Starting phenix.real_space_refine on Thu Nov 20 18:34:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v35_21028/11_2025/6v35_21028.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v35_21028/11_2025/6v35_21028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v35_21028/11_2025/6v35_21028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v35_21028/11_2025/6v35_21028.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v35_21028/11_2025/6v35_21028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v35_21028/11_2025/6v35_21028.map" } resolution = 3.5 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= -0.342 sd= 1.078 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 248 5.16 5 C 23788 2.51 5 N 5828 2.21 5 O 6612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36488 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7287 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 885} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "B" Number of atoms: 7287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7287 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 885} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7287 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 885} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 188 Unusual residues: {'CLR': 1, 'PGW': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-2': 5, 'PGW:plan-1': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 69 Unusual residues: {'CLR': 1, 'NAG': 2, 'PGW': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-1': 2, 'PGW:plan-2': 2, 'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Unusual residues: {'CLR': 1, 'PGW': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PGW:plan-3': 7, 'PGW:plan-1': 5, 'PGW:plan-2': 5} Unresolved non-hydrogen planarities: 56 Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 78 Unusual residues: {'CLR': 1, 'NAG': 2, 'PGW': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 3, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Unusual residues: {'CLR': 1, 'PGW': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-1': 4, 'PGW:plan-3': 4, 'PGW:plan-2': 4} Unresolved non-hydrogen planarities: 40 Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 69 Unusual residues: {'CLR': 1, 'NAG': 2, 'PGW': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-1': 2, 'PGW:plan-2': 2, 'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {'CLR': 1, 'PGW': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PGW:plan-1': 2, 'PGW:plan-2': 2, 'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 78 Unusual residues: {'CLR': 1, 'NAG': 2, 'PGW': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 3, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 28 Restraints were copied for chains: D, F, G, H Time building chain proxies: 13.30, per 1000 atoms: 0.36 Number of scatterers: 36488 At special positions: 0 Unit cell: (159.9, 159.9, 165.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 248 16.00 P 12 15.00 O 6612 8.00 N 5828 7.00 C 23788 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS G2054 " - pdb=" SG CYS G2148 " distance=2.04 Simple disulfide: pdb=" SG CYS H2054 " - pdb=" SG CYS H2148 " distance=2.04 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=8, symmetry=0 Links applied NAG-ASN " NAG E2303 " - " ASN E2053 " " NAG E2304 " - " ASN E2090 " " NAG F2304 " - " ASN F2053 " " NAG F2305 " - " ASN F2090 " " NAG G2303 " - " ASN G2053 " " NAG G2304 " - " ASN G2090 " " NAG H2304 " - " ASN H2053 " " NAG H2305 " - " ASN H2090 " Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.6 seconds 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8456 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 28 sheets defined 51.9% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 22 through 47 removed outlier: 4.089A pdb=" N LEU A 26 " --> pdb=" O TRP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 removed outlier: 4.362A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 148 through 167 removed outlier: 4.261A pdb=" N ILE A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 removed outlier: 3.643A pdb=" N TRP A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.550A pdb=" N LEU A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 259 removed outlier: 3.673A pdb=" N SER A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.537A pdb=" N SER A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 317 Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.533A pdb=" N ASN A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.552A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.795A pdb=" N LEU A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.536A pdb=" N MET A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 529 removed outlier: 3.875A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.503A pdb=" N PHE A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 546 " --> pdb=" O SER A 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 542 through 546' Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.618A pdb=" N VAL A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 625 removed outlier: 3.570A pdb=" N ILE A 625 " --> pdb=" O PRO A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.734A pdb=" N VAL A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 742 Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 759 through 767 removed outlier: 4.301A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 791 Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 817 through 829 removed outlier: 3.885A pdb=" N ILE A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 876 removed outlier: 4.104A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 876 " --> pdb=" O GLY A 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 872 through 876' Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.740A pdb=" N VAL A 888 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 890 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 891 " --> pdb=" O VAL A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 917 through 930 removed outlier: 4.170A pdb=" N ASP A 921 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 926 " --> pdb=" O SER A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 942 Processing helix chain 'A' and resid 946 through 957 removed outlier: 3.992A pdb=" N GLU A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 972 removed outlier: 3.537A pdb=" N ASN A 971 " --> pdb=" O GLN A 967 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A 972 " --> pdb=" O THR A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 992 removed outlier: 4.224A pdb=" N ASP A 989 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP A 992 " --> pdb=" O ASP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'A' and resid 1017 through 1021 removed outlier: 3.697A pdb=" N ALA A1020 " --> pdb=" O LEU A1017 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS A1021 " --> pdb=" O ARG A1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1017 through 1021' Processing helix chain 'E' and resid 2011 through 2036 removed outlier: 3.567A pdb=" N LEU E2032 " --> pdb=" O GLY E2028 " (cutoff:3.500A) Processing helix chain 'E' and resid 2039 through 2047 removed outlier: 3.955A pdb=" N GLN E2045 " --> pdb=" O SER E2041 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP E2046 " --> pdb=" O PRO E2042 " (cutoff:3.500A) Processing helix chain 'E' and resid 2103 through 2110 removed outlier: 3.559A pdb=" N THR E2109 " --> pdb=" O HIS E2105 " (cutoff:3.500A) Processing helix chain 'E' and resid 2122 through 2139 removed outlier: 3.620A pdb=" N TRP E2137 " --> pdb=" O TRP E2133 " (cutoff:3.500A) Processing helix chain 'E' and resid 2166 through 2169 removed outlier: 3.637A pdb=" N VAL E2169 " --> pdb=" O ASP E2166 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2166 through 2169' Processing helix chain 'E' and resid 2170 through 2200 removed outlier: 3.866A pdb=" N PHE E2174 " --> pdb=" O LEU E2170 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP E2176 " --> pdb=" O HIS E2172 " (cutoff:3.500A) Proline residue: E2177 - end of helix removed outlier: 3.621A pdb=" N VAL E2188 " --> pdb=" O GLY E2184 " (cutoff:3.500A) Processing helix chain 'E' and resid 2201 through 2204 removed outlier: 3.738A pdb=" N MET E2204 " --> pdb=" O ALA E2201 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2201 through 2204' Processing helix chain 'B' and resid 22 through 47 removed outlier: 4.089A pdb=" N LEU B 26 " --> pdb=" O TRP B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 101 removed outlier: 4.362A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 109 through 134 Processing helix chain 'B' and resid 148 through 167 removed outlier: 4.260A pdb=" N ILE B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 180 removed outlier: 3.643A pdb=" N TRP B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.550A pdb=" N LEU B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 259 removed outlier: 3.673A pdb=" N SER B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.537A pdb=" N SER B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 317 Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 352 through 364 removed outlier: 3.533A pdb=" N ASN B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 removed outlier: 3.551A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 466 through 472 removed outlier: 3.794A pdb=" N LEU B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 500 Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.535A pdb=" N MET B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 529 removed outlier: 3.875A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.503A pdb=" N PHE B 545 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 546 " --> pdb=" O SER B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 546' Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 601 through 607 removed outlier: 3.618A pdb=" N VAL B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 625 removed outlier: 3.569A pdb=" N ILE B 625 " --> pdb=" O PRO B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.734A pdb=" N VAL B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 742 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 759 through 767 removed outlier: 4.301A pdb=" N ARG B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 766 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 785 through 791 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 817 through 829 removed outlier: 3.884A pdb=" N ILE B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 822 " --> pdb=" O LYS B 818 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 removed outlier: 4.103A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE B 876 " --> pdb=" O GLY B 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 872 through 876' Processing helix chain 'B' and resid 884 through 891 removed outlier: 3.740A pdb=" N VAL B 888 " --> pdb=" O ASP B 885 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE B 890 " --> pdb=" O ASN B 887 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 891 " --> pdb=" O VAL B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 917 through 930 removed outlier: 4.170A pdb=" N ASP B 921 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 926 " --> pdb=" O SER B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 942 Processing helix chain 'B' and resid 946 through 957 removed outlier: 3.993A pdb=" N GLU B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 972 removed outlier: 3.537A pdb=" N ASN B 971 " --> pdb=" O GLN B 967 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B 972 " --> pdb=" O THR B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 992 removed outlier: 4.224A pdb=" N ASP B 989 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP B 992 " --> pdb=" O ASP B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1008 Processing helix chain 'B' and resid 1017 through 1021 removed outlier: 3.697A pdb=" N ALA B1020 " --> pdb=" O LEU B1017 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS B1021 " --> pdb=" O ARG B1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1017 through 1021' Processing helix chain 'F' and resid 2011 through 2036 removed outlier: 3.567A pdb=" N LEU F2032 " --> pdb=" O GLY F2028 " (cutoff:3.500A) Processing helix chain 'F' and resid 2039 through 2047 removed outlier: 3.954A pdb=" N GLN F2045 " --> pdb=" O SER F2041 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F2046 " --> pdb=" O PRO F2042 " (cutoff:3.500A) Processing helix chain 'F' and resid 2103 through 2110 removed outlier: 3.559A pdb=" N THR F2109 " --> pdb=" O HIS F2105 " (cutoff:3.500A) Processing helix chain 'F' and resid 2122 through 2139 removed outlier: 3.619A pdb=" N TRP F2137 " --> pdb=" O TRP F2133 " (cutoff:3.500A) Processing helix chain 'F' and resid 2166 through 2169 removed outlier: 3.637A pdb=" N VAL F2169 " --> pdb=" O ASP F2166 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2166 through 2169' Processing helix chain 'F' and resid 2170 through 2200 removed outlier: 3.867A pdb=" N PHE F2174 " --> pdb=" O LEU F2170 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP F2176 " --> pdb=" O HIS F2172 " (cutoff:3.500A) Proline residue: F2177 - end of helix removed outlier: 3.621A pdb=" N VAL F2188 " --> pdb=" O GLY F2184 " (cutoff:3.500A) Processing helix chain 'F' and resid 2201 through 2204 removed outlier: 3.738A pdb=" N MET