Starting phenix.real_space_refine on Sat Mar 7 02:59:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v35_21028/03_2026/6v35_21028.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v35_21028/03_2026/6v35_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6v35_21028/03_2026/6v35_21028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v35_21028/03_2026/6v35_21028.map" model { file = "/net/cci-nas-00/data/ceres_data/6v35_21028/03_2026/6v35_21028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v35_21028/03_2026/6v35_21028.cif" } 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36488 Number of models: 1 Model: "" Number of chains: 16 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: "F" 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: "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: "G" 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: "D" 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: "H" 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: "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: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 173 Unusual residues: {'CLR': 1, 'PGW': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PGW:plan-3': 5, 'PGW:plan-1': 4, 'PGW:plan-2': 4} Unresolved non-hydrogen planarities: 42 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 Time building chain proxies: 9.45, per 1000 atoms: 0.26 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 F2068 " - pdb=" SG CYS F2119 " distance=2.03 Simple disulfide: pdb=" SG CYS F2072 " - pdb=" SG CYS F2076 " distance=2.02 Simple disulfide: pdb=" SG CYS F2084 " - pdb=" SG CYS F2113 " distance=2.03 Simple disulfide: pdb=" SG CYS G2054 " - pdb=" SG CYS G2148 " distance=2.04 Simple disulfide: pdb=" SG CYS G2068 " - pdb=" SG CYS G2119 " distance=2.03 Simple disulfide: pdb=" SG CYS G2072 " - pdb=" SG CYS G2076 " distance=2.02 Simple disulfide: pdb=" SG CYS G2084 " - pdb=" SG CYS G2113 " distance=2.03 Simple disulfide: pdb=" SG CYS H2054 " - pdb=" SG CYS H2148 " distance=2.04 Simple disulfide: pdb=" SG CYS H2068 " - pdb=" SG CYS H2119 " distance=2.03 Simple disulfide: pdb=" SG CYS H2072 " - pdb=" SG CYS H2076 " distance=2.02 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: 3.30 Conformation dependent library (CDL) restraints added in 1.7 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: 1.46 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: 8.38 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 36.710 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.080 ------------------------------------------------------------------------------- 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 : 1.315 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: 0.7391 (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: 0.8457 (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: 0.8553 (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: 0.8387 (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: 0.2337 time to fit residues: 329.6728 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 : 1.346 ------------------------------------------------------------------------------- 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 : 1.263 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: 0.8894 (OUTLIER) cc_final: 0.8337 (pp) REVERT: A 900 ASP cc_start: 0.8627 (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: 0.7992 (t0) REVERT: B 157 ASN cc_start: 0.9208 (m-40) cc_final: 0.8555 (m110) REVERT: B 162 LEU cc_start: 0.9462 (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: 0.8115 (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: 0.8572 (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: 0.8446 (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: 0.8505 (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: 0.8693 (mm-30) cc_final: 0.8064 (mm-30) REVERT: D 285 MET cc_start: 0.8453 (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: 0.2079 time to fit residues: 214.3405 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 : 1.256 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.066035 restraints weight = 117861.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068284 restraints weight = 55869.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069754 restraints weight = 35365.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070719 restraints weight = 26563.