=" O VAL D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 918 through 921 Processing helix chain 'D' and resid 922 through 930 Processing helix chain 'D' and resid 931 through 942 removed outlier: 4.461A pdb=" N THR D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 956 removed outlier: 3.629A pdb=" N GLU D 950 " --> pdb=" O THR D 946 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 971 Processing helix chain 'D' and resid 972 through 974 No H-bonds generated for 'chain 'D' and resid 972 through 974' Processing helix chain 'D' and resid 987 through 992 removed outlier: 3.620A pdb=" N GLY D 991 " --> pdb=" O ALA D 988 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 992 " --> pdb=" O ASP D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 996 through 1007 Processing helix chain 'H' and resid 2011 through 2039 removed outlier: 3.950A pdb=" N PHE H2037 " --> pdb=" O PHE H2033 " (cutoff:3.500A) Processing helix chain 'H' and resid 2039 through 2049 removed outlier: 3.681A pdb=" N ALA H2049 " --> pdb=" O GLN H2045 " (cutoff:3.500A) Processing helix chain 'H' and resid 2103 through 2110 Processing helix chain 'H' and resid 2122 through 2140 removed outlier: 3.679A pdb=" N GLU H2140 " --> pdb=" O TYR H2136 " (cutoff:3.500A) Processing helix chain 'H' and resid 2168 through 2204 removed outlier: 3.817A pdb=" N PHE H2174 " --> pdb=" O LEU H2170 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TRP H2176 " --> pdb=" O HIS H2172 " (cutoff:3.500A) Proline residue: H2177 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 402 removed outlier: 6.207A pdb=" N ILE A 375 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TYR A 401 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE A 377 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 421 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 540 removed outlier: 6.110A pdb=" N LEU A 594 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 568 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 596 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 564 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.715A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.211A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU A 803 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS A 722 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 976 through 981 removed outlier: 3.901A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 994 through 995 removed outlier: 3.919A pdb=" N GLY A 994 " --> pdb=" O LEU A1043 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 2050 through 2061 removed outlier: 6.871A pdb=" N TYR E2088 " --> pdb=" O LEU E2057 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL E2059 " --> pdb=" O GLN E2086 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN E2086 " --> pdb=" O VAL E2059 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL E2087 " --> pdb=" O LEU E2100 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG E2097 " --> pdb=" O ASP E2157 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL E2159 " --> pdb=" O ARG E2097 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU E2099 " --> pdb=" O VAL E2159 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP E2158 " --> pdb=" O ASN E2151 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN E2151 " --> pdb=" O ASP E2158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2066 through 2067 Processing sheet with id=AB1, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AB2, first strand: chain 'B' and resid 398 through 402 removed outlier: 6.207A pdb=" N ILE B 375 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TYR B 401 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE B 377 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE B 345 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 378 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 347 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 421 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.110A pdb=" N LEU B 594 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 568 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 564 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 686 through 687 removed outlier: 4.715A pdb=" N TYR B 686 " --> pdb=" O GLY B 962 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.210A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 720 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU B 803 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS B 722 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 976 through 981 removed outlier: 3.901A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 994 through 995 removed outlier: 3.918A pdb=" N GLY B 994 " --> pdb=" O LEU B1043 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 2050 through 2061 removed outlier: 6.871A pdb=" N TYR F2088 " --> pdb=" O LEU F2057 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL F2059 " --> pdb=" O GLN F2086 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN F2086 " --> pdb=" O VAL F2059 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL F2087 " --> pdb=" O LEU F2100 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG F2097 " --> pdb=" O ASP F2157 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL F2159 " --> pdb=" O ARG F2097 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU F2099 " --> pdb=" O VAL F2159 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP F2158 " --> pdb=" O ASN F2151 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN F2151 " --> pdb=" O ASP F2158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 2066 through 2067 Processing sheet with id=AC1, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AC2, first strand: chain 'C' and resid 398 through 402 removed outlier: 6.207A pdb=" N ILE C 375 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR C 401 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE C 377 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE C 345 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU C 378 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C 347 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA C 421 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 535 through 540 removed outlier: 6.110A pdb=" N LEU C 594 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE C 568 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE C 596 " --> pdb=" O ILE C 566 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 564 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.715A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.211A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 720 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU C 803 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS C 722 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 976 through 981 removed outlier: 3.901A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 994 through 995 removed outlier: 3.919A pdb=" N GLY C 994 " --> pdb=" O LEU C1043 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 2050 through 2061 removed outlier: 6.870A pdb=" N TYR G2088 " --> pdb=" O LEU G2057 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL G2059 " --> pdb=" O GLN G2086 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN G2086 " --> pdb=" O VAL G2059 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL G2087 " --> pdb=" O LEU G2100 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG G2097 " --> pdb=" O ASP G2157 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL G2159 " --> pdb=" O ARG G2097 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU G2099 " --> pdb=" O VAL G2159 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP G2158 " --> pdb=" O ASN G2151 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN G2151 " --> pdb=" O ASP G2158 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 2066 through 2067 Processing sheet with id=AD1, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AD2, first strand: chain 'D' and resid 398 through 402 removed outlier: 6.207A pdb=" N ILE D 375 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TYR D 401 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE D 377 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE D 345 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU D 378 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL D 347 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA D 421 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N CYS D 422 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN D 459 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE D 424 " --> pdb=" O GLN D 459 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 535 through 540 removed outlier: 6.110A pdb=" N LEU D 594 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE D 568 " --> pdb=" O LEU D 594 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE D 596 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 564 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.715A pdb=" N TYR D 686 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.210A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL D 720 " --> pdb=" O VAL D 801 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU D 803 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS D 722 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 976 through 981 removed outlier: 3.901A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 994 through 995 removed outlier: 3.918A pdb=" N GLY D 994 " --> pdb=" O LEU D1043 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 2050 through 2061 removed outlier: 6.871A pdb=" N TYR H2088 " --> pdb=" O LEU H2057 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL H2059 " --> pdb=" O GLN H2086 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN H2086 " --> pdb=" O VAL H2059 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL H2087 " --> pdb=" O LEU H2100 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG H2097 " --> pdb=" O ASP H2157 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL H2159 " --> pdb=" O ARG H2097 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU H2099 " --> pdb=" O VAL H2159 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP H2158 " --> pdb=" O ASN H2151 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN H2151 " --> pdb=" O ASP H2158 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 2066 through 2067 1624 hydrogen bonds defined for protein. 4620 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: 9.10 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5724 1.30 - 1.43: 10050 1.43 - 1.56: 21312 1.56 - 1.69: 342 1.69 - 1.81: 360 Bond restraints: 37788 Sorted by residual: bond pdb=" C5 CLR A1113 " pdb=" C6 CLR A1113 " ideal model delta sigma weight residual 1.332 1.571 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C5 CLR C1118 " pdb=" C6 CLR C1118 " ideal model delta sigma weight residual 1.332 1.571 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C5 CLR B1118 " pdb=" C6 CLR B1118 " ideal model delta sigma weight residual 1.332 1.571 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C5 CLR D1118 " pdb=" C6 CLR D1118 " ideal model delta sigma weight residual 1.332 1.571 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C5 CLR A1111 " pdb=" C6 CLR A1111 " ideal model delta sigma weight residual 1.332 1.569 -0.237 2.00e-02 2.50e+03 1.40e+02 ... (remaining 37783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 50105 4.10 - 8.20: 767 8.20 - 12.30: 136 12.30 - 16.40: 84 16.40 - 20.50: 40 Bond angle restraints: 51132 Sorted by residual: angle pdb=" O13 POV C1105 " pdb=" P POV C1105 " pdb=" O14 POV C1105 " ideal model delta sigma weight residual 121.11 100.61 20.50 3.00e+00 1.11e-01 4.67e+01 angle pdb=" O13 POV A1122 " pdb=" P POV A1122 " pdb=" O14 POV A1122 " ideal model delta sigma weight residual 121.11 100.61 20.50 3.00e+00 1.11e-01 4.67e+01 angle pdb=" O13 POV D1105 " pdb=" P POV D1105 " pdb=" O14 POV D1105 " ideal model delta sigma weight residual 121.11 100.64 20.47 3.00e+00 1.11e-01 4.66e+01 angle pdb=" O13 POV B1105 " pdb=" P POV B1105 " pdb=" O14 POV B1105 " ideal model delta sigma weight residual 121.11 100.65 20.46 3.00e+00 1.11e-01 4.65e+01 angle pdb=" O13 POV E2301 " pdb=" P POV E2301 " pdb=" O14 POV E2301 " ideal model delta sigma weight residual 121.11 100.70 20.41 3.00e+00 1.11e-01 4.63e+01 ... (remaining 51127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 21352 33.89 - 67.77: 720 67.77 - 101.66: 80 101.66 - 135.54: 16 135.54 - 169.43: 16 Dihedral angle restraints: 22184 sinusoidal: 9360 harmonic: 12824 Sorted by residual: dihedral pdb=" CB CYS G2054 " pdb=" SG CYS G2054 " pdb=" SG CYS G2148 " pdb=" CB CYS G2148 " ideal model delta sinusoidal sigma weight residual -86.00 -158.77 72.77 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS F2054 " pdb=" SG CYS F2054 " pdb=" SG CYS F2148 " pdb=" CB CYS F2148 " ideal model delta sinusoidal sigma weight residual -86.00 -158.73 72.73 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS H2054 " pdb=" SG CYS H2054 " pdb=" SG CYS H2148 " pdb=" CB CYS H2148 " ideal model delta sinusoidal sigma weight residual -86.00 -158.73 72.73 1 1.00e+01 1.00e-02 6.75e+01 ... (remaining 22181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4744 0.069 - 0.138: 855 0.138 - 0.207: 105 0.207 - 0.276: 12 0.276 - 0.345: 40 Chirality restraints: 5756 Sorted by residual: chirality pdb=" C13 CLR B1117 " pdb=" C12 CLR B1117 " pdb=" C14 CLR B1117 " pdb=" C17 CLR B1117 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C13 CLR D1117 " pdb=" C12 CLR D1117 " pdb=" C14 CLR D1117 " pdb=" C17 CLR D1117 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C13 CLR C1117 " pdb=" C12 CLR C1117 " pdb=" C14 CLR C1117 " pdb=" C17 CLR C1117 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 5753 not shown) Planarity restraints: 6204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B1111 " 0.154 2.00e-02 2.50e+03 3.41e-01 1.16e+03 pdb=" C29 POV B1111 " -0.452 2.00e-02 2.50e+03 pdb="C210 POV B1111 " 0.459 2.00e-02 2.50e+03 pdb="C211 POV B1111 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D1111 " -0.154 2.00e-02 2.50e+03 3.41e-01 1.16e+03 pdb=" C29 POV D1111 " 0.452 2.00e-02 2.50e+03 pdb="C210 POV D1111 " -0.459 2.00e-02 2.50e+03 pdb="C211 POV D1111 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C1111 " -0.153 2.00e-02 2.50e+03 3.41e-01 1.16e+03 pdb=" C29 POV C1111 " 0.452 2.00e-02 2.50e+03 pdb="C210 POV C1111 " -0.459 2.00e-02 2.50e+03 pdb="C211 POV C1111 " 0.160 2.00e-02 2.50e+03 ... (remaining 6201 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.83: 11986 2.83 - 3.41: 38111 3.41 - 3.99: 68345 3.99 - 4.56: 97381 4.56 - 5.14: 143826 Nonbonded interactions: 