F2204 " --> pdb=" O ALA F2201 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2201 through 2204' Processing helix chain 'C' and resid 22 through 47 removed outlier: 4.089A pdb=" N LEU C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 4.362A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 148 through 167 removed outlier: 4.260A pdb=" N ILE C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP C 153 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 180 removed outlier: 3.644A pdb=" N TRP C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.550A pdb=" N LEU C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 259 removed outlier: 3.673A pdb=" N SER C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 273 through 286 removed outlier: 3.537A pdb=" N SER C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 352 through 364 removed outlier: 3.533A pdb=" N ASN C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 384 through 392 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.552A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 466 through 472 removed outlier: 3.795A pdb=" N LEU C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.536A pdb=" N MET C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 529 removed outlier: 3.875A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.503A pdb=" N PHE C 545 " --> pdb=" O SER C 542 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 546 " --> pdb=" O SER C 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 542 through 546' Processing helix chain 'C' and resid 549 through 561 Processing helix chain 'C' and resid 601 through 607 removed outlier: 3.618A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 607 " --> pdb=" O LYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 625 removed outlier: 3.570A pdb=" N ILE C 625 " --> pdb=" O PRO C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 704 removed outlier: 3.734A pdb=" N VAL C 703 " --> pdb=" O GLU C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 742 Proline residue: C 740 - end of helix Processing helix chain 'C' and resid 759 through 767 removed outlier: 4.300A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 766 " --> pdb=" O TYR C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 785 through 791 Processing helix chain 'C' and resid 812 through 816 Processing helix chain 'C' and resid 817 through 829 removed outlier: 3.885A pdb=" N ILE C 821 " --> pdb=" O ASP C 817 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 822 " --> pdb=" O LYS C 818 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 876 removed outlier: 4.104A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE C 876 " --> pdb=" O GLY C 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 872 through 876' Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.740A pdb=" N VAL C 888 " --> pdb=" O ASP C 885 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 890 " --> pdb=" O ASN C 887 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 891 " --> pdb=" O VAL C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 917 through 930 removed outlier: 4.170A pdb=" N ASP C 921 " --> pdb=" O VAL C 917 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 926 " --> pdb=" O SER C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 942 Processing helix chain 'C' and resid 946 through 957 removed outlier: 3.992A pdb=" N GLU C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 972 removed outlier: 3.537A pdb=" N ASN C 971 " --> pdb=" O GLN C 967 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG C 972 " --> pdb=" O THR C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 removed outlier: 4.223A pdb=" N ASP C 989 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP C 992 " --> pdb=" O ASP C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 Processing helix chain 'C' and resid 1017 through 1021 removed outlier: 3.697A pdb=" N ALA C1020 " --> pdb=" O LEU C1017 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS C1021 " --> pdb=" O ARG C1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1017 through 1021' Processing helix chain 'G' and resid 2011 through 2036 removed outlier: 3.566A pdb=" N LEU G2032 " --> pdb=" O GLY G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2039 through 2047 removed outlier: 3.955A pdb=" N GLN G2045 " --> pdb=" O SER G2041 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP G2046 " --> pdb=" O PRO G2042 " (cutoff:3.500A) Processing helix chain 'G' and resid 2103 through 2110 removed outlier: 3.559A pdb=" N THR G2109 " --> pdb=" O HIS G2105 " (cutoff:3.500A) Processing helix chain 'G' and resid 2122 through 2139 removed outlier: 3.620A pdb=" N TRP G2137 " --> pdb=" O TRP G2133 " (cutoff:3.500A) Processing helix chain 'G' and resid 2166 through 2169 removed outlier: 3.637A pdb=" N VAL G2169 " --> pdb=" O ASP G2166 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2166 through 2169' Processing helix chain 'G' and resid 2170 through 2200 removed outlier: 3.867A pdb=" N PHE G2174 " --> pdb=" O LEU G2170 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP G2176 " --> pdb=" O HIS G2172 " (cutoff:3.500A) Proline residue: G2177 - end of helix removed outlier: 3.621A pdb=" N VAL G2188 " --> pdb=" O GLY G2184 " (cutoff:3.500A) Processing helix chain 'G' and resid 2201 through 2204 removed outlier: 3.739A pdb=" N MET G2204 " --> pdb=" O ALA G2201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2201 through 2204' Processing helix chain 'D' and resid 22 through 47 removed outlier: 4.088A pdb=" N LEU D 26 " --> pdb=" O TRP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 removed outlier: 4.361A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 109 through 134 Processing helix chain 'D' and resid 148 through 167 removed outlier: 4.261A pdb=" N ILE D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 180 removed outlier: 3.643A pdb=" N TRP D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.550A pdb=" N LEU D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 259 removed outlier: 3.672A pdb=" N SER D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 273 through 286 removed outlier: 3.537A pdb=" N SER D 286 " --> pdb=" O MET D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 317 Processing helix chain 'D' and resid 322 through 326 Processing helix chain 'D' and resid 352 through 364 removed outlier: 3.532A pdb=" N ASN D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 384 through 392 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 432 through 451 removed outlier: 3.553A pdb=" N GLU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 465 No H-bonds generated for 'chain 'D' and resid 463 through 465' Processing helix chain 'D' and resid 466 through 472 removed outlier: 3.795A pdb=" N LEU D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.536A pdb=" N MET D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 512 " --> pdb=" O ALA D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 529 removed outlier: 3.874A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 removed outlier: 3.503A pdb=" N PHE D 545 " --> pdb=" O SER D 542 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 546 " --> pdb=" O SER D 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 542 through 546' Processing helix chain 'D' and resid 549 through 561 Processing helix chain 'D' and resid 601 through 607 removed outlier: 3.618A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 607 " --> pdb=" O LYS D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 625 removed outlier: 3.570A pdb=" N ILE D 625 " --> pdb=" O PRO D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 704 removed outlier: 3.734A pdb=" N VAL D 703 " --> pdb=" O GLU D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 742 Proline residue: D 740 - end of helix Processing helix chain 'D' and resid 759 through 767 removed outlier: 4.300A pdb=" N ARG D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU D 766 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 785 through 791 Processing helix chain 'D' and resid 812 through 816 Processing helix chain 'D' and resid 817 through 829 removed outlier: 3.884A pdb=" N ILE D 821 " --> pdb=" O ASP D 817 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 822 " --> pdb=" O LYS D 818 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA D 823 " --> pdb=" O GLU D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 876 removed outlier: 4.103A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE D 876 " --> pdb=" O GLY D 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 872 through 876' Processing helix chain 'D' and resid 884 through 891 removed outlier: 3.740A pdb=" N VAL D 888 " --> pdb=" O ASP D 885 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE D 890 " --> pdb=" O ASN D 887 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 891 " --> pdb=" O VAL D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 917 through 930 removed outlier: 4.170A pdb=" N ASP D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 926 " --> pdb=" O SER D 922 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 942 Processing helix chain 'D' and resid 946 through 957 removed outlier: 3.993A pdb=" N GLU D 956 " --> pdb=" O LEU D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 972 removed outlier: 3.538A pdb=" N ASN D 971 " --> pdb=" O GLN D 967 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 972 " --> pdb=" O THR D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 992 removed outlier: 4.224A pdb=" N ASP D 989 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP D 992 " --> pdb=" O ASP D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1008 Processing helix chain 'D' and resid 1017 through 1021 removed outlier: 3.697A pdb=" N ALA D1020 " --> pdb=" O LEU D1017 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS D1021 " --> pdb=" O ARG D1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1017 through 1021' Processing helix chain 'H' and resid 2011 through 2036 removed outlier: 3.567A pdb=" N LEU H2032 " --> pdb=" O GLY H2028 " (cutoff:3.500A) Processing helix chain 'H' and resid 2039 through 2047 removed outlier: 3.955A pdb=" N GLN H2045 " --> pdb=" O SER H2041 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP H2046 " --> pdb=" O PRO H2042 " (cutoff:3.500A) Processing helix chain 'H' and resid 2103 through 2110 removed outlier: 3.559A pdb=" N THR H2109 " --> pdb=" O HIS H2105 " (cutoff:3.500A) Processing helix chain 'H' and resid 2122 through 2139 removed outlier: 3.619A pdb=" N TRP H2137 " --> pdb=" O TRP H2133 " (cutoff:3.500A) Processing helix chain 'H' and resid 2166 through 2169 removed outlier: 3.636A pdb=" N VAL H2169 " --> pdb=" O ASP H2166 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 2166 through 2169' Processing helix chain 'H' and resid 2170 through 2200 removed outlier: 3.866A pdb=" N PHE H2174 " --> pdb=" O LEU H2170 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP H2176 " --> pdb=" O HIS H2172 " (cutoff:3.500A) Proline residue: H2177 - end of helix removed outlier: 3.621A pdb=" N VAL H2188 " --> pdb=" O GLY H2184 " (cutoff:3.500A) Processing helix chain 'H' and resid 2201 through 2204 removed outlier: 3.737A pdb=" N MET H2204 " --> pdb=" O ALA H2201 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 2201 through 2204' Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 402 removed outlier: 6.914A pdb=" N LYS A 343 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL A 376 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA A 421 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 540 removed outlier: 6.618A pdb=" N PHE A 596 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 564 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 569 through 570 removed outlier: 3.611A pdb=" N TYR A 570 " --> pdb=" O ARG A 578 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 578 " --> pdb=" O TYR A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.406A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 978 through 981 removed outlier: 3.558A pdb=" N ILE A1049 " --> pdb=" O LEU A 980 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 2050 through 2061 removed outlier: 6.778A pdb=" N TYR E2088 " --> pdb=" O LEU E2057 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL E2059 " --> pdb=" O GLN E2086 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN E2086 " --> pdb=" O VAL E2059 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL E2087 " --> pdb=" O LEU E2100 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N VAL E2159 " --> pdb=" O ARG E2097 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU E2099 " --> pdb=" O VAL E2159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 2066 through 2067 Processing sheet with id=AA8, first strand: chain 'B' and resid 398 through 402 removed outlier: 6.914A pdb=" N LYS B 343 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL B 376 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE B 345 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 378 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 347 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA B 421 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.618A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 564 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 569 through 570 removed outlier: 3.611A pdb=" N TYR B 570 " --> pdb=" O ARG B 578 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 578 " --> pdb=" O TYR B 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.405A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 978 through 981 removed outlier: 3.559A pdb=" N ILE B1049 " --> pdb=" O LEU B 980 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 2050 through 2061 removed outlier: 6.778A pdb=" N TYR F2088 " --> pdb=" O LEU F2057 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL F2059 " --> pdb=" O GLN F2086 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLN F2086 " --> pdb=" O VAL F2059 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL F2087 " --> pdb=" O LEU F2100 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N VAL F2159 " --> pdb=" O ARG F2097 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU F2099 " --> pdb=" O VAL F2159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 2066 through 2067 Processing sheet with id=AB6, first strand: chain 'C' and resid 398 through 402 removed outlier: 6.914A pdb=" N LYS C 343 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 376 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE C 345 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU C 378 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 347 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA C 421 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 535 through 540 removed outlier: 6.617A pdb=" N PHE C 596 " --> pdb=" O ILE C 566 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C 564 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 569 through 570 removed outlier: 3.611A pdb=" N TYR C 570 " --> pdb=" O ARG C 578 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 578 " --> pdb=" O TYR C 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.406A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 719 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL C 757 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL C 721 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 978 through 981 removed outlier: 3.558A pdb=" N ILE C1049 " --> pdb=" O LEU C 980 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 2050 through 2061 removed outlier: 6.778A pdb=" N TYR G2088 " --> pdb=" O LEU G2057 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL G2059 " --> pdb=" O GLN G2086 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLN G2086 " --> pdb=" O VAL G2059 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL G2087 " --> pdb=" O LEU G2100 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL G2159 " --> pdb=" O ARG G2097 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU G2099 " --> pdb=" O VAL G2159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 2066 through 2067 Processing sheet with id=AC4, first strand: chain 'D' and resid 398 through 402 removed outlier: 6.914A pdb=" N LYS D 343 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL D 376 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE D 345 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU D 378 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 347 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA D 421 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 535 through 540 removed outlier: 6.618A pdb=" N PHE D 596 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 564 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 569 through 570 removed outlier: 3.611A pdb=" N TYR D 570 " --> pdb=" O ARG D 578 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 578 " --> pdb=" O TYR D 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.406A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL D 719 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL D 757 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL D 721 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 978 through 981 removed outlier: 3.558A pdb=" N ILE D1049 " --> pdb=" O LEU D 980 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 2050 through 2061 removed outlier: 6.778A pdb=" N TYR H2088 " --> pdb=" O LEU H2057 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL H2059 " --> pdb=" O GLN H2086 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN H2086 " --> pdb=" O VAL H2059 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL H2087 " --> pdb=" O LEU H2100 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N VAL H2159 " --> pdb=" O ARG H2097 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU H2099 " --> pdb=" O VAL H2159 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 2066 through 2067 1448 hydrogen bonds defined for protein. 4056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.56 Time building geometry restraints manager: 4.34 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: 5780 1.30 - 1.43: 9993 1.43 - 1.56: 21021 1.56 - 1.69: 150 1.69 - 1.81: 356 Bond restraints: 37300 Sorted by residual: bond pdb=" C5 CLR H2306 " pdb=" C6 CLR H2306 " ideal model delta sigma weight residual 1.332 1.575 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR E2305 " pdb=" C6 CLR E2305 " ideal model delta sigma weight residual 1.332 1.575 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR G2305 " pdb=" C6 CLR G2305 " ideal model delta sigma weight residual 1.332 1.575 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR F2306 " pdb=" C6 CLR F2306 " ideal model delta sigma weight residual 1.332 1.574 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR C1107 " pdb=" C6 CLR C1107 " ideal model delta sigma weight residual 1.332 1.566 -0.234 2.00e-02 2.50e+03 1.37e+02 ... (remaining 37295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 49675 3.82 - 7.63: 713 7.63 - 11.45: 76 11.45 - 15.26: 26 15.26 - 19.08: 14 Bond angle restraints: 50504 Sorted by residual: angle pdb=" O13 PGW B1104 " pdb=" P PGW B1104 " pdb=" O14 PGW B1104 " ideal model delta sigma weight residual 119.81 100.73 19.08 3.00e+00 1.11e-01 4.05e+01 angle pdb=" O13 PGW D1104 " pdb=" P PGW D1104 " pdb=" O14 PGW D1104 " ideal model delta sigma weight residual 119.81 100.73 19.08 3.00e+00 1.11e-01 4.04e+01 angle pdb=" O13 PGW A3001 " pdb=" P PGW A3001 " pdb=" O14 PGW A3001 " ideal model delta sigma weight residual 119.81 100.75 19.06 3.00e+00 1.11e-01 4.04e+01 angle pdb=" O13 PGW C1102 " pdb=" P PGW C1102 " pdb=" O14 PGW C1102 " ideal model delta sigma weight residual 119.81 100.75 19.06 3.00e+00 1.11e-01 4.04e+01 angle pdb=" O13 PGW D1101 " pdb=" P PGW D1101 " pdb=" O14 PGW D1101 " ideal model delta sigma weight residual 119.81 100.97 18.84 3.00e+00 1.11e-01 3.94e+01 ... (remaining 50499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.77: 21886 26.77 - 53.54: 566 53.54 - 80.32: 168 80.32 - 107.09: 56 107.09 - 133.86: 28 Dihedral angle restraints: 22704 sinusoidal: 9660 harmonic: 13044 Sorted by residual: dihedral pdb=" CB CYS F2054 " pdb=" SG CYS F2054 " pdb=" SG CYS F2148 " pdb=" CB CYS F2148 " ideal model delta sinusoidal sigma weight residual 93.00 178.44 -85.44 1 1.00e+01 1.00e-02 8.84e+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 93.00 178.42 -85.42 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS E2054 " pdb=" SG CYS E2054 " pdb=" SG CYS E2148 " pdb=" CB CYS E2148 " ideal model delta sinusoidal sigma weight residual 93.00 178.41 -85.41 1 1.00e+01 1.00e-02 8.83e+01 ... (remaining 22701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 5362 0.135 - 0.270: 355 0.270 - 0.406: 26 0.406 - 0.541: 5 0.541 - 0.676: 8 Chirality restraints: 5756 Sorted by residual: chirality pdb=" C1 NAG F2304 " pdb=" ND2 ASN F2053 " pdb=" C2 NAG F2304 " pdb=" O5 NAG F2304 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG E2303 " pdb=" ND2 ASN E2053 " pdb=" C2 NAG E2303 " pdb=" O5 NAG E2303 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG G2303 " pdb=" ND2 ASN G2053 " pdb=" C2 NAG G2303 " pdb=" O5 NAG G2303 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 5753 not shown) Planarity restraints: 6248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B1104 " 0.119 2.00e-02 2.50e+03 1.91e-01 3.64e+02 pdb=" C10 PGW B1104 " -0.242 2.00e-02 2.50e+03 pdb=" C8 PGW B1104 " -0.119 2.00e-02 2.50e+03 pdb=" C9 PGW B1104 " 0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C1102 " 0.119 2.00e-02 2.50e+03 1.91e-01 3.63e+02 pdb=" C10 PGW C1102 " -0.242 2.00e-02 2.50e+03 pdb=" C8 PGW C1102 " -0.119 2.00e-02 2.50e+03 pdb=" C9 PGW C1102 " 0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A3001 " -0.119 2.00e-02 2.50e+03 1.91e-01 3.63e+02 pdb=" C10 PGW A3001 " 0.242 2.00e-02 2.50e+03 pdb=" C8 PGW A3001 " 0.119 2.00e-02 2.50e+03 pdb=" C9 PGW A3001 " -0.242 2.00e-02 2.50e+03 ... (remaining 6245 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 10819 2.82 - 3.34: 34138 3.34 - 3.86: 61205 3.86 - 4.38: 69709 4.38 - 4.90: 117097 Nonbonded interactions: 292968 Sorted by model distance: nonbonded pdb=" O LEU D 214 " pdb=" OG SER D 240 " model vdw 2.296 3.040 nonbonded pdb=" O LEU A 214 " pdb=" OG SER A 240 " model vdw 2.296 3.040 nonbonded pdb=" O LEU B 214 " pdb=" OG SER B 240 " model vdw 2.297 3.040 nonbonded pdb=" O LEU C 214 " pdb=" OG SER C 240 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR D 290 " model vdw 2.302 3.040 ... (remaining 292963 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 19 through 1056 or resid 3003 or (resid 3005 and (name C20 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27)))) selection = (chain 'B' and (resid 19 through 1056 or resid 1103 or (resid 1105 and (name C20 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27)))) selection = (chain 'C' and (resid 19 through 1056 or (resid 1103 and (name C1 or name C2 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 1105 and (name C20 or name C21 or name C22 or name C23 or name C24 or nam \ e C25 or name C26 or name C27)))) selection = (chain 'D' and (resid 19 through 1056 or resid 1103 or (resid 1105 and (name C20 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27)))) } ncs_group { reference = (chain 'E' and (resid 2008 through 2302 or resid 2304)) selection = (chain 'F' and (resid 2008 through 2205 or (resid 2301 and (name C1 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 2302 and (nam \ e C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 2304)) selection = (chain 'G' and (resid 2008 through 2302 or resid 2304)) selection = (chain 'H' and (resid 2008 through 2205 or (resid 2301 and (name C1 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 2302 and (nam \ e C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 2304)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 39.870 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.011 0.243 37332 Z= 0.585 Angle : 1.242 19.081 50560 Z= 0.683 Chirality : 0.075 0.676 5756 Planarity : 0.008 0.191 6240 Dihedral : 14.970 133.861 14200 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.81 % Allowed : 4.27 % Favored : 94.92 % Cbeta Deviations : 0.09 % 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: -3.13 (0.11), residues: 4408 helix: -2.06 (0.09), residues: 1936 sheet: -1.71 (0.21), residues: 576 loop : -2.04 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1031 TYR 0.026 0.002 TYR C1015 PHE 0.033 0.003 PHE C 164 TRP 0.041 0.003 TRP B 246 HIS 0.011 0.002 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.01105 (37300) covalent geometry : angle 1.23293 (50504) SS BOND : bond 0.00514 ( 16) SS BOND : angle 0.75239 ( 32) hydrogen bonds : bond 0.20858 ( 1448) hydrogen bonds : angle 8.37568 ( 4056) Misc. bond : bond 0.00278 ( 8) link_NAG-ASN : bond 0.01787 ( 8) link_NAG-ASN : angle 6.99993 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 847 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9439 (tp) cc_final: 0.9143 (tp) REVERT: A 30 MET cc_start: 0.8565 (ttm) cc_final: 0.8314 (mmm) REVERT: A 214 LEU cc_start: 0.9273 (mt) cc_final: 0.8949 (mp) REVERT: A 276 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 282 MET cc_start: 0.8784 (tpp) cc_final: 0.8555 (tpp) REVERT: A 356 VAL cc_start: 0.9738 (t) cc_final: 0.9499 (t) REVERT: A 374 GLU cc_start: 0.7848 (tt0) cc_final: 0.7390 (tp30) REVERT: A 460 MET cc_start: 0.9049 (mmm) cc_final: 0.8683 (mmm) REVERT: A 878 ILE cc_start: 0.9086 (pt) cc_final: 0.8882 (mt) REVERT: E 2015 ASP cc_start: 0.8841 (t70) cc_final: 0.8527 (t0) REVERT: E 2016 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8340 (tptt) REVERT: E 2046 ASP cc_start: 0.8773 (t70) cc_final: 0.8384 (t0) REVERT: E 2077 ARG cc_start: 0.8914 (mmt90) cc_final: 0.8666 (mmm160) REVERT: E 2115 TYR cc_start: 0.9182 (t80) cc_final: 0.8757 (t80) REVERT: E 2163 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.7820 (mtt-85) REVERT: E 2168 ILE cc_start: 0.8433 (tt) cc_final: 0.8179 (tt) REVERT: B 214 LEU cc_start: 0.9191 (mt) cc_final: 0.8926 (mp) REVERT: B 276 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7881 (mm-30) REVERT: B 282 MET cc_start: 0.8706 (tpp) cc_final: 0.8458 (tpp) REVERT: B 356 VAL cc_start: 0.9728 (t) cc_final: 0.9494 (t) REVERT: B 374 GLU cc_start: 0.7803 (tt0) cc_final: 0.7507 (tp30) REVERT: B 460 MET cc_start: 0.9078 (mmm) cc_final: 0.8775 (mmm) REVERT: F 2015 ASP cc_start: 0.8949 (t70) cc_final: 0.8729 (t0) REVERT: F 2016 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8348 (tptt) REVERT: F 2046 ASP cc_start: 0.8701 (t70) cc_final: 0.8188 (t0) REVERT: F 2077 ARG cc_start: 0.8948 (mmt90) cc_final: 0.8676 (mmm160) REVERT: F 2115 TYR cc_start: 0.9192 (t80) cc_final: 0.8758 (t80) REVERT: F 2163 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.7698 (mtt-85) REVERT: F 2168 ILE