359649 Sorted by model distance: nonbonded pdb=" O ARG A 938 " pdb=" OG1 THR A 942 " model vdw 2.257 3.040 nonbonded pdb=" O ARG D 938 " pdb=" OG1 THR D 942 " model vdw 2.257 3.040 nonbonded pdb=" O ARG B 938 " pdb=" OG1 THR B 942 " model vdw 2.257 3.040 nonbonded pdb=" O ARG C 938 " pdb=" OG1 THR C 942 " model vdw 2.258 3.040 nonbonded pdb=" OE2 GLU B 399 " pdb="MG MG B1106 " model vdw 2.277 2.170 ... (remaining 359644 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 16 through 1056 or (resid 1104 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or resid 1105 or (resid 1109 and (n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38)))) selection = (chain 'B' and (resid 16 through 1056 or (resid 1104 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or (resid 1105 and (name C31 or nam \ e C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name O31 or name O32 or name C310 or name C311)) or (resid 1109 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38)))) selection = (chain 'C' and (resid 16 through 1056 or (resid 1104 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or (resid 1105 and (name C31 or nam \ e C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name O31 or name O32 or name C310 or name C311)) or (resid 1109 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38)))) selection = (chain 'D' and (resid 16 through 1056 or (resid 1104 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or (resid 1105 and (name C31 or nam \ e C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name O31 or name O32 or name C310 or name C311)) or (resid 1109 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 40.840 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 : 0.014 0.239 37828 Z= 0.673 Angle : 1.410 20.498 51188 Z= 0.576 Chirality : 0.060 0.345 5756 Planarity : 0.019 0.341 6196 Dihedral : 17.768 169.427 13824 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.21 % Allowed : 8.01 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.10), residues: 4332 helix: -2.75 (0.07), residues: 2148 sheet: -1.61 (0.22), residues: 516 loop : -2.08 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 786 TYR 0.015 0.002 TYR D 48 PHE 0.023 0.002 PHE G2070 TRP 0.016 0.002 TRP C 767 HIS 0.006 0.001 HIS C 771 Details of bonding type rmsd/Z covalent geometry : bond 0.01397 / 0.67 (37788) covalent geometry : angle 1.41021 / 0.58 (51132) SS BOND : bond 0.00507 / 0.34 ( 16) SS BOND : angle 0.65201 / 0.40 ( 32) hydrogen bonds : bond 0.19065 / 12.20 ( 1624) hydrogen bonds : angle 7.39501 / 5.17 ( 4620) Misc. bond : bond 0.00569 / 0.49 ( 16) link_NAG-ASN : bond 0.00584 / 0.38 ( 8) link_NAG-ASN : angle 2.11078 / 1.37 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 345 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8250 (mt-10) REVERT: A 691 MET cc_start: 0.9120 (mmt) cc_final: 0.8858 (mmt) REVERT: A 1053 MET cc_start: 0.8385 (mtp) cc_final: 0.8182 (mtm) REVERT: E 2015 ASP cc_start: 0.8586 (t0) cc_final: 0.8356 (t0) REVERT: E 2112 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8846 (ttmt) REVERT: E 2163 ARG cc_start: 0.7802 (mtt-85) cc_final: 0.7435 (mtt-85) REVERT: E 2168 ILE cc_start: 0.9261 (tt) cc_final: 0.8945 (tt) REVERT: B 691 MET cc_start: 0.9133 (mmt) cc_final: 0.8870 (mmt) REVERT: B 1053 MET cc_start: 0.8352 (mtp) cc_final: 0.8142 (mtm) REVERT: F 2015 ASP cc_start: 0.8582 (t0) cc_final: 0.8377 (t0) REVERT: F 2019 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7829 (mtt90) REVERT: F 2112 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8845 (ttmt) REVERT: F 2163 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7419 (mtt-85) REVERT: F 2166 ASP cc_start: 0.7935 (t0) cc_final: 0.7710 (t0) REVERT: F 2168 ILE cc_start: 0.9257 (tt) cc_final: 0.8925 (tt) REVERT: C 691 MET cc_start: 0.9110 (mmt) cc_final: 0.8839 (mmt) REVERT: C 1053 MET cc_start: 0.8339 (mtp) cc_final: 0.8137 (mtm) REVERT: G 2019 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7820 (mtt90) REVERT: G 2112 LYS cc_start: 0.9109 (mtmt) cc_final: 0.8851 (ttmt) REVERT: G 2163 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7441 (mtt-85) REVERT: G 2168 ILE cc_start: 0.9248 (tt) cc_final: 0.8925 (tt) REVERT: D 691 MET cc_start: 0.9134 (mmt) cc_final: 0.8873 (mmt) REVERT: D 1053 MET cc_start: 0.8365 (mtp) cc_final: 0.8147 (mtm) REVERT: H 2015 ASP cc_start: 0.8592 (t0) cc_final: 0.8386 (t0) REVERT: H 2019 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7832 (mtt90) REVERT: H 2112 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8844 (ttmt) REVERT: H 2163 ARG cc_start: 0.7798 (mtt-85) cc_final: 0.7416 (mtt-85) REVERT: H 2166 ASP cc_start: 0.7936 (t0) cc_final: 0.7711 (t0) REVERT: H 2168 ILE cc_start: 0.9256 (tt) cc_final: 0.8924 (tt) outliers start: 8 outliers final: 0 residues processed: 353 average time/residue: 0.2942 time to fit residues: 160.0121 Evaluate side-chains 246 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 GLN A 143 ASN A 200 ASN A 407 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN A 534 ASN A 793 ASN A 884 ASN E2144 GLN B 142 GLN B 143 ASN B 200 ASN B 407 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN B 534 ASN B 793 ASN B 884 ASN B1054 GLN F2144 GLN C 142 GLN C 143 ASN C 200 ASN C 407 ASN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN C 534 ASN C 793 ASN C 884 ASN C1054 GLN G2144 GLN D 142 GLN D 143 ASN D 200 ASN D 407 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN D 534 ASN D 793 ASN D 884 ASN D1054 GLN H2144 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.090750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.067340 restraints weight = 87358.873| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.71 r_work: 0.2816 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37828 Z= 0.124 Angle : 0.519 9.689 51188 Z= 0.269 Chirality : 0.040 0.163 5756 Planarity : 0.004 0.044 6196 Dihedral : 15.578 135.267 5772 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.16 % Allowed : 9.94 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.12), residues: 4332 helix: -0.32 (0.10), residues: 2144 sheet: -1.07 (0.23), residues: 524 loop : -1.54 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 974 TYR 0.012 0.001 TYR C 48 PHE 0.017 0.001 PHE B 120 TRP 0.014 0.001 TRP C 263 HIS 0.003 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (37788) covalent geometry : angle 0.51812 / 0.27 (51132) SS BOND : bond 0.00295 / 0.19 ( 16) SS BOND : angle 0.77191 / 0.50 ( 32) hydrogen bonds : bond 0.04826 / 3.17 ( 1624) hydrogen bonds : angle 4.61225 / 3.21 ( 4620) Misc. bond : bond 0.00231 / 0.14 ( 16) link_NAG-ASN : bond 0.00505 / 0.32 ( 8) link_NAG-ASN : angle 1.62317 / 1.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 286 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2015 ASP cc_start: 0.8923 (t0) cc_final: 0.8657 (t0) REVERT: E 2019 ARG cc_start: 0.8583 (mtt-85) cc_final: 0.8001 (mtt90) REVERT: E 2157 ASP cc_start: 0.8558 (m-30) cc_final: 0.8256 (p0) REVERT: E 2163 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7576 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8319 (t0) cc_final: 0.7976 (t0) REVERT: E 2168 ILE cc_start: 0.9218 (tt) cc_final: 0.8954 (tt) REVERT: B 799 MET cc_start: 0.9359 (tpp) cc_final: 0.9139 (tpp) REVERT: F 2015 ASP cc_start: 0.8938 (t0) cc_final: 0.8660 (t0) REVERT: F 2019 ARG cc_start: 0.8586 (mtt-85) cc_final: 0.8000 (mtt90) REVERT: F 2112 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8760 (ttmt) REVERT: F 2157 ASP cc_start: 0.8556 (m-30) cc_final: 0.8249 (p0) REVERT: F 2163 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7587 (mtt-85) REVERT: C 799 MET cc_start: 0.9358 (tpp) cc_final: 0.9135 (tpp) REVERT: G 2015 ASP cc_start: 0.8923 (t0) cc_final: 0.8715 (t0) REVERT: G 2019 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.7924 (mtt90) REVERT: G 2157 ASP cc_start: 0.8539 (m-30) cc_final: 0.8233 (p0) REVERT: G 2163 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7578 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8326 (t0) cc_final: 0.7982 (t0) REVERT: G 2168 ILE cc_start: 0.9206 (tt) cc_final: 0.8948 (tt) REVERT: D 799 MET cc_start: 0.9362 (tpp) cc_final: 0.9145 (tpp) REVERT: H 2015 ASP cc_start: 0.8942 (t0) cc_final: 0.8663 (t0) REVERT: H 2019 ARG cc_start: 0.8575 (mtt-85) cc_final: 0.7991 (mtt90) REVERT: H 2112 LYS cc_start: 0.9057 (mtmt) cc_final: 0.8755 (ttmt) REVERT: H 2157 ASP cc_start: 0.8564 (m-30) cc_final: 0.8258 (p0) REVERT: H 2163 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7603 (mtt-85) outliers start: 45 outliers final: 16 residues processed: 318 average time/residue: 0.2388 time to fit residues: 125.7920 Evaluate side-chains 277 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 261 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 239 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 350 optimal weight: 0.6980 chunk 338 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 357 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 402 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 887 ASN C 465 ASN C 887 ASN D 465 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.091793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068355 restraints weight = 87732.436| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.70 r_work: 0.2843 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 37828 Z= 0.104 Angle : 0.463 8.104 51188 Z= 0.240 Chirality : 0.039 0.164 5756 Planarity : 0.003 0.036 6196 Dihedral : 13.997 115.528 5772 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.39 % Allowed : 11.23 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 4332 helix: 0.76 (0.11), residues: 2116 sheet: -0.80 (0.23), residues: 524 loop : -1.01 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 765 TYR 0.011 0.001 TYR C 48 PHE 0.014 0.001 PHE C 120 TRP 0.012 0.001 TRP E2176 HIS 0.004 0.001 HIS F2165 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (37788) covalent geometry : angle 0.46172 / 0.24 (51132) SS BOND : bond 0.00231 / 0.15 ( 16) SS BOND : angle 0.51971 / 0.33 ( 32) hydrogen bonds : bond 0.04159 / 2.73 ( 1624) hydrogen bonds : angle 4.18949 / 2.92 ( 4620) Misc. bond : bond 0.00162 / 0.12 ( 16) link_NAG-ASN : bond 0.00438 / 0.28 ( 8) link_NAG-ASN : angle 1.44852 / 0.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 1.444 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: A 234 LYS cc_start: 0.8925 (tttt) cc_final: 0.8721 (ttmt) REVERT: A 257 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8691 (mm-30) REVERT: A 314 MET cc_start: 0.9394 (tmm) cc_final: 0.9140 (ttp) REVERT: E 2015 ASP cc_start: 0.8936 (t0) cc_final: 0.8621 (t0) REVERT: E 2019 ARG cc_start: 0.8508 (mtt-85) cc_final: 0.7950 (mtt90) REVERT: E 2155 ARG cc_start: 0.8661 (mtm110) cc_final: 0.8342 (mpp80) REVERT: E 2157 ASP cc_start: 0.8563 (m-30) cc_final: 0.8358 (p0) REVERT: E 2163 ARG cc_start: 0.7956 (mtt-85) cc_final: 0.7569 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8443 (t0) cc_final: 0.8134 (t0) REVERT: E 2168 ILE cc_start: 0.9225 (tt) cc_final: 0.8931 (tt) REVERT: B 234 LYS cc_start: 0.8917 (tttt) cc_final: 0.8711 (ttmt) REVERT: B 314 MET cc_start: 0.9404 (tmm) cc_final: 0.9141 (ttp) REVERT: F 2015 ASP cc_start: 0.8932 (t0) cc_final: 0.8631 (t0) REVERT: F 2019 ARG cc_start: 0.8483 (mtt-85) cc_final: 0.7923 (mtt90) REVERT: F 2112 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8755 (ttmt) REVERT: F 2155 ARG cc_start: 0.8672 (mtm110) cc_final: 0.8346 (mpp80) REVERT: F 2163 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.7583 (mtt-85) REVERT: C 234 LYS cc_start: 0.8926 (tttt) cc_final: 0.8717 (ttmt) REVERT: C 314 MET cc_start: 0.9396 (tmm) cc_final: 0.9133 (ttp) REVERT: G 2015 ASP cc_start: 0.8912 (t0) cc_final: 0.8669 (t0) REVERT: G 2019 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.7890 (mtt90) REVERT: G 2157 ASP cc_start: 0.8632 (m-30) cc_final: 0.8422 (p0) REVERT: G 2163 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7505 (mtt-85) REVERT: D 234 LYS cc_start: 0.8929 (tttt) cc_final: 0.8724 (ttmt) REVERT: D 314 MET cc_start: 0.9408 (tmm) cc_final: 0.9149 (ttp) REVERT: H 2015 ASP cc_start: 0.8928 (t0) cc_final: 0.8624 (t0) REVERT: H 2019 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.7914 (mtt90) REVERT: H 2112 LYS cc_start: 0.9021 (mtmt) cc_final: 0.8755 (ttmt) REVERT: H 2155 ARG cc_start: 0.8675 (mtm110) cc_final: 0.8350 (mpp80) REVERT: H 2163 ARG cc_start: 0.7971 (mtt-85) cc_final: 0.7598 (mtt-85) outliers start: 54 outliers final: 38 residues processed: 321 average time/residue: 0.2474 time to fit residues: 128.7734 Evaluate side-chains 289 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 62 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 294 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 393 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 377 optimal weight: 7.9990 chunk 341 optimal weight: 0.9990 chunk 413 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 HIS A1054 GLN E2091 ASN B 254 HIS C 254 HIS D 254 HIS H2091 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.064887 restraints weight = 87035.519| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.62 r_work: 0.2758 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 37828 Z= 0.244 Angle : 0.566 6.253 51188 Z= 0.293 Chirality : 0.043 0.162 5756 Planarity : 0.004 0.034 6196 Dihedral : 14.352 110.473 5772 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.96 % Allowed : 12.45 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 4332 helix: 0.87 (0.11), residues: 2156 sheet: -0.96 (0.23), residues: 540 loop : -0.81 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 368 TYR 0.016 0.001 TYR D 928 PHE 0.020 0.002 PHE A 120 TRP 0.018 0.002 TRP A 263 HIS 0.004 0.001 HIS A 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 (37788) covalent geometry : angle 0.56541 / 0.29 (51132) SS BOND : bond 0.00351 / 0.22 ( 16) SS BOND : angle 0.59036 / 0.39 ( 32) hydrogen bonds : bond 0.04978 / 3.27 ( 1624) hydrogen bonds : angle 4.43124 / 3.10 ( 4620) Misc. bond : bond 0.00215 / 0.15 ( 16) link_NAG-ASN : bond 0.00518 / 0.33 ( 8) link_NAG-ASN : angle 1.49620 / 0.