cc_start: 0.8484 (tt) cc_final: 0.8181 (mt) REVERT: F 2191 THR cc_start: 0.9092 (m) cc_final: 0.8828 (m) REVERT: C 26 LEU cc_start: 0.9438 (tp) cc_final: 0.9142 (tp) REVERT: C 30 MET cc_start: 0.8579 (ttm) cc_final: 0.8319 (mmm) REVERT: C 214 LEU cc_start: 0.9273 (mt) cc_final: 0.8951 (mp) REVERT: C 276 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7907 (mm-30) REVERT: C 282 MET cc_start: 0.8785 (tpp) cc_final: 0.8554 (tpp) REVERT: C 356 VAL cc_start: 0.9731 (t) cc_final: 0.9458 (p) REVERT: C 374 GLU cc_start: 0.7775 (tt0) cc_final: 0.7464 (tp30) REVERT: C 460 MET cc_start: 0.9042 (mmm) cc_final: 0.8669 (mmm) REVERT: G 2015 ASP cc_start: 0.8841 (t70) cc_final: 0.8521 (t0) REVERT: G 2016 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8339 (tptt) REVERT: G 2046 ASP cc_start: 0.8775 (t70) cc_final: 0.8388 (t0) REVERT: G 2077 ARG cc_start: 0.8921 (mmt90) cc_final: 0.8663 (mmm160) REVERT: G 2115 TYR cc_start: 0.9177 (t80) cc_final: 0.8759 (t80) REVERT: G 2155 ARG cc_start: 0.8153 (mpp-170) cc_final: 0.7673 (mtt90) REVERT: G 2163 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.7753 (mtt-85) REVERT: D 26 LEU cc_start: 0.9463 (tp) cc_final: 0.9261 (tp) REVERT: D 214 LEU cc_start: 0.9181 (mt) cc_final: 0.8937 (mp) REVERT: D 276 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7799 (mm-30) REVERT: D 282 MET cc_start: 0.8689 (tpp) cc_final: 0.8424 (tpp) REVERT: D 356 VAL cc_start: 0.9741 (t) cc_final: 0.9537 (t) REVERT: D 362 ASP cc_start: 0.8148 (t0) cc_final: 0.7709 (t0) REVERT: D 374 GLU cc_start: 0.7977 (tt0) cc_final: 0.7538 (tp30) REVERT: D 460 MET cc_start: 0.9055 (mmm) cc_final: 0.8722 (mmm) REVERT: D 513 MET cc_start: 0.7499 (mmm) cc_final: 0.7285 (mmm) REVERT: D 1030 LYS cc_start: 0.9137 (mttt) cc_final: 0.8670 (mtmt) REVERT: H 2015 ASP cc_start: 0.8944 (t70) cc_final: 0.8727 (t0) REVERT: H 2016 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8327 (tptt) REVERT: H 2046 ASP cc_start: 0.8752 (t70) cc_final: 0.8136 (t0) REVERT: H 2077 ARG cc_start: 0.8901 (mmt90) cc_final: 0.8617 (mmm160) REVERT: H 2115 TYR cc_start: 0.9250 (t80) cc_final: 0.8742 (t80) REVERT: H 2163 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7560 (mtp180) REVERT: H 2168 ILE cc_start: 0.8557 (tt) cc_final: 0.8287 (mt) REVERT: H 2191 THR cc_start: 0.9082 (m) cc_final: 0.8824 (m) outliers start: 32 outliers final: 10 residues processed: 879 average time/residue: 0.2469 time to fit residues: 347.6865 Evaluate side-chains 469 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 459 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN A 267 GLN A 379 HIS A 440 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN A 809 ASN E2106 GLN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 379 HIS B 440 ASN B 465 ASN B 471 ASN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN B 809 ASN F2106 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 379 HIS C 440 ASN C 465 ASN C 471 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN ** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN C 809 ASN G2106 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 379 HIS D 440 ASN D 465 ASN D 471 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN D 809 ASN H2124 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.087474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.068254 restraints weight = 117077.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070518 restraints weight = 55244.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072070 restraints weight = 34835.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073076 restraints weight = 26024.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073624 restraints weight = 21601.541| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37332 Z= 0.150 Angle : 0.658 12.177 50560 Z= 0.330 Chirality : 0.044 0.396 5756 Planarity : 0.005 0.046 6240 Dihedral : 13.940 134.482 5996 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.52 % Allowed : 9.17 % Favored : 88.31 % 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: -1.64 (0.12), residues: 4408 helix: -0.37 (0.11), residues: 1980 sheet: -1.60 (0.19), residues: 632 loop : -1.58 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E2155 TYR 0.016 0.001 TYR D 48 PHE 0.024 0.002 PHE G2033 TRP 0.041 0.002 TRP E2176 HIS 0.007 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00334 (37300) covalent geometry : angle 0.64880 (50504) SS BOND : bond 0.00278 ( 16) SS BOND : angle 0.90966 ( 32) hydrogen bonds : bond 0.04127 ( 1448) hydrogen bonds : angle 5.13194 ( 4056) Misc. bond : bond 0.00048 ( 8) link_NAG-ASN : bond 0.01517 ( 8) link_NAG-ASN : angle 5.08116 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 540 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9446 (tp) cc_final: 0.9162 (tp) REVERT: A 38 PHE cc_start: 0.9157 (m-10) cc_final: 0.8885 (m-80) REVERT: A 48 TYR cc_start: 0.8597 (m-80) cc_final: 0.8179 (m-10) REVERT: A 118 LEU cc_start: 0.9348 (tp) cc_final: 0.9057 (pp) REVERT: A 153 ASP cc_start: 0.8578 (t0) cc_final: 0.7917 (t0) REVERT: A 157 ASN cc_start: 0.9227 (m-40) cc_final: 0.8512 (m110) REVERT: A 162 LEU cc_start: 0.9421 (mt) cc_final: 0.9005 (pp) REVERT: A 282 MET cc_start: 0.8864 (tpp) cc_final: 0.8624 (tpp) REVERT: A 285 MET cc_start: 0.8438 (mmm) cc_final: 0.8212 (mmm) REVERT: A 362 ASP cc_start: 0.8227 (t0) cc_final: 0.7581 (t0) REVERT: A 561 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8337 (pp) REVERT: A 900 ASP cc_start: 0.8628 (p0) cc_final: 0.8324 (p0) REVERT: A 1053 MET cc_start: 0.8510 (mtp) cc_final: 0.8278 (mtp) REVERT: E 2015 ASP cc_start: 0.8929 (t70) cc_final: 0.8676 (t0) REVERT: E 2016 LYS cc_start: 0.9051 (ttmt) cc_final: 0.8452 (tptt) REVERT: E 2046 ASP cc_start: 0.8759 (t70) cc_final: 0.8464 (t70) REVERT: E 2077 ARG cc_start: 0.8961 (mmt90) cc_final: 0.8603 (mmm160) REVERT: E 2163 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.7367 (mmm160) REVERT: B 118 LEU cc_start: 0.9265 (tp) cc_final: 0.8976 (pp) REVERT: B 153 ASP cc_start: 0.8613 (t0) cc_final: 0.7993 (t0) REVERT: B 157 ASN cc_start: 0.9208 (m-40) cc_final: 0.8555 (m110) REVERT: B 162 LEU cc_start: 0.9461 (mm) cc_final: 0.9246 (mm) REVERT: B 182 ASN cc_start: 0.7506 (t160) cc_final: 0.7055 (t0) REVERT: B 282 MET cc_start: 0.8866 (tpp) cc_final: 0.8614 (tpp) REVERT: B 285 MET cc_start: 0.8350 (mmm) cc_final: 0.8114 (mmm) REVERT: B 362 ASP cc_start: 0.8268 (t0) cc_final: 0.7692 (t0) REVERT: B 460 MET cc_start: 0.8919 (mmm) cc_final: 0.8595 (mmm) REVERT: B 561 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8477 (pp) REVERT: B 900 ASP cc_start: 0.8732 (p0) cc_final: 0.8506 (p0) REVERT: F 2015 ASP cc_start: 0.8931 (t70) cc_final: 0.8663 (t0) REVERT: F 2016 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8418 (tptt) REVERT: F 2046 ASP cc_start: 0.8743 (t70) cc_final: 0.8413 (t70) REVERT: F 2077 ARG cc_start: 0.8968 (mmt90) cc_final: 0.8596 (mmm160) REVERT: F 2163 ARG cc_start: 0.8205 (mtt-85) cc_final: 0.7380 (mmm160) REVERT: C 26 LEU cc_start: 0.9447 (tp) cc_final: 0.9168 (tp) REVERT: C 38 PHE cc_start: 0.9167 (m-10) cc_final: 0.8854 (m-80) REVERT: C 48 TYR cc_start: 0.8571 (m-80) cc_final: 0.8154 (m-10) REVERT: C 118 LEU cc_start: 0.9345 (tp) cc_final: 0.9058 (pp) REVERT: C 153 ASP cc_start: 0.8576 (t0) cc_final: 0.7902 (t0) REVERT: C 157 ASN cc_start: 0.9215 (m-40) cc_final: 0.8485 (m110) REVERT: C 162 LEU cc_start: 0.9418 (mt) cc_final: 0.8999 (pp) REVERT: C 282 MET cc_start: 0.8854 (tpp) cc_final: 0.8611 (tpp) REVERT: C 285 MET cc_start: 0.8447 (mmm) cc_final: 0.8222 (mmm) REVERT: C 362 ASP cc_start: 0.8234 (t0) cc_final: 0.7668 (t0) REVERT: C 561 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8325 (pp) REVERT: C 1053 MET cc_start: 0.8506 (mtp) cc_final: 0.8277 (mtp) REVERT: G 2015 ASP cc_start: 0.8919 (t70) cc_final: 0.8667 (t0) REVERT: G 2016 LYS cc_start: 0.9100 (ttmt) cc_final: 0.8572 (tptt) REVERT: G 2046 ASP cc_start: 0.8772 (t70) cc_final: 0.8460 (t70) REVERT: G 2077 ARG cc_start: 0.8952 (mmt90) cc_final: 0.8600 (mmm160) REVERT: G 2163 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7348 (mmm160) REVERT: D 21 MET cc_start: 0.8658 (mmm) cc_final: 0.8364 (mmm) REVERT: D 118 LEU cc_start: 0.9301 (tp) cc_final: 0.8921 (pp) REVERT: D 153 ASP cc_start: 0.8516 (t0) cc_final: 0.7908 (t0) REVERT: D 157 ASN cc_start: 0.9118 (m-40) cc_final: 0.8276 (m110) REVERT: D 276 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8063 (mm-30) REVERT: D 285 MET cc_start: 0.8454 (mmm) cc_final: 0.7941 (mmm) REVERT: D 303 PHE cc_start: 0.8098 (t80) cc_final: 0.7872 (t80) REVERT: D 307 PHE cc_start: 0.8092 (t80) cc_final: 0.7673 (t80) REVERT: D 362 ASP cc_start: 0.8313 (t0) cc_final: 0.7718 (t0) REVERT: D 460 MET cc_start: 0.8962 (mmm) cc_final: 0.8584 (mmm) REVERT: D 561 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8520 (pp) REVERT: D 900 ASP cc_start: 0.8574 (p0) cc_final: 0.8354 (p0) REVERT: H 2015 ASP cc_start: 0.8912 (t70) cc_final: 0.8669 (t0) REVERT: H 2016 LYS cc_start: 0.8987 (ttmt) cc_final: 0.8209 (tptt) REVERT: H 2046 ASP cc_start: 0.8769 (t70) cc_final: 0.8521 (t70) REVERT: H 2077 ARG cc_start: 0.8886 (mmt90) cc_final: 0.8558 (mmm160) REVERT: H 2115 TYR cc_start: 0.9295 (t80) cc_final: 0.9037 (t80) REVERT: H 2141 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.7965 (tt) REVERT: H 2163 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7688 (mtp180) outliers start: 99 outliers final: 39 residues processed: 612 average time/residue: 0.2209 time to fit residues: 227.7682 Evaluate side-chains 459 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 415 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2204 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2188 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain C residue 987 PHE Chi-restraints excluded: chain G residue 2187 ILE Chi-restraints excluded: chain G residue 2188 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 814 SER Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 949 LEU Chi-restraints excluded: chain D residue 987 PHE Chi-restraints excluded: chain H residue 2141 ILE Chi-restraints excluded: chain H residue 2188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 135 optimal weight: 0.8980 chunk 376 optimal weight: 3.9990 chunk 371 optimal weight: 2.9990 chunk 337 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 chunk 418 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN A 182 ASN A 216 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN B 143 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 216 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN ** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN G2101 HIS ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.085331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.066055 restraints weight = 117861.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068288 restraints weight = 55716.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069755 restraints weight = 35333.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070720 restraints weight = 26555.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071313 restraints weight = 22139.087| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37332 Z= 0.184 Angle : 0.620 10.901 50560 Z= 0.311 Chirality : 0.043 0.349 5756 Planarity : 0.004 0.052 6240 Dihedral : 12.327 151.957 5978 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.87 % Allowed : 10.65 % Favored : 86.48 % 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: -1.01 (0.13), residues: 4408 helix: 0.31 (0.12), residues: 2032 sheet: -1.52 (0.20), residues: 592 loop : -1.42 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 213 TYR 0.015 0.001 TYR F2008 PHE 0.026 0.002 PHE H2033 TRP 0.056 0.002 TRP E2176 HIS 0.008 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00414 (37300) covalent geometry : angle 0.61164 (50504) SS BOND : bond 0.00187 ( 16) SS BOND : angle 0.80517 ( 32) hydrogen bonds : bond 0.03570 ( 1448) hydrogen bonds : angle 4.70335 ( 4056) Misc. bond : bond 0.00050 ( 8) link_NAG-ASN : bond 0.01371 ( 8) link_NAG-ASN : angle 4.55367 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 457 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8695 (mmm) cc_final: 0.8433 (mmm) REVERT: A 118 LEU cc_start: 0.9350 (tp) cc_final: 0.9022 (pp) REVERT: A 285 MET cc_start: 0.8483 (mmm) cc_final: 0.8226 (mmm) REVERT: A 303 PHE cc_start: 0.8274 (t80) cc_final: 0.7972 (t80) REVERT: A 362 ASP cc_start: 0.8318 (t0) cc_final: 0.7741 (t0) REVERT: A 561 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8415 (pp) REVERT: A 715 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.7905 (pp) REVERT: A 878 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8908 (mp) REVERT: A 1053 MET cc_start: 0.8627 (mtp) cc_final: 0.8395 (mtm) REVERT: E 2015 ASP cc_start: 0.8905 (t70) cc_final: 0.8674 (t0) REVERT: E 2016 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8531 (tptt) REVERT: E 2046 ASP cc_start: 0.8746 (t70) cc_final: 0.8484 (t70) REVERT: E 2077 ARG cc_start: 0.8888 (mmt90) cc_final: 0.8511 (mmm160) REVERT: E 2163 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.7373 (mmm160) REVERT: B 118 LEU cc_start: 0.9294 (tp) cc_final: 0.8978 (pp) REVERT: B 153 ASP cc_start: 0.8683 (t0) cc_final: 0.8022 (t0) REVERT: B 157 ASN cc_start: 0.9167 (m-40) cc_final: 0.8451 (m110) REVERT: B 162 LEU cc_start: 0.9436 (mm) cc_final: 0.9004 (pp) REVERT: B 362 ASP cc_start: 0.8325 (t0) cc_final: 0.7760 (t0) REVERT: B 561 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8463 (pp) REVERT: B 715 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.7932 (pp) REVERT: F 2015 ASP cc_start: 0.8891 (t70) cc_final: 0.8599 (t0) REVERT: F 2016 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8411 (tptt) REVERT: F 2046 ASP cc_start: 0.8710 (t70) cc_final: 0.8435 (t70) REVERT: F 2077 ARG cc_start: 0.8996 (mmt90) cc_final: 0.8533 (mmm160) REVERT: F 2163 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.7394 (mmm160) REVERT: F 2166 ASP cc_start: 0.8335 (p0) cc_final: 0.8037 (p0) REVERT: C 21 MET cc_start: 0.8689 (mmm) cc_final: 0.8428 (mmm) REVERT: C 118 LEU cc_start: 0.9354 (tp) cc_final: 0.9024 (pp) REVERT: C 285 MET cc_start: 0.8472 (mmm) cc_final: 0.8227 (mmm) REVERT: C 303 PHE cc_start: 0.8272 (t80) cc_final: 0.7967 (t80) REVERT: C 362 ASP cc_start: 0.8322 (t0) cc_final: 0.7748 (t0) REVERT: C 561 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8399 (pp) REVERT: C 715 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.7962 (pp) REVERT: C 830 MET cc_start: 0.8268 (ttm) cc_final: 0.7909 (mmm) REVERT: C 1053 MET cc_start: 0.8631 (mtp) cc_final: 0.8270 (mtp) REVERT: G 2015 ASP cc_start: 0.8908 (t70) cc_final: 0.8662 (t0) REVERT: G 2016 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8561 (tptt) REVERT: G 2046 ASP cc_start: 0.8745 (t70) cc_final: 0.8483 (t70) REVERT: G 2077 ARG cc_start: 0.8891 (mmt90) cc_final: 0.8507 (mmm160) REVERT: G 2120 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8442 (mptt) REVERT: G 2163 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7389 (mmm160) REVERT: D 30 MET cc_start: 0.8646 (mmm) cc_final: 0.8370 (mmm) REVERT: D 118 LEU cc_start: 0.9268 (tp) cc_final: 0.8906 (pp) REVERT: D 153 ASP cc_start: 0.8587 (t0) cc_final: 0.7929 (t0) REVERT: D 157 ASN cc_start: 0.9183 (m-40) cc_final: 0.8335 (m110) REVERT: D 162 LEU cc_start: 0.9351 (mm) cc_final: 0.8964 (pp) REVERT: D 182 ASN cc_start: 0.7755 (t160) cc_final: 0.7122 (t0) REVERT: D 285 MET cc_start: 0.8496 (mmm) cc_final: 0.8253 (mmm) REVERT: D 303 PHE cc_start: 0.8259 (t80) cc_final: 0.7942 (t80) REVERT: D 362 ASP cc_start: 0.8345 (t0) cc_final: 0.7869 (t0) REVERT: D 561 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8473 (pp) REVERT: D 715 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8256 (pp) REVERT: D 900 ASP cc_start: 0.8568 (p0) cc_final: 0.8289 (p0) REVERT: H 2015 ASP cc_start: 0.8896 (t70) cc_final: 0.8591 (t0) REVERT: H 2016 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8354 (tptt) REVERT: H 2046 ASP cc_start: 0.8701 (t70) cc_final: 0.8487 (t70) REVERT: H 2077 ARG cc_start: 0.8891 (mmt90) cc_final: 0.8531 (mmm160) REVERT: H 2115 TYR cc_start: 0.9302 (t80) cc_final: 0.8875 (t80) REVERT: H 2141 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8008 (tt) REVERT: H 2163 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7799 (mtp180) REVERT: H 2166 ASP cc_start: 0.8022 (p0) cc_final: 0.7516 (p0) outliers start: 113 outliers final: 53 residues processed: 536 average time/residue: 0.2132 time to fit residues: 192.6554 Evaluate side-chains 462 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 399 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain F residue 2188 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain G residue 2188 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 927 THR Chi-restraints excluded: chain H residue 2141 ILE Chi-restraints excluded: chain H residue 2188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 199 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 355 optimal weight: 0.7980 chunk 271 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 428 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 182 ASN A 216 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN B 182 ASN B 216 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN B 907 GLN C 143 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN C 745 ASN D 143 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN D 932 ASN H2061 GLN H2134 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.085887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.066714 restraints weight = 117239.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.069013 restraints weight = 55160.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070564 restraints weight = 34353.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071571 restraints weight = 25420.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072162 restraints weight = 20994.316| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37332 Z= 0.131 Angle : 0.573 10.778 50560 Z= 0.286 Chirality : 0.042 0.343 5756 Planarity : 0.004 0.046 6240 Dihedral : 11.272 153.131 5978 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.41 % Allowed : 11.89 % Favored : 85.70 % 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: -0.66 (0.13), residues: 4408 helix: 0.70 (0.12), residues: 2020 sheet: -1.53 (0.20), residues: 608 loop : -1.30 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 213 TYR 0.016 0.001 TYR G2008 PHE 0.022 0.001 PHE E2033 TRP 0.036 0.001 TRP E2176 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00297 (37300) covalent geometry : angle 0.56636 (50504) SS BOND : bond 0.00165 ( 16) SS BOND : angle 0.50768 ( 32) hydrogen bonds : bond 0.03274 ( 1448) hydrogen bonds : angle 4.46123 ( 4056) Misc. bond : bond 0.00048 ( 8) link_NAG-ASN : bond 0.01378 ( 8) link_NAG-ASN : angle 4.01604 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 446 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8722 (mmm) cc_final: 0.8302 (mmm) REVERT: A 118 LEU cc_start: 0.9313 (tp) cc_final: 0.9046 (pp) REVERT: A 153 ASP cc_start: 0.8554 (t0) cc_final: 0.8157 (t70) REVERT: A 162 LEU cc_start: 0.9412 (mm) cc_final: 0.9076 (pp) REVERT: A 182 ASN cc_start: 0.7310 (t160) cc_final: 0.7034 (t0) REVERT: A 213 ARG cc_start: 0.9114 (ttt90) cc_final: 0.8859 (tpp80) REVERT: A 285 MET cc_start: 0.8526 (mmm) cc_final: 0.7976 (mmm) REVERT: A 303 PHE cc_start: 0.8167 (t80) cc_final: 0.7946 (t80) REVERT: A 307 PHE cc_start: 0.8119 (t80) cc_final: 0.7742 (t80) REVERT: A 362 ASP cc_start: 0.8353 (t0) cc_final: 0.7782 (t0) REVERT: A 561 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8376 (pp) REVERT: A 715 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.7871 (pp) REVERT: A 878 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8916 (mp) REVERT: A 900 ASP cc_start: 0.8631 (p0) cc_final: 0.8344 (p0) REVERT: A 1053 MET cc_start: 0.8614 (mtp) cc_final: 0.8380 (mtm) REVERT: E 2015 ASP cc_start: 0.8912 (t70) cc_final: 0.8680 (t0) REVERT: E 2016 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8513 (tptt) REVERT: E 2046 ASP cc_start: 0.8772 (t70) cc_final: 0.8510 (t70) REVERT: E 2077 ARG cc_start: 0.8933 (mmt90) cc_final: 0.8491 (mmm160) REVERT: E 2120 LYS cc_start: 0.8763 (mmtm) cc_final: 0.8464 (mptt) REVERT: E 2163 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7297 (mmm160) REVERT: B 118 LEU cc_start: 0.9251 (tp) cc_final: 0.8996 (pp) REVERT: B 162 LEU cc_start: 0.9417 (mm) cc_final: 0.8956 (pp) REVERT: B 214 LEU cc_start: 0.9545 (mt) cc_final: 0.9048 (mt) REVERT: B 362 ASP cc_start: 0.8386 (t0) cc_final: 0.7926 (t0) REVERT: B 601 ASP cc_start: 0.7472 (p0) cc_final: 0.6690 (p0) REVERT: B 715 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.7910 (pp) REVERT: B 900 ASP cc_start: 0.8734 (p0) cc_final: 0.8499 (p0) REVERT: F 2015 ASP cc_start: 0.8927 (t70) cc_final: 0.8621 (t0) REVERT: F 2016 LYS cc_start: 0.9020 (ttmt) cc_final: 0.8364 (tptt) REVERT: F 2046 ASP cc_start: 0.8736 (t70) cc_final: 0.8460 (t70) REVERT: F 2077 ARG cc_start: 0.8923 (mmt90) cc_final: 0.8483 (mmm160) REVERT: F 2120 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8462 (mptt) REVERT: F 2163 ARG cc_start: 0.8193 (mtt-85) cc_final: 0.7325 (mmm160) REVERT: C 21 MET cc_start: 0.8722 (mmm) cc_final: 0.8301 (mmm) REVERT: C 118 LEU cc_start: 0.9309 (tp) cc_final: 0.9042 (pp) REVERT: C 153 ASP cc_start: 0.8564 (t0) cc_final: 0.8169 (t70) REVERT: C 162 LEU cc_start: 0.9409 (mm) cc_final: 0.9071 (pp) REVERT: C 285 MET cc_start: 0.8523 (mmm) cc_final: 0.7984 (mmm) REVERT: C 303 PHE cc_start: 0.8159 (t80) cc_final: 0.7946 (t80) REVERT: C 307 PHE cc_start: 0.8103 (t80) cc_final: 0.7730 (t80) REVERT: C 362 ASP cc_start: 0.8382 (t0) cc_final: 0.7795 (t0) REVERT: C 561 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8396 (pp) REVERT: C 715 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.7959 (pp) REVERT: C 739 MET cc_start: 0.8441 (mtp) cc_final: 0.8027 (mtp) REVERT: G 2015 ASP cc_start: 0.8927 (t70) cc_final: 0.8673 (t0) REVERT: G 2016 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8529 (tptt) REVERT: G 2046 ASP cc_start: 0.8763 (t70) cc_final: 0.8497 (t70) REVERT: G 2077 ARG cc_start: 0.8901 (mmt90) cc_final: 0.8462 (mmm160) REVERT: G 2163 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7224 (mmm160) REVERT: D 30 MET cc_start: 0.8582 (mmm) cc_final: 0.8326 (mmm) REVERT: D 118 LEU cc_start: 0.9223 (tp) cc_final: 0.8871 (pp) REVERT: D 153 ASP cc_start: 0.8675 (t0) cc_final: 0.7999 (t0) REVERT: D 157 ASN cc_start: 0.9224 (m-40) cc_final: 0.8439 (m110) REVERT: D 162 LEU cc_start: 0.9402 (mm) cc_final: 0.8933 (pp) REVERT: D 285 MET cc_start: 0.8516 (mmm) cc_final: 0.7955 (mmm) REVERT: D 303 PHE cc_start: 0.8154 (t80) cc_final: 0.7925 (t80) REVERT: D 306 PHE cc_start: 0.8632 (t80) cc_final: 0.8428 (t80) REVERT: D 307 PHE cc_start: 0.8122 (t80) cc_final: 0.7708 (t80) REVERT: D 362 ASP cc_start: 0.8374 (t0) cc_final: 0.7901 (t0) REVERT: D 442 MET cc_start: 0.8910 (tpp) cc_final: 0.8630 (tpp) REVERT: D 601 ASP cc_start: 0.7529 (p0) cc_final: 0.6759 (p0) REVERT: D 715 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8053 (pp) REVERT: D 878 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8881 (mp) REVERT: D 900 ASP cc_start: 0.8664 (p0) cc_final: 0.8408 (p0) REVERT: H 2015 ASP cc_start: 0.8901 (t70) cc_final: 0.8579 (t0) REVERT: H 2016 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8375 (tptt) REVERT: H 2077 ARG cc_start: 0.8906 (mmt90) cc_final: 0.8472 (mmm160) REVERT: H 2141 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8007 (tt) REVERT: H 2163 ARG cc_start: 0.8191 (mtt-85) cc_final: 0.7796 (mtp180) outliers start: 95 outliers final: 48 residues processed: 516 average time/residue: 0.2132 time to fit residues: 187.1495 Evaluate side-chains 462 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 405 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2187 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2141 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 116 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 424 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 347 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN C 745 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN H2061 GLN H2134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.086724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.067839 restraints weight = 117269.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070177 restraints weight = 54596.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071721 restraints weight = 33932.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.072703 restraints weight = 25048.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073341 restraints weight = 20694.628| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 37332 Z= 0.110 Angle : 0.551 10.256 50560 Z= 0.276 Chirality : 0.041 0.327 5756 Planarity : 0.003 0.047 6240 Dihedral : 10.266 129.210 5978 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.26 % Allowed : 12.80 % Favored : 84.93 % 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: -0.49 (0.13), residues: 4408 helix: 0.90 (0.12), residues: 2032 sheet: -1.64 (0.20), residues: 628 loop : -1.21 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 786 TYR 0.010 0.001 TYR G2008 PHE 0.020 0.001 PHE G2033 TRP 0.026 0.001 TRP E2176 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00247 (37300) covalent geometry : angle 0.54560 (50504) SS BOND : bond 0.00134 ( 16) SS BOND : angle 0.42128 ( 32) hydrogen bonds : bond 0.03069 ( 1448) hydrogen bonds : angle 4.30329 ( 4056) Misc. bond : bond 0.00044 ( 8) link_NAG-ASN : bond 0.01356 ( 8) link_NAG-ASN : angle 3.68226 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 450 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9296 (tp) cc_final: 0.9045 (pp) REVERT: A 153 ASP cc_start: 0.8538 (t0) cc_final: 0.8072 (t0) REVERT: A 162 LEU cc_start: 0.9405 (mm) cc_final: 0.9077 (pp) REVERT: A 182 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7273 (t0) REVERT: A 213 ARG cc_start: 0.9107 (ttt90) cc_final: 0.8901 (tpp80) REVERT: A 273 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8702 (p) REVERT: A 285 MET cc_start: 0.8524 (mmm) cc_final: 0.7999 (mmm) REVERT: A 303 PHE cc_start: 0.8115 (t80) cc_final: 0.7822 (t80) REVERT: A 307 PHE cc_start: 0.8070 (t80) cc_final: 0.7766 (t80) REVERT: A 362 ASP cc_start: 0.8380 (t0) cc_final: 0.7815 (t0) REVERT: A 561 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8606 (pp) REVERT: A 715 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7849 (pp) REVERT: A 739 MET cc_start: 0.8349 (mtp) cc_final: 0.8015 (mtp) REVERT: A 900 ASP cc_start: 0.8613 (p0) cc_final: 0.8316 (p0) REVERT: E 2015 ASP cc_start: 0.8891 (t70) cc_final: 0.8667 (t0) REVERT: E 2016 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8504 (tptt) REVERT: E 2046 ASP cc_start: 0.8732 (t70) cc_final: 0.8421 (t70) REVERT: E 2077 ARG cc_start: 0.8919 (mmt90) cc_final: 0.8498 (mmm160) REVERT: E 2131 MET cc_start: 0.8529 (mmm) cc_final: 0.8324 (mmp) REVERT: E 2163 ARG cc_start: 0.8156 (mtt-85) cc_final: 0.7255 (mmm160) REVERT: B 118 LEU cc_start: 0.9222 (tp) cc_final: 0.9013 (pp) REVERT: B 153 ASP cc_start: 0.8631 (t0) cc_final: 0.7884 (t0) REVERT: B 157 ASN cc_start: 0.9427 (m-40) cc_final: 0.8655 (m110) REVERT: B 162 LEU cc_start: 0.9413 (mm) cc_final: 0.9141 (mm) REVERT: B 273 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8665 (p) REVERT: B 306 PHE cc_start: 0.8560 (t80) cc_final: 0.8335 (t80) REVERT: B 362 ASP cc_start: 0.8377 (t0) cc_final: 0.7921 (t0) REVERT: B 715 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.7905 (pp) REVERT: B 739 MET cc_start: 0.8337 (mtp) cc_final: 0.8119 (mtp) REVERT: B 900 ASP cc_start: 0.8581 (p0) cc_final: 0.8275 (p0) REVERT: F 2015 ASP cc_start: 0.8979 (t70) cc_final: 0.8638 (t0) REVERT: F 2016 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8499 (tptt) REVERT: F 2023 PHE cc_start: 0.9125 (t80) cc_final: 0.8844 (t80) REVERT: F 2077 ARG cc_start: 0.8894 (mmt90) cc_final: 0.8510 (mmm160) REVERT: F 2163 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7894 (mtp180) REVERT: C 118 LEU cc_start: 0.9291 (tp) cc_final: 0.9041 (pp) REVERT: C 153 ASP cc_start: 0.8541 (t0) cc_final: 0.8077 (t0) REVERT: C 162 LEU cc_start: 0.9401 (mm) cc_final: 0.9075 (pp) REVERT: C 273 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8646 (p) REVERT: C 285 MET cc_start: 0.8537 (mmm) cc_final: 0.8023 (mmm) REVERT: C 303 PHE cc_start: 0.8115 (t80) cc_final: 0.7822 (t80) REVERT: C 307 PHE cc_start: 0.8063 (t80) cc_final: 0.7765 (t80) REVERT: C 362 ASP cc_start: 0.8379 (t0) cc_final: 0.7811 (t0) REVERT: C 561 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8664 (pp) REVERT: C 715 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.7789 (pp) REVERT: C 739 MET cc_start: 0.8418 (mtp) cc_final: 0.8040 (mtp) REVERT: C 900 ASP cc_start: 0.8605 (p0) cc_final: 0.8331 (p0) REVERT: G 2015 ASP cc_start: 0.8921 (t70) cc_final: 0.8665 (t0) REVERT: G 2016 LYS cc_start: 0.9085 (ttmt) cc_final: 0.8525 (tptt) REVERT: G 2046 ASP cc_start: 0.8689 (t70) cc_final: 0.8141 (t0) REVERT: G 2077 ARG cc_start: 0.8895 (mmt90) cc_final: 0.8462 (mmm160) REVERT: G 2131 MET cc_start: 0.8523 (mmm) cc_final: 0.8322 (mmp) REVERT: G 2163 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7187 (mmm160) REVERT: D 118 LEU cc_start: 0.9225 (tp) cc_final: 0.8964 (pp) REVERT: D 153 ASP cc_start: 0.8711 (t0) cc_final: 0.8088 (t0) REVERT: D 157 ASN cc_start: 0.9100 (m-40) cc_final: 0.8357 (m110) REVERT: D 159 PHE cc_start: 0.9064 (t80) cc_final: 0.8658 (t80) REVERT: D 162 LEU cc_start: 0.9404 (mm) cc_final: 0.9143 (mm) REVERT: D 273 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8738 (p) REVERT: D 276 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8334 (mm-30) REVERT: D 285 MET cc_start: 0.8517 (mmm) cc_final: 0.8018 (mmm) REVERT: D 303 PHE cc_start: 0.8060 (t80) cc_final: 0.7718 (t80) REVERT: D 306 PHE cc_start: 0.8646 (t80) cc_final: 0.8430 (t80) REVERT: D 307 PHE cc_start: 0.8046 (t80) cc_final: 0.7809 (t80) REVERT: D 386 GLU cc_start: 0.7924 (tp30) cc_final: 0.7672 (tp30) REVERT: D 442 MET cc_start: 0.8983 (tpp) cc_final: 0.8750 (tpp) REVERT: D 627 LYS cc_start: 0.7756 (tptt) cc_final: 0.7520 (tppt) REVERT: D 715 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.7984 (pp) REVERT: D 739 MET cc_start: 0.8297 (mtp) cc_final: 0.7995 (mtp) REVERT: D 878 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8869 (mp) REVERT: D 900 ASP cc_start: 0.8678 (p0) cc_final: 0.8439 (p0) REVERT: H 2015 ASP cc_start: 0.8961 (t70) cc_final: 0.8622 (t0) REVERT: H 2016 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8393 (tptt) REVERT: H 2023 PHE cc_start: 0.9120 (t80) cc_final: 0.8866 (t80) REVERT: H 2046 ASP cc_start: 0.8553 (t70) cc_final: 0.8172 (t0) REVERT: H 2077 ARG cc_start: 0.8889 (mmt90) cc_final: 0.8454 (mmm160) REVERT: H 2131 MET cc_start: 0.8662 (mmp) cc_final: 0.8143 (mmp) REVERT: H 2141 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8102 (tt) outliers start: 89 outliers final: 53 residues processed: 511 average time/residue: 0.2103 time to fit residues: 183.1576 Evaluate side-chains 480 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 414 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2168 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2187 ILE Chi-restraints excluded: chain G residue 2188 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2141 ILE Chi-restraints excluded: chain H residue 2157 ASP Chi-restraints excluded: chain H residue 2168 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 426 optimal weight: 3.9990 chunk 315 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 414 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 147 optimal weight: 0.0570 chunk 48 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.085766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.066632 restraints weight = 117668.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068949 restraints weight = 54752.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070475 restraints weight = 34179.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071465 restraints weight = 25346.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.072025 restraints weight = 20980.932| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37332 Z= 0.145 Angle : 0.576 10.611 50560 Z= 0.286 Chirality : 0.041 0.317 5756 Planarity : 0.003 0.046 6240 Dihedral : 9.870 120.428 5978 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.64 % Allowed : 13.31 % Favored : 84.04 % 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: -0.37 (0.13), residues: 4408 helix: 1.00 (0.12), residues: 2036 sheet: -1.63 (0.20), residues: 632 loop : -1.13 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 976 TYR 0.007 0.001 TYR G2008 PHE 0.023 0.001 PHE G2033 TRP 0.024 0.001 TRP E2176 HIS 0.006 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00329 (37300) covalent geometry : angle 0.57066 (50504) SS BOND : bond 0.00142 ( 16) SS BOND : angle 0.41220 ( 32) hydrogen bonds : bond 0.03126 ( 1448) hydrogen bonds : angle 4.30917 ( 4056) Misc. bond : bond 0.00051 ( 8) link_NAG-ASN : bond 0.01309 ( 8) link_NAG-ASN : angle 3.59195 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 418 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8572 (t0) cc_final: 0.8081 (t0) REVERT: A 162 LEU cc_start: 0.9409 (mm) cc_final: 0.9080 (pp) REVERT: A 213 ARG cc_start: 0.9117 (ttt90) cc_final: 0.8913 (tpp80) REVERT: A 273 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8672 (p) REVERT: A 285 MET cc_start: 0.8542 (mmm) cc_final: 0.7963 (mmm) REVERT: A 306 PHE cc_start: 0.8623 (t80) cc_final: 0.8414 (t80) REVERT: A 307 PHE cc_start: 0.8158 (t80) cc_final: 0.7656 (t80) REVERT: A 362 ASP cc_start: 0.8406 (t0) cc_final: 0.7861 (t0) REVERT: A 561 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8584 (pp) REVERT: A 627 LYS cc_start: 0.7379 (tptt) cc_final: 0.7033 (tppt) REVERT: A 715 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.7955 (pp) REVERT: A 878 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8916 (mp) REVERT: E 2015 ASP cc_start: 0.8939 (t70) cc_final: 0.8706 (t0) REVERT: E 2016 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8576 (tptt) REVERT: E 2046 ASP cc_start: 0.8747 (t70) cc_final: 0.8398 (t0) REVERT: E 2077 ARG cc_start: 0.8971 (mmt90) cc_final: 0.8478 (mmm160) REVERT: E 2131 MET cc_start: 0.8531 (mmm) cc_final: 0.8328 (mmp) REVERT: E 2163 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7815 (mtp180) REVERT: B 118 LEU cc_start: 0.9203 (tp) cc_final: 0.8968 (pp) REVERT: B 153 ASP cc_start: 0.8695 (t0) cc_final: 0.8315 (t70) REVERT: B 162 LEU cc_start: 0.9435 (mm) cc_final: 0.9167 (mm) REVERT: B 164 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8094 (t80) REVERT: B 273 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8670 (p) REVERT: B 306 PHE cc_start: 0.8696 (t80) cc_final: 0.8462 (t80) REVERT: B 362 ASP cc_start: 0.8414 (t0) cc_final: 0.7963 (t0) REVERT: B 428 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8900 (mmtm) REVERT: B 575 ARG cc_start: 0.6542 (mpp-170) cc_final: 0.6203 (mpp-170) REVERT: B 715 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7879 (pp) REVERT: F 2015 ASP cc_start: 0.8988 (t70) cc_final: 0.8640 (t0) REVERT: F 2016 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8500 (tptt) REVERT: F 2023 PHE cc_start: 0.9097 (t80) cc_final: 0.8875 (t80) REVERT: F 2024 LEU cc_start: 0.8985 (mp) cc_final: 0.8762 (tp) REVERT: F 2046 ASP cc_start: 0.8530 (t70) cc_final: 0.8146 (t0) REVERT: F 2077 ARG cc_start: 0.8913 (mmt90) cc_final: 0.8461 (mmm160) REVERT: F 2163 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7757 (mtp180) REVERT: C 153 ASP cc_start: 0.8584 (t0) cc_final: 0.8095 (t0) REVERT: C 162 LEU cc_start: 0.9423 (mm) cc_final: 0.9100 (pp) REVERT: C 273 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8641 (p) REVERT: C 285 MET cc_start: 0.8587 (mmm) cc_final: 0.8030 (mmm) REVERT: C 306 PHE cc_start: 0.8619 (t80) cc_final: 0.8406 (t80) REVERT: C 307 PHE cc_start: 0.8123 (t80) cc_final: 0.7617 (t80) REVERT: C 362 ASP cc_start: 0.8407 (t0) cc_final: 0.7861 (t0) REVERT: C 561 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8591 (pp) REVERT: C 715 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.7910 (pp) REVERT: C 878 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8904 (mp) REVERT: G 2015 ASP cc_start: 0.9000 (t70) cc_final: 0.8755 (t0) REVERT: G 2016 LYS cc_start: 0.9097 (ttmt) cc_final: 0.8524 (tptt) REVERT: G 2046 ASP cc_start: 0.8714 (t70) cc_final: 0.8497 (t70) REVERT: G 2077 ARG cc_start: 0.8963 (mmt90) cc_final: 0.8478 (mmm160) REVERT: G 2131 MET cc_start: 0.8534 (mmm) cc_final: 0.8315 (mmp) REVERT: G 2163 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7694 (mtp180) REVERT: D 118 LEU cc_start: 0.9218 (tp) cc_final: 0.8866 (pp) REVERT: D 162 LEU cc_start: 0.9418 (mm) cc_final: 0.9158 (mm) REVERT: D 273 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8705 (p) REVERT: D 276 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8355 (mm-30) REVERT: D 285 MET cc_start: 0.8545 (mmm) cc_final: 0.7955 (mmm) REVERT: D 306 PHE cc_start: 0.8692 (t80) cc_final: 0.8474 (t80) REVERT: D 307 PHE cc_start: 0.8145 (t80) cc_final: 0.7682 (t80) REVERT: D 442 MET cc_start: 0.9237 (tpp) cc_final: 0.8846 (tpp) REVERT: D 715 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.7958 (pp) REVERT: D 878 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8899 (mp) REVERT: D 900 ASP cc_start: 0.8635 (p0) cc_final: 0.8396 (p0) REVERT: H 2015 ASP cc_start: 0.8936 (t70) cc_final: 0.8633 (t0) REVERT: H 2016 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8398 (tptt) REVERT: H 2023 PHE cc_start: 0.9105 (t80) cc_final: 0.8884 (t80) REVERT: H 2046 ASP cc_start: 0.8550 (t70) cc_final: 0.8320 (t0) REVERT: H 2077 ARG cc_start: 0.8918 (mmt90) cc_final: 0.8465 (mmm160) REVERT: H 2141 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8034 (tt) outliers start: 104 outliers final: 57 residues processed: 492 average time/residue: 0.2123 time to fit residues: 177.2951 Evaluate side-chains 481 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 408 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2204 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2168 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2187 ILE Chi-restraints excluded: chain G residue 2188 VAL Chi-restraints excluded: chain G residue 2204 MET Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2141 ILE Chi-restraints excluded: chain H residue 2168 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 311 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 chunk 434 optimal weight: 0.0470 chunk 248 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 372 optimal weight: 0.9980 chunk 368 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.068177 restraints weight = 117278.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070526 restraints weight = 54569.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072046 restraints weight = 33909.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.073059 restraints weight = 25113.