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 249 time to evaluate : 1.458 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: A 513 MET cc_start: 0.9159 (mmm) cc_final: 0.8957 (mmm) REVERT: A 799 MET cc_start: 0.9293 (tpp) cc_final: 0.9017 (tpp) REVERT: E 2015 ASP cc_start: 0.8994 (t0) cc_final: 0.8663 (t0) REVERT: E 2019 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.7938 (mtt90) REVERT: E 2138 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8393 (mtpt) REVERT: E 2155 ARG cc_start: 0.8685 (mtm110) cc_final: 0.8363 (mpp80) REVERT: E 2157 ASP cc_start: 0.8569 (m-30) cc_final: 0.8345 (p0) REVERT: E 2163 ARG cc_start: 0.8000 (mtt-85) cc_final: 0.7609 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8307 (t0) cc_final: 0.7973 (t0) REVERT: E 2168 ILE cc_start: 0.9261 (tt) cc_final: 0.8938 (tt) REVERT: B 513 MET cc_start: 0.9144 (mmm) cc_final: 0.8938 (mmm) REVERT: F 2015 ASP cc_start: 0.8995 (t0) cc_final: 0.8664 (t0) REVERT: F 2019 ARG cc_start: 0.8539 (mtt-85) cc_final: 0.7949 (mtt90) REVERT: F 2138 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8392 (mtpt) REVERT: F 2155 ARG cc_start: 0.8664 (mtm110) cc_final: 0.8384 (mpp80) REVERT: F 2163 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7607 (mtt-85) REVERT: F 2166 ASP cc_start: 0.8613 (t0) cc_final: 0.8328 (t0) REVERT: F 2168 ILE cc_start: 0.9232 (tt) cc_final: 0.8976 (tt) REVERT: C 513 MET cc_start: 0.9142 (mmm) cc_final: 0.8939 (mmm) REVERT: G 2015 ASP cc_start: 0.8975 (t0) cc_final: 0.8735 (t0) REVERT: G 2019 ARG cc_start: 0.8489 (mtt-85) cc_final: 0.7898 (mtt90) REVERT: G 2138 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8363 (mtpt) REVERT: G 2163 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7600 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8553 (t0) cc_final: 0.8212 (t0) REVERT: G 2168 ILE cc_start: 0.9205 (tt) cc_final: 0.8927 (tt) REVERT: D 513 MET cc_start: 0.9155 (mmm) cc_final: 0.8949 (mmm) REVERT: H 2015 ASP cc_start: 0.9002 (t0) cc_final: 0.8676 (t0) REVERT: H 2019 ARG cc_start: 0.8528 (mtt-85) cc_final: 0.7935 (mtt90) REVERT: H 2138 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8394 (mtpt) REVERT: H 2155 ARG cc_start: 0.8668 (mtm110) cc_final: 0.8384 (mpp80) REVERT: H 2163 ARG cc_start: 0.7998 (mtt-85) cc_final: 0.7607 (mtt-85) REVERT: H 2166 ASP cc_start: 0.8610 (t0) cc_final: 0.8329 (t0) REVERT: H 2168 ILE cc_start: 0.9234 (tt) cc_final: 0.8977 (tt) outliers start: 76 outliers final: 51 residues processed: 309 average time/residue: 0.2465 time to fit residues: 125.1437 Evaluate side-chains 291 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2041 SER Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2041 SER Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain F residue 2157 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2041 SER Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2041 SER Chi-restraints excluded: chain H residue 2146 PHE Chi-restraints excluded: chain H residue 2157 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 236 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 358 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 400 optimal weight: 0.9980 chunk 74 optimal weight: 0.0170 chunk 119 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 330 optimal weight: 2.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 887 ASN A 957 ASN A1008 ASN E2091 ASN E2165 HIS B 957 ASN B1008 ASN C 957 ASN C1008 ASN D 887 ASN D 957 ASN D1008 ASN H2091 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.091230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.067758 restraints weight = 87386.780| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.71 r_work: 0.2827 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 37828 Z= 0.101 Angle : 0.461 7.254 51188 Z= 0.237 Chirality : 0.040 0.164 5756 Planarity : 0.003 0.032 6196 Dihedral : 13.299 97.890 5772 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.12 % Allowed : 12.76 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4332 helix: 1.32 (0.11), residues: 2132 sheet: -0.80 (0.23), residues: 532 loop : -0.60 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 765 TYR 0.011 0.001 TYR B 928 PHE 0.014 0.001 PHE C 120 TRP 0.013 0.001 TRP G2176 HIS 0.003 0.001 HIS C 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (37788) covalent geometry : angle 0.45987 / 0.24 (51132) SS BOND : bond 0.00161 / 0.10 ( 16) SS BOND : angle 0.40904 / 0.27 ( 32) hydrogen bonds : bond 0.04015 / 2.64 ( 1624) hydrogen bonds : angle 4.00763 / 2.79 ( 4620) Misc. bond : bond 0.00112 / 0.08 ( 16) link_NAG-ASN : bond 0.00446 / 0.28 ( 8) link_NAG-ASN : angle 1.39334 / 0.91 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 288 time to evaluate : 1.480 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: A 148 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7080 (t80) REVERT: A 234 LYS cc_start: 0.8949 (tttt) cc_final: 0.8734 (ttmt) REVERT: E 2015 ASP cc_start: 0.8921 (t0) cc_final: 0.8614 (t0) REVERT: E 2019 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8013 (mtt90) REVERT: E 2131 MET cc_start: 0.8634 (mmm) cc_final: 0.8143 (mmm) REVERT: E 2138 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8459 (mtpt) REVERT: E 2155 ARG cc_start: 0.8650 (mtm110) cc_final: 0.8379 (mpp80) REVERT: E 2163 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7594 (mtt-85) REVERT: B 234 LYS cc_start: 0.8941 (tttt) cc_final: 0.8729 (ttmt) REVERT: B 370 ASP cc_start: 0.7595 (m-30) cc_final: 0.7158 (t0) REVERT: F 2015 ASP cc_start: 0.8921 (t0) cc_final: 0.8611 (t0) REVERT: F 2019 ARG cc_start: 0.8538 (mtt-85) cc_final: 0.7980 (mtt90) REVERT: F 2131 MET cc_start: 0.8655 (mmm) cc_final: 0.8169 (mmm) REVERT: F 2138 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8456 (mtpt) REVERT: F 2155 ARG cc_start: 0.8648 (mtm110) cc_final: 0.8425 (mpp80) REVERT: F 2163 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7588 (mtt-85) REVERT: F 2166 ASP cc_start: 0.8602 (t0) cc_final: 0.8319 (t0) REVERT: F 2168 ILE cc_start: 0.9216 (tt) cc_final: 0.8912 (tt) REVERT: C 234 LYS cc_start: 0.8946 (tttt) cc_final: 0.8730 (ttmt) REVERT: G 2015 ASP cc_start: 0.8961 (t0) cc_final: 0.8703 (t0) REVERT: G 2019 ARG cc_start: 0.8483 (mtt-85) cc_final: 0.7897 (mtt90) REVERT: G 2131 MET cc_start: 0.8622 (mmm) cc_final: 0.8130 (mmm) REVERT: G 2138 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8477 (mtpt) REVERT: G 2163 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7568 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8519 (t0) cc_final: 0.8178 (t0) REVERT: G 2168 ILE cc_start: 0.9197 (tt) cc_final: 0.8898 (tt) REVERT: D 148 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7120 (t80) REVERT: D 234 LYS cc_start: 0.8954 (tttt) cc_final: 0.8737 (ttmt) REVERT: D 370 ASP cc_start: 0.7611 (m-30) cc_final: 0.7164 (t0) REVERT: H 2015 ASP cc_start: 0.8930 (t0) cc_final: 0.8625 (t0) REVERT: H 2019 ARG cc_start: 0.8523 (mtt-85) cc_final: 0.7963 (mtt90) REVERT: H 2131 MET cc_start: 0.8661 (mmm) cc_final: 0.8178 (mmm) REVERT: H 2138 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8459 (mtpt) REVERT: H 2155 ARG cc_start: 0.8646 (mtm110) cc_final: 0.8421 (mpp80) REVERT: H 2163 ARG cc_start: 0.7956 (mtt-85) cc_final: 0.7591 (mtt-85) REVERT: H 2166 ASP cc_start: 0.8600 (t0) cc_final: 0.8320 (t0) REVERT: H 2168 ILE cc_start: 0.9221 (tt) cc_final: 0.8917 (tt) outliers start: 82 outliers final: 52 residues processed: 349 average time/residue: 0.2459 time to fit residues: 141.1935 Evaluate side-chains 318 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 264 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 987 PHE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2008 TYR Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain G residue 2157 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 987 PHE Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 419 optimal weight: 6.9990 chunk 182 optimal weight: 0.1980 chunk 176 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 227 optimal weight: 0.5980 chunk 34 optimal weight: 0.0070 chunk 361 optimal weight: 0.9990 chunk 366 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 358 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 ASN B 957 ASN C 957 ASN D 957 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.091957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.068704 restraints weight = 86753.175| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.74 r_work: 0.2842 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 37828 Z= 0.095 Angle : 0.452 7.570 51188 Z= 0.235 Chirality : 0.040 0.235 5756 Planarity : 0.003 0.032 6196 Dihedral : 12.597 89.900 5772 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.17 % Allowed : 12.91 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.13), residues: 4332 helix: 1.48 (0.11), residues: 2164 sheet: -0.59 (0.24), residues: 524 loop : -0.51 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H2077 TYR 0.010 0.001 TYR A 928 PHE 0.012 0.001 PHE A 120 TRP 0.010 0.001 TRP G2176 HIS 0.003 0.000 HIS C 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (37788) covalent geometry : angle 0.45140 / 0.23 (51132) SS BOND : bond 0.00148 / 0.09 ( 16) SS BOND : angle 0.39369 / 0.25 ( 32) hydrogen bonds : bond 0.03761 / 2.46 ( 1624) hydrogen bonds : angle 3.84592 / 2.69 ( 4620) Misc. bond : bond 0.00206 / 0.15 ( 16) link_NAG-ASN : bond 0.00441 / 0.28 ( 8) link_NAG-ASN : angle 1.36329 / 0.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 294 time to evaluate : 1.460 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: A 513 MET cc_start: 0.8657 (mmm) cc_final: 0.8127 (mmm) REVERT: E 2015 ASP cc_start: 0.8905 (t0) cc_final: 0.8598 (t0) REVERT: E 2019 ARG cc_start: 0.8452 (mtt-85) cc_final: 0.7915 (mtt90) REVERT: E 2131 MET cc_start: 0.8641 (mmm) cc_final: 0.8139 (mmm) REVERT: E 2138 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8591 (mtpt) REVERT: E 2163 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7599 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8561 (t0) cc_final: 0.8234 (t0) REVERT: E 2168 ILE cc_start: 0.9149 (tt) cc_final: 0.8894 (tt) REVERT: B 513 MET cc_start: 0.8671 (mmm) cc_final: 0.8114 (mmm) REVERT: B 976 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7461 (ttp80) REVERT: F 2015 ASP cc_start: 0.8919 (t0) cc_final: 0.8617 (t0) REVERT: F 2019 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.7927 (mtt90) REVERT: F 2131 MET cc_start: 0.8655 (mmm) cc_final: 0.8151 (mmm) REVERT: F 2138 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8598 (mtpt) REVERT: F 2163 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7618 (mtt-85) REVERT: F 2200 LYS cc_start: 0.7775 (mttt) cc_final: 0.7530 (mttp) REVERT: C 513 MET cc_start: 0.8642 (mmm) cc_final: 0.8112 (mmm) REVERT: C 976 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7460 (ttp80) REVERT: G 2015 ASP cc_start: 0.8909 (t0) cc_final: 0.8655 (t0) REVERT: G 2019 ARG cc_start: 0.8424 (mtt-85) cc_final: 0.7884 (mtt90) REVERT: G 2131 MET cc_start: 0.8639 (mmm) cc_final: 0.8137 (mmm) REVERT: G 2138 LYS cc_start: 0.8852 (mmmt) cc_final: 0.8597 (mtpt) REVERT: G 2163 ARG cc_start: 0.7962 (mtt-85) cc_final: 0.7569 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8511 (t0) cc_final: 0.8290 (t0) REVERT: G 2200 LYS cc_start: 0.7843 (mttt) cc_final: 0.7635 (mttm) REVERT: D 513 MET cc_start: 0.8666 (mmm) cc_final: 0.8112 (mmm) REVERT: D 976 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7462 (ttp80) REVERT: H 2015 ASP cc_start: 0.8919 (t0) cc_final: 0.8616 (t0) REVERT: H 2019 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.7931 (mtt90) REVERT: H 2131 MET cc_start: 0.8636 (mmm) cc_final: 0.8134 (mmm) REVERT: H 2138 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8598 (mtpt) REVERT: H 2163 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7606 (mtt-85) REVERT: H 2200 LYS cc_start: 0.7774 (mttt) cc_final: 0.7532 (mttp) outliers start: 84 outliers final: 68 residues processed: 350 average time/residue: 0.2443 time to fit residues: 138.9501 Evaluate side-chains 333 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 262 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 987 PHE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 987 PHE Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2008 TYR Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 987 PHE Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 301 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 339 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 391 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 396 optimal weight: 0.2980 chunk 431 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 ASN B 957 ASN C 957 ASN D 957 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.067717 restraints weight = 86742.141| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.74 r_work: 0.2819 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37828 Z= 0.112 Angle : 0.456 6.363 51188 Z= 0.237 Chirality : 0.040 0.187 5756 Planarity : 0.003 0.032 6196 Dihedral : 12.459 89.412 5772 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.99 % Allowed : 13.84 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.13), residues: 4332 helix: 1.57 (0.11), residues: 2164 sheet: -0.60 (0.24), residues: 532 loop : -0.37 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H2077 TYR 0.011 0.001 TYR E2008 PHE 0.013 0.001 PHE B 120 TRP 0.010 0.001 TRP G2176 HIS 0.003 0.000 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (37788) covalent geometry : angle 0.45497 / 0.24 (51132) SS BOND : bond 0.00190 / 0.12 ( 16) SS BOND : angle 0.35388 / 0.23 ( 32) hydrogen bonds : bond 0.03894 / 2.56 ( 1624) hydrogen bonds : angle 3.87324 / 2.71 ( 4620) Misc. bond : bond 0.00188 / 0.14 ( 16) link_NAG-ASN : bond 0.00452 / 0.29 ( 8) link_NAG-ASN : angle 1.34751 / 0.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 261 time to evaluate : 1.489 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: E 2015 ASP cc_start: 0.8913 (t0) cc_final: 0.8607 (t0) REVERT: E 2019 ARG cc_start: 0.8449 (mtt-85) cc_final: 0.7933 (mtt90) REVERT: E 2163 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.7584 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8574 (t0) cc_final: 0.8236 (t0) REVERT: E 2168 ILE cc_start: 0.9183 (tt) cc_final: 0.8885 (tt) REVERT: F 2015 ASP cc_start: 0.8907 (t0) cc_final: 0.8604 (t0) REVERT: F 2019 ARG cc_start: 0.8444 (mtt-85) cc_final: 0.7931 (mtt90) REVERT: F 2163 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.7585 (mtt-85) REVERT: F 2168 ILE cc_start: 0.9147 (tt) cc_final: 0.8927 (tt) REVERT: F 2200 LYS cc_start: 0.7880 (mttt) cc_final: 0.7628 (mttp) REVERT: G 2015 ASP cc_start: 0.8853 (t0) cc_final: 0.8603 (t0) REVERT: G 2019 ARG cc_start: 0.8407 (mtt-85) cc_final: 0.7883 (mtt90) REVERT: G 2155 ARG cc_start: 0.8770 (mpp80) cc_final: 0.7838 (mpt-90) REVERT: G 2163 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.7486 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8490 (t0) cc_final: 0.8167 (t0) REVERT: G 2168 ILE cc_start: 0.9221 (tt) cc_final: 0.8902 (tt) REVERT: G 2200 LYS cc_start: 0.7856 (mttt) cc_final: 0.7641 (mttm) REVERT: H 2015 ASP cc_start: 0.8908 (t0) cc_final: 0.8603 (t0) REVERT: H 2019 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.7940 (mtt90) REVERT: H 2163 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.7585 (mtt-85) REVERT: H 