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073631 restraints weight = 20717.027| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 37332 Z= 0.103 Angle : 0.556 9.867 50560 Z= 0.275 Chirality : 0.041 0.303 5756 Planarity : 0.003 0.048 6240 Dihedral : 9.310 124.552 5978 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.13 % Allowed : 13.69 % 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: -0.25 (0.13), residues: 4408 helix: 1.09 (0.12), residues: 2020 sheet: -1.37 (0.21), residues: 604 loop : -1.14 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 213 TYR 0.010 0.001 TYR A 48 PHE 0.025 0.001 PHE F2033 TRP 0.023 0.001 TRP G2176 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00230 (37300) covalent geometry : angle 0.55144 (50504) SS BOND : bond 0.00109 ( 16) SS BOND : angle 0.35414 ( 32) hydrogen bonds : bond 0.02993 ( 1448) hydrogen bonds : angle 4.20192 ( 4056) Misc. bond : bond 0.00047 ( 8) link_NAG-ASN : bond 0.01332 ( 8) link_NAG-ASN : angle 3.40232 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 464 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9296 (tp) cc_final: 0.8925 (pp) REVERT: A 153 ASP cc_start: 0.8636 (t0) cc_final: 0.8137 (t0) REVERT: A 162 LEU cc_start: 0.9381 (mm) cc_final: 0.9070 (pp) REVERT: A 273 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 276 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8410 (mm-30) REVERT: A 285 MET cc_start: 0.8604 (mmm) cc_final: 0.7969 (mmm) REVERT: A 303 PHE cc_start: 0.8235 (t80) cc_final: 0.7944 (t80) REVERT: A 307 PHE cc_start: 0.8095 (t80) cc_final: 0.7660 (t80) REVERT: A 362 ASP cc_start: 0.8378 (t0) cc_final: 0.7887 (t0) REVERT: A 459 GLN cc_start: 0.9098 (mt0) cc_final: 0.8889 (mt0) REVERT: A 601 ASP cc_start: 0.7460 (t0) cc_final: 0.7033 (t0) REVERT: A 627 LYS cc_start: 0.7373 (tptt) cc_final: 0.7022 (tppt) REVERT: A 715 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.7931 (pp) REVERT: A 878 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8896 (mp) REVERT: E 2015 ASP cc_start: 0.8910 (t70) cc_final: 0.8666 (t0) REVERT: E 2016 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8522 (tptt) REVERT: E 2046 ASP cc_start: 0.8717 (t70) cc_final: 0.8371 (t0) REVERT: E 2077 ARG cc_start: 0.8948 (mmt90) cc_final: 0.8458 (mmm160) REVERT: E 2131 MET cc_start: 0.8500 (mmm) cc_final: 0.8294 (mmp) REVERT: E 2163 ARG cc_start: 0.7961 (mtt-85) cc_final: 0.7704 (mtp180) REVERT: B 159 PHE cc_start: 0.9052 (t80) cc_final: 0.8673 (t80) REVERT: B 162 LEU cc_start: 0.9434 (mm) cc_final: 0.9168 (mm) REVERT: B 273 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8575 (p) REVERT: B 362 ASP cc_start: 0.8409 (t0) cc_final: 0.8035 (t0) REVERT: B 575 ARG cc_start: 0.6313 (mpp-170) cc_final: 0.6067 (mpp-170) REVERT: B 715 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7836 (pp) REVERT: B 900 ASP cc_start: 0.8578 (p0) cc_final: 0.8347 (p0) REVERT: F 2015 ASP cc_start: 0.8823 (t70) cc_final: 0.8501 (t0) REVERT: F 2016 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8456 (tptt) REVERT: F 2046 ASP cc_start: 0.8529 (t70) cc_final: 0.8176 (t0) REVERT: F 2077 ARG cc_start: 0.8896 (mmt90) cc_final: 0.8427 (mmm160) REVERT: F 2131 MET cc_start: 0.8422 (mmp) cc_final: 0.7876 (mmp) REVERT: C 118 LEU cc_start: 0.9293 (tp) cc_final: 0.8926 (pp) REVERT: C 153 ASP cc_start: 0.8636 (t0) cc_final: 0.8140 (t0) REVERT: C 162 LEU cc_start: 0.9378 (mm) cc_final: 0.9066 (pp) REVERT: C 273 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8628 (p) REVERT: C 276 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8481 (mm-30) REVERT: C 285 MET cc_start: 0.8645 (mmm) cc_final: 0.8359 (mmm) REVERT: C 303 PHE cc_start: 0.8233 (t80) cc_final: 0.7936 (t80) REVERT: C 362 ASP cc_start: 0.8372 (t0) cc_final: 0.7884 (t0) REVERT: C 442 MET cc_start: 0.8839 (tpp) cc_final: 0.8630 (tpp) REVERT: C 459 GLN cc_start: 0.8958 (mt0) cc_final: 0.8740 (mt0) REVERT: C 601 ASP cc_start: 0.7463 (t0) cc_final: 0.7027 (t0) REVERT: C 715 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.7881 (pp) REVERT: G 2015 ASP cc_start: 0.8971 (t70) cc_final: 0.8722 (t0) REVERT: G 2016 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8458 (tptt) REVERT: G 2046 ASP cc_start: 0.8671 (t70) cc_final: 0.8461 (t70) REVERT: G 2077 ARG cc_start: 0.8938 (mmt90) cc_final: 0.8453 (mmm160) REVERT: G 2131 MET cc_start: 0.8495 (mmm) cc_final: 0.8291 (mmp) REVERT: G 2163 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7608 (mtp180) REVERT: D 118 LEU cc_start: 0.9196 (tp) cc_final: 0.8937 (pp) REVERT: D 153 ASP cc_start: 0.8738 (t0) cc_final: 0.8049 (t0) REVERT: D 157 ASN cc_start: 0.9405 (m-40) cc_final: 0.8792 (m110) REVERT: D 159 PHE cc_start: 0.8974 (t80) cc_final: 0.8578 (t80) REVERT: D 221 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9273 (tt) REVERT: D 273 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8745 (p) REVERT: D 285 MET cc_start: 0.8552 (mmm) cc_final: 0.8043 (mmm) REVERT: D 303 PHE cc_start: 0.8273 (t80) cc_final: 0.7959 (t80) REVERT: D 307 PHE cc_start: 0.8023 (t80) cc_final: 0.7691 (t80) REVERT: D 442 MET cc_start: 0.9220 (tpp) cc_final: 0.8724 (tpp) REVERT: D 715 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8161 (pp) REVERT: D 878 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8867 (mp) REVERT: D 900 ASP cc_start: 0.8642 (p0) cc_final: 0.8401 (p0) REVERT: H 2015 ASP cc_start: 0.8778 (t70) cc_final: 0.8457 (t0) REVERT: H 2016 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8370 (tptt) REVERT: H 2023 PHE cc_start: 0.8998 (t80) cc_final: 0.8706 (t80) REVERT: H 2024 LEU cc_start: 0.8988 (mp) cc_final: 0.8663 (tp) REVERT: H 2046 ASP cc_start: 0.8544 (t70) cc_final: 0.8310 (t0) REVERT: H 2077 ARG cc_start: 0.8900 (mmt90) cc_final: 0.8454 (mmm160) REVERT: H 2141 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8089 (tt) outliers start: 84 outliers final: 45 residues processed: 520 average time/residue: 0.2132 time to fit residues: 188.1448 Evaluate side-chains 479 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 422 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2168 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2187 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2141 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 26 optimal weight: 6.9990 chunk 166 optimal weight: 0.4980 chunk 262 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 421 optimal weight: 8.9990 chunk 340 optimal weight: 0.8980 chunk 263 optimal weight: 0.9980 chunk 211 optimal weight: 9.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.085633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066444 restraints weight = 118246.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068755 restraints weight = 55603.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.070262 restraints weight = 34769.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071262 restraints weight = 25887.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071832 restraints weight = 21461.944| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37332 Z= 0.152 Angle : 0.601 10.165 50560 Z= 0.300 Chirality : 0.041 0.294 5756 Planarity : 0.003 0.050 6240 Dihedral : 9.061 123.881 5978 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.31 % Allowed : 14.13 % Favored : 83.56 % 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: -0.19 (0.13), residues: 4408 helix: 1.14 (0.12), residues: 2020 sheet: -1.32 (0.21), residues: 592 loop : -1.11 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 213 TYR 0.009 0.001 TYR D 163 PHE 0.037 0.001 PHE G2023 TRP 0.024 0.001 TRP G2176 HIS 0.006 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00344 (37300) covalent geometry : angle 0.59640 (50504) SS BOND : bond 0.00160 ( 16) SS BOND : angle 0.45486 ( 32) hydrogen bonds : bond 0.03159 ( 1448) hydrogen bonds : angle 4.24102 ( 4056) Misc. bond : bond 0.00056 ( 8) link_NAG-ASN : bond 0.01270 ( 8) link_NAG-ASN : angle 3.38491 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 415 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9287 (tp) cc_final: 0.8908 (pp) REVERT: A 153 ASP cc_start: 0.8656 (t0) cc_final: 0.8132 (t0) REVERT: A 162 LEU cc_start: 0.9428 (mm) cc_final: 0.9110 (pp) REVERT: A 273 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8697 (p) REVERT: A 285 MET cc_start: 0.8570 (mmm) cc_final: 0.8268 (mmm) REVERT: A 303 PHE cc_start: 0.8291 (t80) cc_final: 0.7995 (t80) REVERT: A 362 ASP cc_start: 0.8389 (t0) cc_final: 0.7928 (t0) REVERT: A 627 LYS cc_start: 0.7449 (tptt) cc_final: 0.7055 (tppt) REVERT: A 715 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.7887 (pp) REVERT: A 739 MET cc_start: 0.8422 (mtm) cc_final: 0.8062 (mtp) REVERT: A 878 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8947 (mp) REVERT: E 2015 ASP cc_start: 0.8970 (t70) cc_final: 0.8731 (t0) REVERT: E 2016 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8448 (tptt) REVERT: E 2046 ASP cc_start: 0.8753 (t70) cc_final: 0.8339 (t0) REVERT: E 2077 ARG cc_start: 0.8971 (mmt90) cc_final: 0.8405 (mmm160) REVERT: E 2163 ARG cc_start: 0.7852 (mtt-85) cc_final: 0.7540 (mtp180) REVERT: B 157 ASN cc_start: 0.9482 (m-40) cc_final: 0.8698 (m110) REVERT: B 162 LEU cc_start: 0.9449 (mm) cc_final: 0.9189 (mm) REVERT: B 273 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8669 (p) REVERT: B 715 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7931 (pp) REVERT: B 739 MET cc_start: 0.8374 (mtm) cc_final: 0.8025 (mtp) REVERT: B 1009 MET cc_start: 0.7446 (ttm) cc_final: 0.7000 (tpp) REVERT: F 2015 ASP cc_start: 0.8826 (t70) cc_final: 0.8496 (t0) REVERT: F 2016 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8403 (tptt) REVERT: F 2046 ASP cc_start: 0.8478 (t70) cc_final: 0.8257 (t0) REVERT: F 2077 ARG cc_start: 0.8928 (mmt90) cc_final: 0.8427 (mmm160) REVERT: C 48 TYR cc_start: 0.8626 (m-80) cc_final: 0.8338 (m-10) REVERT: C 118 LEU cc_start: 0.9289 (tp) cc_final: 0.8912 (pp) REVERT: C 153 ASP cc_start: 0.8651 (t0) cc_final: 0.8133 (t0) REVERT: C 162 LEU cc_start: 0.9424 (mm) cc_final: 0.9106 (pp) REVERT: C 273 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8647 (p) REVERT: C 276 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8490 (mm-30) REVERT: C 285 MET cc_start: 0.8611 (mmm) cc_final: 0.8326 (mmm) REVERT: C 303 PHE cc_start: 0.8287 (t80) cc_final: 0.7992 (t80) REVERT: C 459 GLN cc_start: 0.9070 (mt0) cc_final: 0.8804 (mt0) REVERT: C 575 ARG cc_start: 0.6325 (mpp-170) cc_final: 0.6050 (mpp-170) REVERT: C 627 LYS cc_start: 0.7450 (tptt) cc_final: 0.7050 (tppt) REVERT: C 715 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.7922 (pp) REVERT: C 739 MET cc_start: 0.8363 (mtm) cc_final: 0.8011 (mtp) REVERT: C 878 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8921 (mp) REVERT: G 2015 ASP cc_start: 0.8983 (t70) cc_final: 0.8725 (t0) REVERT: G 2016 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8424 (tptt) REVERT: G 2046 ASP cc_start: 0.8700 (t70) cc_final: 0.8466 (t70) REVERT: G 2077 ARG cc_start: 0.8961 (mmt90) cc_final: 0.8414 (mmm160) REVERT: G 2163 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.7571 (mtp180) REVERT: D 118 LEU cc_start: 0.9201 (tp) cc_final: 0.8929 (pp) REVERT: D 153 ASP cc_start: 0.8598 (t0) cc_final: 0.7925 (t0) REVERT: D 157 ASN cc_start: 0.9434 (m-40) cc_final: 0.8634 (m110) REVERT: D 221 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9251 (tt) REVERT: D 273 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8739 (p) REVERT: D 285 MET cc_start: 0.8569 (mmm) cc_final: 0.8276 (mmm) REVERT: D 303 PHE cc_start: 0.8298 (t80) cc_final: 0.8030 (t80) REVERT: D 442 MET cc_start: 0.9182 (tpp) cc_final: 0.8703 (tpp) REVERT: D 627 LYS cc_start: 0.7647 (tptt) cc_final: 0.7282 (tppt) REVERT: D 715 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.7911 (pp) REVERT: D 739 MET cc_start: 0.8366 (mtm) cc_final: 0.8024 (mtp) REVERT: D 878 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8917 (mp) REVERT: D 892 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7448 (t70) REVERT: H 2015 ASP cc_start: 0.8783 (t70) cc_final: 0.8456 (t0) REVERT: H 2016 LYS cc_start: 0.9094 (ttmt) cc_final: 0.8374 (tptt) REVERT: H 2023 PHE cc_start: 0.8983 (t80) cc_final: 0.8781 (t80) REVERT: H 2046 ASP cc_start: 0.8565 (t70) cc_final: 0.8328 (t0) REVERT: H 2077 ARG cc_start: 0.8931 (mmt90) cc_final: 0.8478 (mmm160) REVERT: H 2141 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8057 (tt) outliers start: 91 outliers final: 58 residues processed: 482 average time/residue: 0.2160 time to fit residues: 176.8357 Evaluate side-chains 471 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 399 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2168 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2187 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2141 ILE Chi-restraints excluded: chain H residue 2157 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 1 optimal weight: 6.9990 chunk 419 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 290 optimal weight: 6.9990 chunk 283 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.086407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.067343 restraints weight = 118144.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.069659 restraints weight = 55060.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071189 restraints weight = 34352.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072175 restraints weight = 25489.