2168 ILE cc_start: 0.9144 (tt) cc_final: 0.8925 (tt) REVERT: H 2200 LYS cc_start: 0.7878 (mttt) cc_final: 0.7627 (mttp) outliers start: 77 outliers final: 70 residues processed: 316 average time/residue: 0.2521 time to fit residues: 129.7732 Evaluate side-chains 326 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 256 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 987 PHE Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2008 TYR Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 217 optimal weight: 0.5980 chunk 210 optimal weight: 0.7980 chunk 427 optimal weight: 0.2980 chunk 83 optimal weight: 9.9990 chunk 357 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 428 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 ASN C 957 ASN D 957 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.068351 restraints weight = 86509.841| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.74 r_work: 0.2832 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 37828 Z= 0.100 Angle : 0.446 6.036 51188 Z= 0.232 Chirality : 0.039 0.176 5756 Planarity : 0.003 0.032 6196 Dihedral : 12.131 89.917 5772 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.01 % Allowed : 14.10 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4332 helix: 1.73 (0.11), residues: 2136 sheet: -0.54 (0.24), residues: 520 loop : -0.22 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H2077 TYR 0.010 0.001 TYR B 928 PHE 0.012 0.001 PHE C 120 TRP 0.010 0.001 TRP G2176 HIS 0.003 0.000 HIS C 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (37788) covalent geometry : angle 0.44569 / 0.23 (51132) SS BOND : bond 0.00169 / 0.11 ( 16) SS BOND : angle 0.32399 / 0.21 ( 32) hydrogen bonds : bond 0.03779 / 2.48 ( 1624) hydrogen bonds : angle 3.80692 / 2.66 ( 4620) Misc. bond : bond 0.00161 / 0.12 ( 16) link_NAG-ASN : bond 0.00443 / 0.28 ( 8) link_NAG-ASN : angle 1.33158 / 0.87 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 276 time to evaluate : 1.942 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: E 2015 ASP cc_start: 0.8880 (t0) cc_final: 0.8560 (t0) REVERT: E 2019 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.7858 (mtt90) REVERT: E 2131 MET cc_start: 0.8652 (mmt) cc_final: 0.8413 (mmm) REVERT: E 2163 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7561 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8597 (t0) cc_final: 0.8276 (t0) REVERT: E 2168 ILE cc_start: 0.9185 (tt) cc_final: 0.8873 (tt) REVERT: F 2015 ASP cc_start: 0.8875 (t0) cc_final: 0.8556 (t0) REVERT: F 2019 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.7938 (mtt90) REVERT: F 2131 MET cc_start: 0.8658 (mmt) cc_final: 0.8421 (mmm) REVERT: F 2163 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7562 (mtt-85) REVERT: F 2200 LYS cc_start: 0.7871 (mttt) cc_final: 0.7561 (mttm) REVERT: C 48 TYR cc_start: 0.8418 (m-10) cc_final: 0.8201 (m-10) REVERT: C 818 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8847 (ttmt) REVERT: G 2015 ASP cc_start: 0.8847 (t0) cc_final: 0.8497 (t0) REVERT: G 2019 ARG cc_start: 0.8410 (mtt-85) cc_final: 0.7874 (mtt90) REVERT: G 2131 MET cc_start: 0.8649 (mmt) cc_final: 0.8410 (mmm) REVERT: G 2153 HIS cc_start: 0.8022 (t-90) cc_final: 0.7690 (t-90) REVERT: G 2155 ARG cc_start: 0.8807 (mpp80) cc_final: 0.8120 (mpt-90) REVERT: G 2163 ARG cc_start: 0.7965 (mtt-85) cc_final: 0.7574 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8425 (t0) cc_final: 0.8209 (t0) REVERT: G 2200 LYS cc_start: 0.7780 (mttt) cc_final: 0.7527 (mttp) REVERT: H 2015 ASP cc_start: 0.8875 (t0) cc_final: 0.8556 (t0) REVERT: H 2019 ARG cc_start: 0.8468 (mtt-85) cc_final: 0.7946 (mtt90) REVERT: H 2131 MET cc_start: 0.8648 (mmt) cc_final: 0.8412 (mmm) REVERT: H 2163 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7564 (mtt-85) REVERT: H 2200 LYS cc_start: 0.7870 (mttt) cc_final: 0.7560 (mttm) outliers start: 78 outliers final: 69 residues processed: 331 average time/residue: 0.2564 time to fit residues: 138.0879 Evaluate side-chains 335 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 265 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2008 TYR Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 987 PHE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 818 LYS Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 987 PHE Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2008 TYR Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 987 PHE Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 419 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 418 optimal weight: 7.9990 chunk 400 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 335 optimal weight: 0.9990 chunk 326 optimal weight: 2.9990 chunk 317 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 ASN B 957 ASN C 957 ASN D 957 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.067101 restraints weight = 86614.780| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.73 r_work: 0.2801 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37828 Z= 0.133 Angle : 0.480 11.904 51188 Z= 0.246 Chirality : 0.040 0.169 5756 Planarity : 0.003 0.032 6196 Dihedral : 12.180 89.685 5772 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.12 % Allowed : 14.20 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.14), residues: 4332 helix: 1.59 (0.11), residues: 2168 sheet: -0.57 (0.24), residues: 520 loop : -0.21 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H2077 TYR 0.012 0.001 TYR B 928 PHE 0.014 0.001 PHE B 120 TRP 0.011 0.001 TRP H2039 HIS 0.003 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (37788) covalent geometry : angle 0.47907 / 0.25 (51132) SS BOND : bond 0.00214 / 0.14 ( 16) SS BOND : angle 0.33447 / 0.22 ( 32) hydrogen bonds : bond 0.04028 / 2.65 ( 1624) hydrogen bonds : angle 3.92671 / 2.74 ( 4620) Misc. bond : bond 0.00181 / 0.13 ( 16) link_NAG-ASN : bond 0.00441 / 0.28 ( 8) link_NAG-ASN : angle 1.32348 / 0.86 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 271 time to evaluate : 1.689 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: E 2015 ASP cc_start: 0.8887 (t0) cc_final: 0.8585 (t0) REVERT: E 2019 ARG cc_start: 0.8404 (mtt-85) cc_final: 0.7856 (mtt90) REVERT: E 2077 ARG cc_start: 0.7464 (mmp80) cc_final: 0.7226 (mmp80) REVERT: E 2131 MET cc_start: 0.8662 (mmt) cc_final: 0.8415 (mmm) REVERT: E 2155 ARG cc_start: 0.8857 (mpp80) cc_final: 0.8097 (mpt-90) REVERT: E 2163 ARG cc_start: 0.7988 (mtt-85) cc_final: 0.7586 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8609 (t0) cc_final: 0.8280 (t0) REVERT: E 2168 ILE cc_start: 0.9217 (tt) cc_final: 0.8906 (tt) REVERT: E 2200 LYS cc_start: 0.7819 (mttt) cc_final: 0.7558 (mttp) REVERT: B 818 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8828 (ttmt) REVERT: F 2015 ASP cc_start: 0.8876 (t0) cc_final: 0.8554 (t0) REVERT: F 2019 ARG cc_start: 0.8401 (mtt-85) cc_final: 0.7853 (mtt90) REVERT: F 2077 ARG cc_start: 0.7471 (mmp80) cc_final: 0.7229 (mmp80) REVERT: F 2131 MET cc_start: 0.8660 (mmt) cc_final: 0.8413 (mmm) REVERT: F 2163 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7612 (mtt-85) REVERT: C 818 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8843 (ttmt) REVERT: G 2015 ASP cc_start: 0.8828 (t0) cc_final: 0.8476 (t0) REVERT: G 2019 ARG cc_start: 0.8409 (mtt-85) cc_final: 0.7847 (mtt90) REVERT: G 2077 ARG cc_start: 0.7453 (mmp80) cc_final: 0.7213 (mmp80) REVERT: G 2131 MET cc_start: 