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072732 restraints weight = 21134.887| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37332 Z= 0.121 Angle : 0.588 9.360 50560 Z= 0.293 Chirality : 0.041 0.287 5756 Planarity : 0.003 0.050 6240 Dihedral : 8.720 126.518 5978 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.06 % Allowed : 14.25 % Favored : 83.69 % 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: -0.15 (0.13), residues: 4408 helix: 1.17 (0.12), residues: 2024 sheet: -1.38 (0.21), residues: 608 loop : -1.06 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 213 TYR 0.014 0.001 TYR F2008 PHE 0.028 0.001 PHE H2033 TRP 0.023 0.001 TRP G2176 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00276 (37300) covalent geometry : angle 0.58360 (50504) SS BOND : bond 0.00112 ( 16) SS BOND : angle 0.37034 ( 32) hydrogen bonds : bond 0.03073 ( 1448) hydrogen bonds : angle 4.20436 ( 4056) Misc. bond : bond 0.00050 ( 8) link_NAG-ASN : bond 0.01289 ( 8) link_NAG-ASN : angle 3.28720 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 426 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9298 (tp) cc_final: 0.8935 (pp) REVERT: A 153 ASP cc_start: 0.8644 (t0) cc_final: 0.8119 (t0) REVERT: A 162 LEU cc_start: 0.9419 (mm) cc_final: 0.9110 (pp) REVERT: A 273 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8646 (p) REVERT: A 285 MET cc_start: 0.8551 (mmm) cc_final: 0.8248 (mmm) REVERT: A 303 PHE cc_start: 0.8230 (t80) cc_final: 0.7919 (t80) REVERT: A 362 ASP cc_start: 0.8380 (t0) cc_final: 0.7917 (t0) REVERT: A 627 LYS cc_start: 0.7420 (tptt) cc_final: 0.7040 (tppt) REVERT: A 715 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.7870 (pp) REVERT: A 739 MET cc_start: 0.8311 (mtm) cc_final: 0.7961 (mtp) REVERT: A 878 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8927 (mp) REVERT: E 2015 ASP cc_start: 0.8948 (t70) cc_final: 0.8688 (t0) REVERT: E 2016 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8429 (tptt) REVERT: E 2046 ASP cc_start: 0.8749 (t70) cc_final: 0.8333 (t0) REVERT: E 2077 ARG cc_start: 0.8959 (mmt90) cc_final: 0.8408 (mmm160) REVERT: B 153 ASP cc_start: 0.8537 (t0) cc_final: 0.7779 (t0) REVERT: B 157 ASN cc_start: 0.9393 (m-40) cc_final: 0.8792 (m110) REVERT: B 162 LEU cc_start: 0.9444 (mm) cc_final: 0.9182 (mm) REVERT: B 187 PHE cc_start: 0.8491 (t80) cc_final: 0.8231 (t80) REVERT: B 273 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8572 (p) REVERT: B 715 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8104 (pp) REVERT: B 739 MET cc_start: 0.8305 (mtm) cc_final: 0.7938 (mtp) REVERT: B 1053 MET cc_start: 0.8721 (tpp) cc_final: 0.8509 (mmm) REVERT: F 2015 ASP cc_start: 0.8748 (t70) cc_final: 0.8399 (t0) REVERT: F 2016 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8407 (tptt) REVERT: F 2046 ASP cc_start: 0.8465 (t70) cc_final: 0.8239 (t0) REVERT: F 2077 ARG cc_start: 0.8916 (mmt90) cc_final: 0.8407 (mmm160) REVERT: C 30 MET cc_start: 0.8846 (mmp) cc_final: 0.8571 (mmm) REVERT: C 48 TYR cc_start: 0.8614 (m-80) cc_final: 0.8333 (m-10) REVERT: C 118 LEU cc_start: 0.9270 (tp) cc_final: 0.8918 (pp) REVERT: C 153 ASP cc_start: 0.8679 (t0) cc_final: 0.8177 (t0) REVERT: C 162 LEU cc_start: 0.9415 (mm) cc_final: 0.9105 (pp) REVERT: C 273 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8617 (p) REVERT: C 276 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8487 (mm-30) REVERT: C 285 MET cc_start: 0.8622 (mmm) cc_final: 0.8321 (mmm) REVERT: C 303 PHE cc_start: 0.8224 (t80) cc_final: 0.7913 (t80) REVERT: C 428 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8685 (mmtm) REVERT: C 459 GLN cc_start: 0.8874 (mt0) cc_final: 0.8635 (mt0) REVERT: C 627 LYS cc_start: 0.7428 (tptt) cc_final: 0.7036 (tppt) REVERT: C 715 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.7931 (pp) REVERT: C 739 MET cc_start: 0.8303 (mtm) cc_final: 0.7930 (mtp) REVERT: C 878 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8903 (mp) REVERT: G 2015 ASP cc_start: 0.8966 (t70) cc_final: 0.8694 (t0) REVERT: G 2016 LYS cc_start: 0.9037 (ttmt) cc_final: 0.8436 (tptt) REVERT: G 2046 ASP cc_start: 0.8661 (t70) cc_final: 0.8419 (t70) REVERT: G 2077 ARG cc_start: 0.8945 (mmt90) cc_final: 0.8410 (mmm160) REVERT: D 118 LEU cc_start: 0.9179 (tp) cc_final: 0.8919 (pp) REVERT: D 153 ASP cc_start: 0.8704 (t0) cc_final: 0.7960 (t0) REVERT: D 157 ASN cc_start: 0.9413 (m-40) cc_final: 0.8629 (m110) REVERT: D 162 LEU cc_start: 0.9365 (mm) cc_final: 0.8982 (pp) REVERT: D 187 PHE cc_start: 0.8587 (t80) cc_final: 0.8276 (t80) REVERT: D 221 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9241 (tt) REVERT: D 273 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8689 (p) REVERT: D 285 MET cc_start: 0.8625 (mmm) cc_final: 0.8323 (mmm) REVERT: D 303 PHE cc_start: 0.8208 (t80) cc_final: 0.7939 (t80) REVERT: D 442 MET cc_start: 0.9126 (tpp) cc_final: 0.8720 (tpp) REVERT: D 627 LYS cc_start: 0.7571 (tptt) cc_final: 0.7196 (tppt) REVERT: D 715 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.7962 (pp) REVERT: D 739 MET cc_start: 0.8295 (mtm) cc_final: 0.7944 (mtp) REVERT: D 878 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8905 (mp) REVERT: D 892 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7323 (t70) REVERT: H 2015 ASP cc_start: 0.8751 (t70) cc_final: 0.8405 (t0) REVERT: H 2016 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8437 (tptt) REVERT: H 2046 ASP cc_start: 0.8510 (t70) cc_final: 0.8273 (t0) REVERT: H 2077 ARG cc_start: 0.8941 (mmt90) cc_final: 0.8459 (mmm160) REVERT: H 2141 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8103 (tt) outliers start: 81 outliers final: 55 residues processed: 486 average time/residue: 0.2125 time to fit residues: 175.1136 Evaluate side-chains 480 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 410 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2187 ILE Chi-restraints excluded: chain G residue 2204 MET Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2141 ILE Chi-restraints excluded: chain H residue 2157 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 55 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 176 optimal weight: 0.0980 chunk 346 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 425 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.085602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066392 restraints weight = 118503.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068696 restraints weight = 55300.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070219 restraints weight = 34597.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071194 restraints weight = 25710.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.071817 restraints weight = 21368.839| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37332 Z= 0.160 Angle : 0.622 9.976 50560 Z= 0.311 Chirality : 0.042 0.282 5756 Planarity : 0.003 0.051 6240 Dihedral : 8.618 126.616 5978 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.98 % Allowed : 14.74 % Favored : 83.28 % 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: 4408 helix: 1.04 (0.12), residues: 2076 sheet: -1.56 (0.20), residues: 616 loop : -0.98 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 575 TYR 0.008 0.001 TYR B1039 PHE 0.031 0.001 PHE G2033 TRP 0.025 0.001 TRP G2176 HIS 0.006 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00364 (37300) covalent geometry : angle 0.61806 (50504) SS BOND : bond 0.00139 ( 16) SS BOND : angle 0.42697 ( 32) hydrogen bonds : bond 0.03173 ( 1448) hydrogen bonds : angle 4.24959 ( 4056) Misc. bond : bond 0.00060 ( 8) link_NAG-ASN : bond 0.01238 ( 8) link_NAG-ASN : angle 3.28162 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 401 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9289 (tp) cc_final: 0.8914 (pp) REVERT: A 153 ASP cc_start: 0.8649 (t0) cc_final: 0.8423 (t0) REVERT: A 162 LEU cc_start: 0.9437 (mm) cc_final: 0.9158 (pp) REVERT: A 186 ASP cc_start: 0.8417 (m-30) cc_final: 0.8111 (m-30) REVERT: A 213 ARG cc_start: 0.9072 (ttt90) cc_final: 0.8838 (ttm-80) REVERT: A 273 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8697 (p) REVERT: A 285 MET cc_start: 0.8558 (mmm) cc_final: 0.8246 (mmm) REVERT: A 303 PHE cc_start: 0.8289 (t80) cc_final: 0.7991 (t80) REVERT: A 362 ASP cc_start: 0.8413 (t0) cc_final: 0.7945 (t0) REVERT: A 627 LYS cc_start: 0.7533 (tptt) cc_final: 0.7148 (tppt) REVERT: A 715 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8048 (pp) REVERT: A 739 MET cc_start: 0.8368 (mtm) cc_final: 0.8015 (mtp) REVERT: A 878 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8969 (mp) REVERT: E 2015 ASP cc_start: 0.8959 (t70) cc_final: 0.8688 (t0) REVERT: E 2016 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8366 (tptt) REVERT: E 2077 ARG cc_start: 0.8986 (mmt90) cc_final: 0.8423 (mmm160) REVERT: B 153 ASP cc_start: 0.8494 (t0) cc_final: 0.7720 (t0) REVERT: B 157 ASN cc_start: 0.9403 (m-40) cc_final: 0.8726 (m110) REVERT: B 159 PHE cc_start: 0.9158 (t80) cc_final: 0.8930 (t80) REVERT: B 162 LEU cc_start: 0.9444 (mm) cc_final: 0.8998 (pp) REVERT: B 186 ASP cc_start: 0.8436 (m-30) cc_final: 0.8161 (m-30) REVERT: B 187 PHE cc_start: 0.8467 (t80) cc_final: 0.8046 (t80) REVERT: B 273 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8619 (p) REVERT: B 627 LYS cc_start: 0.7488 (tptt) cc_final: 0.7090 (tppt) REVERT: B 715 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8062 (pp) REVERT: B 739 MET cc_start: 0.8354 (mtm) cc_final: 0.7984 (mtp) REVERT: F 2015 ASP cc_start: 0.8764 (t70) cc_final: 0.8407 (t0) REVERT: F 2016 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8465 (tptt) REVERT: F 2046 ASP cc_start: 0.8440 (t70) cc_final: 0.8215 (t0) REVERT: F 2077 ARG cc_start: 0.8929 (mmt90) cc_final: 0.8398 (mmm160) REVERT: C 48 TYR cc_start: 0.8569 (m-80) cc_final: 0.8246 (m-10) REVERT: C 118 LEU cc_start: 0.9278 (tp) cc_final: 0.8925 (pp) REVERT: C 153 ASP cc_start: 0.8664 (t0) cc_final: 0.8133 (t0) REVERT: C 162 LEU cc_start: 0.9443 (mm) cc_final: 0.9153 (pp) REVERT: C 187 PHE cc_start: 0.8590 (t80) cc_final: 0.8380 (t80) REVERT: C 273 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8628 (p) REVERT: C 276 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8531 (mm-30) REVERT: C 285 MET cc_start: 0.8548 (mmm) cc_final: 0.8251 (mmm) REVERT: C 303 PHE cc_start: 0.8284 (t80) cc_final: 0.7991 (t80) REVERT: C 428 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8765 (mmtm) REVERT: C 627 LYS cc_start: 0.7471 (tptt) cc_final: 0.7064 (tppt) REVERT: C 715 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8025 (pp) REVERT: C 739 MET cc_start: 0.8357 (mtm) cc_final: 0.8009 (mtp) REVERT: C 878 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8929 (mp) REVERT: G 2015 ASP cc_start: 0.8992 (t70) cc_final: 0.8691 (t0) REVERT: G 2016 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8442 (tptt) REVERT: G 2077 ARG cc_start: 0.8972 (mmt90) cc_final: 0.8420 (mmm160) REVERT: G 2120 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8563 (mmtm) REVERT: D 118 LEU cc_start: 0.9184 (tp) cc_final: 0.8922 (pp) REVERT: D 153 ASP cc_start: 0.8698 (t0) cc_final: 0.8334 (t70) REVERT: D 187 PHE cc_start: 0.8443 (t80) cc_final: 0.8023 (t80) REVERT: D 221 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9260 (tt) REVERT: D 273 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8681 (p) REVERT: D 285 MET cc_start: 0.8635 (mmm) cc_final: 0.8340 (mmm) REVERT: D 303 PHE cc_start: 0.8300 (t80) cc_final: 0.7998 (t80) REVERT: D 626 LYS cc_start: 0.8682 (mmmt) cc_final: 0.8230 (mmmt) REVERT: D 691 MET cc_start: 0.8262 (mmt) cc_final: 0.7985 (mmm) REVERT: D 715 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8355 (pp) REVERT: D 739 MET cc_start: 0.8338 (mtm) cc_final: 0.7982 (mtp) REVERT: D 878 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8943 (mp) REVERT: D 892 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7300 (t70) REVERT: D 1053 MET cc_start: 0.8487 (mmm) cc_final: 0.8226 (mmm) REVERT: H 2015 ASP cc_start: 0.8691 (t70) cc_final: 0.8347 (t0) REVERT: H 2016 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8449 (tptt) REVERT: H 2046 ASP cc_start: 0.8512 (t70) cc_final: 0.8278 (t0) REVERT: H 2077 ARG cc_start: 0.8923 (mmt90) cc_final: 0.8461 (mmm160) REVERT: H 2141 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8068 (tt) outliers start: 78 outliers final: 62 residues processed: 462 average time/residue: 0.2267 time to fit residues: 179.0677 Evaluate side-chains 468 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 391 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2157 ASP Chi-restraints excluded: chain F residue 2168 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2187 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2141 ILE Chi-restraints excluded: chain H residue 2157 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 172 optimal weight: 0.7980 chunk 287 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 213 optimal weight: 5.9990 chunk 424 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN B 200 ASN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN F2061 GLN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.084925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065669 restraints weight = 118185.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067938 restraints weight = 55248.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069480 restraints weight = 34570.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070453 restraints weight = 25698.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071024 restraints weight = 21367.051| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37332 Z= 0.176 Angle : 0.644 12.470 50560 Z= 0.321 Chirality : 0.042 0.278 5756 Planarity : 0.003 0.052 6240 Dihedral : 8.482 126.553 5978 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.18 % Allowed : 14.84 % Favored : 82.98 % 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: -0.20 (0.13), residues: 4408 helix: 1.03 (0.12), residues: 2068 sheet: -1.62 (0.20), residues: 612 loop : -0.90 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 575 TYR 0.014 0.001 TYR F2008 PHE 0.026 0.001 PHE G2023 TRP 0.024 0.001 TRP G2176 HIS 0.007 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00402 (37300) covalent geometry : angle 0.63984 (50504) SS BOND : bond 0.00141 ( 16) SS BOND : angle 0.45644 ( 32) hydrogen bonds : bond 0.03222 ( 1448) hydrogen bonds : angle 4.31390 ( 4056) Misc. bond : bond 0.00065 ( 8) link_NAG-ASN : bond 0.01208 ( 8) link_NAG-ASN : angle 3.26842 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6472.30 seconds wall clock time: 112 minutes 54.17 seconds (6774.17 seconds total)