0.8651 (mmt) cc_final: 0.8402 (mmm) REVERT: G 2153 HIS cc_start: 0.8071 (t-90) cc_final: 0.7767 (t-90) REVERT: G 2155 ARG cc_start: 0.8842 (mpp80) cc_final: 0.8183 (mpt-90) REVERT: G 2163 ARG cc_start: 0.7949 (mtt-85) cc_final: 0.7548 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8359 (t0) cc_final: 0.8023 (t0) REVERT: G 2168 ILE cc_start: 0.9225 (tt) cc_final: 0.8899 (tt) REVERT: G 2200 LYS cc_start: 0.7815 (mttt) cc_final: 0.7562 (mttp) REVERT: D 818 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8821 (ttmt) REVERT: H 2015 ASP cc_start: 0.8879 (t0) cc_final: 0.8556 (t0) REVERT: H 2019 ARG cc_start: 0.8404 (mtt-85) cc_final: 0.7856 (mtt90) REVERT: H 2131 MET cc_start: 0.8659 (mmt) cc_final: 0.8413 (mmm) REVERT: H 2163 ARG cc_start: 0.7994 (mtt-85) cc_final: 0.7612 (mtt-85) outliers start: 82 outliers final: 67 residues processed: 332 average time/residue: 0.2533 time to fit residues: 136.8963 Evaluate side-chains 340 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 270 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2008 TYR Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 818 LYS Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 987 PHE Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2008 TYR Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 818 LYS Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 394 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 368 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 391 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 342 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 296 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 ASN C 957 ASN D 957 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.068005 restraints weight = 86537.208| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.74 r_work: 0.2824 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 37828 Z= 0.102 Angle : 0.465 12.239 51188 Z= 0.238 Chirality : 0.040 0.165 5756 Planarity : 0.003 0.032 6196 Dihedral : 11.923 88.407 5772 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.76 % Allowed : 14.77 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.14), residues: 4332 helix: 1.74 (0.11), residues: 2144 sheet: -0.51 (0.24), residues: 528 loop : -0.05 (0.17), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E2077 TYR 0.010 0.001 TYR B 928 PHE 0.012 0.001 PHE B 120 TRP 0.011 0.001 TRP F2176 HIS 0.003 0.000 HIS C 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (37788) covalent geometry : angle 0.46450 / 0.24 (51132) SS BOND : bond 0.00175 / 0.11 ( 16) SS BOND : angle 0.29880 / 0.19 ( 32) hydrogen bonds : bond 0.03818 / 2.51 ( 1624) hydrogen bonds : angle 3.84239 / 2.68 ( 4620) Misc. bond : bond 0.00155 / 0.11 ( 16) link_NAG-ASN : bond 0.00422 / 0.26 ( 8) link_NAG-ASN : angle 1.31425 / 0.85 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 277 time to evaluate : 1.428 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: E 2015 ASP cc_start: 0.8881 (t0) cc_final: 0.8477 (t0) REVERT: E 2019 ARG cc_start: 0.8398 (mtt-85) cc_final: 0.7856 (mtt90) REVERT: E 2077 ARG cc_start: 0.7481 (mmp80) cc_final: 0.7218 (mmp80) REVERT: E 2131 MET cc_start: 0.8668 (mmt) cc_final: 0.8417 (mmm) REVERT: E 2163 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7585 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8604 (t0) cc_final: 0.8270 (t0) REVERT: E 2168 ILE cc_start: 0.9192 (tt) cc_final: 0.8866 (tt) REVERT: E 2200 LYS cc_start: 0.7782 (mttt) cc_final: 0.7529 (mttp) REVERT: B 818 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8811 (ttmt) REVERT: F 2015 ASP cc_start: 0.8865 (t0) cc_final: 0.8541 (t0) REVERT: F 2019 ARG cc_start: 0.8399 (mtt-85) cc_final: 0.7868 (mtt90) REVERT: F 2077 ARG cc_start: 0.7491 (mmp80) cc_final: 0.7233 (mmp80) REVERT: F 2131 MET cc_start: 0.8665 (mmt) cc_final: 0.8414 (mmm) REVERT: F 2155 ARG cc_start: 0.8769 (mpp80) cc_final: 0.7908 (mpt-90) REVERT: F 2163 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7604 (mtt-85) REVERT: C 610 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8122 (t80) REVERT: C 818 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8815 (ttmt) REVERT: G 2015 ASP cc_start: 0.8815 (t0) cc_final: 0.8545 (t0) REVERT: G 2019 ARG cc_start: 0.8407 (mtt-85) cc_final: 0.7874 (mtt90) REVERT: G 2077 ARG cc_start: 0.7436 (mmp80) cc_final: 0.7174 (mmp80) REVERT: G 2131 MET cc_start: 0.8654 (mmt) cc_final: 0.8402 (mmm) REVERT: G 2153 HIS cc_start: 0.8077 (t-90) cc_final: 0.7771 (t-90) REVERT: G 2155 ARG cc_start: 0.8795 (mpp80) cc_final: 0.8177 (mpt-90) REVERT: G 2163 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7552 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8370 (t0) cc_final: 0.8158 (t0) REVERT: G 2200 LYS cc_start: 0.7872 (mttt) cc_final: 0.7631 (mttp) REVERT: D 818 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8814 (ttmt) REVERT: H 2015 ASP cc_start: 0.8870 (t0) cc_final: 0.8546 (t0) REVERT: H 2019 ARG cc_start: 0.8401 (mtt-85) cc_final: 0.7871 (mtt90) REVERT: H 2131 MET cc_start: 0.8649 (mmt) cc_final: 0.8400 (mmm) REVERT: H 2155 ARG cc_start: 0.8765 (mpp80) cc_final: 0.7899 (mpt-90) REVERT: H 2163 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7604 (mtt-85) outliers start: 68 outliers final: 63 residues processed: 326 average time/residue: 0.2451 time to fit residues: 129.4886 Evaluate side-chains 339 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 272 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2008 TYR Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 818 LYS Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 987 PHE Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2008 TYR Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 818 LYS Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 246 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 361 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 227 optimal weight: 0.4980 chunk 399 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 228 optimal weight: 0.6980 chunk 172 optimal weight: 0.1980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 ASN B 957 ASN D 957 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.067538 restraints weight = 86359.613| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.73 r_work: 0.2814 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37828 Z= 0.120 Angle : 0.474 11.913 51188 Z= 0.243 Chirality : 0.040 0.168 5756 Planarity : 0.003 0.032 6196 Dihedral : 11.926 87.512 5772 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.78 % Allowed : 14.70 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.14), residues: 4332 helix: 1.72 (0.11), residues: 2144 sheet: -0.59 (0.24), residues: 540 loop : 0.02 (0.17), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F2077 TYR 0.011 0.001 TYR B 928 PHE 0.013 0.001 PHE D 120 TRP 0.010 0.001 TRP G2176 HIS 0.003 0.000 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (37788) covalent geometry : angle 0.47327 / 0.24 (51132) SS BOND : bond 0.00201 / 0.13 ( 16) SS BOND : angle 0.29974 / 0.20 ( 32) hydrogen bonds : bond 0.03912 / 2.57 ( 1624) hydrogen bonds : angle 3.87987 / 2.71 ( 4620) Misc. bond : bond 0.00166 / 0.12 ( 16) link_NAG-ASN : bond 0.00429 / 0.27 ( 8) link_NAG-ASN : angle 1.30980 / 0.85 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8141.09 seconds wall clock time: 140 minutes 55.43 seconds (8455.43 seconds total)