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071328 restraints weight = 22142.018| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- 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 : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8695 (mmm) cc_final: 0.8434 (mmm) REVERT: A 118 LEU cc_start: 0.9350 (tp) cc_final: 0.9023 (pp) REVERT: A 285 MET cc_start: 0.8483 (mmm) cc_final: 0.8228 (mmm) REVERT: A 303 PHE cc_start: 0.8275 (t80) cc_final: 0.7972 (t80) REVERT: A 362 ASP cc_start: 0.8314 (t0) cc_final: 0.7739 (t0) REVERT: A 561 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8415 (pp) REVERT: A 715 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.7906 (pp) REVERT: A 878 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8908 (mp) REVERT: A 1053 MET cc_start: 0.8628 (mtp) cc_final: 0.8394 (mtm) REVERT: E 2015 ASP cc_start: 0.8905 (t70) cc_final: 0.8673 (t0) REVERT: E 2016 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8532 (tptt) REVERT: E 2046 ASP cc_start: 0.8746 (t70) cc_final: 0.8485 (t70) REVERT: E 2077 ARG cc_start: 0.8887 (mmt90) cc_final: 0.8511 (mmm160) REVERT: E 2163 ARG cc_start: 0.8243 (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: 0.8680 (t0) cc_final: 0.8020 (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: 0.7761 (t0) REVERT: B 561 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8461 (pp) REVERT: B 715 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.7935 (pp) REVERT: F 2015 ASP cc_start: 0.8888 (t70) cc_final: 0.8598 (t0) REVERT: F 2016 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8412 (tptt) REVERT: F 2046 ASP cc_start: 0.8709 (t70) cc_final: 0.8435 (t70) REVERT: F 2077 ARG cc_start: 0.8995 (mmt90) cc_final: 0.8532 (mmm160) REVERT: F 2163 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7395 (mmm160) REVERT: F 2166 ASP cc_start: 0.8333 (p0) cc_final: 0.8036 (p0) REVERT: C 21 MET cc_start: 0.8689 (mmm) cc_final: 0.8427 (mmm) REVERT: C 118 LEU cc_start: 0.9354 (tp) cc_final: 0.9024 (pp) REVERT: C 285 MET cc_start: 0.8478 (mmm) cc_final: 0.8231 (mmm) REVERT: C 303 PHE cc_start: 0.8273 (t80) cc_final: 0.7969 (t80) REVERT: C 362 ASP cc_start: 0.8327 (t0) cc_final: 0.7749 (t0) REVERT: C 561 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8400 (pp) REVERT: C 715 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.7962 (pp) REVERT: C 830 MET cc_start: 0.8264 (ttm) cc_final: 0.7911 (mmm) REVERT: C 1053 MET cc_start: 0.8635 (mtp) cc_final: 0.8267 (mtp) REVERT: G 2015 ASP cc_start: 0.8905 (t70) cc_final: 0.8659 (t0) REVERT: G 2016 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8561 (tptt) REVERT: G 2046 ASP cc_start: 0.8744 (t70) cc_final: 0.8483 (t70) REVERT: G 2077 ARG cc_start: 0.8889 (mmt90) cc_final: 0.8507 (mmm160) REVERT: G 2120 LYS cc_start: 0.8692 (mmtm) cc_final: 0.8444 (mptt) REVERT: G 2163 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7391 (mmm160) REVERT: D 30 MET cc_start: 0.8645 (mmm) cc_final: 0.8369 (mmm) REVERT: D 118 LEU cc_start: 0.9269 (tp) cc_final: 0.8906 (pp) REVERT: D 153 ASP cc_start: 0.8586 (t0) cc_final: 0.7930 (t0) REVERT: D 157 ASN cc_start: 0.9182 (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: 0.7756 (t160) cc_final: 0.7126 (t0) REVERT: D 285 MET cc_start: 0.8499 (mmm) cc_final: 0.8254 (mmm) REVERT: D 303 PHE cc_start: 0.8261 (t80) cc_final: 0.7942 (t80) REVERT: D 362 ASP cc_start: 0.8345 (t0) cc_final: 0.7868 (t0) REVERT: D 561 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8473 (pp) REVERT: D 715 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8257 (pp) REVERT: D 900 ASP cc_start: 0.8568 (p0) cc_final: 0.8290 (p0) REVERT: H 2015 ASP cc_start: 0.8895 (t70) cc_final: 0.8590 (t0) REVERT: H 2016 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8355 (tptt) REVERT: H 2046 ASP cc_start: 0.8698 (t70) cc_final: 0.8486 (t70) REVERT: H 2077 ARG cc_start: 0.8891 (mmt90) cc_final: 0.8532 (mmm160) REVERT: H 2115 TYR cc_start: 0.9301 (t80) cc_final: 0.8874 (t80) REVERT: H 2141 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8008 (tt) REVERT: H 2163 ARG cc_start: 0.8219 (mtt-85) cc_final: 0.7800 (mtp180) REVERT: H 2166 ASP cc_start: 0.8020 (p0) cc_final: 0.7514 (p0) outliers start: 113 outliers final: 53 residues processed: 536 average time/residue: 0.2071 time to fit residues: 187.7807 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 : 1.346 ------------------------------------------------------------------------------- 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: 3.9990 chunk 175 optimal weight: 3.9990 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: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.085679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.066572 restraints weight = 117126.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068877 restraints weight = 55154.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070418 restraints weight = 34204.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.071416 restraints weight = 25292.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.072009 restraints weight = 20843.125| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37332 Z= 0.138 Angle : 0.575 10.806 50560 Z= 0.287 Chirality : 0.042 0.343 5756 Planarity : 0.004 0.046 6240 Dihedral : 11.244 153.323 5978 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.41 % Allowed : 11.94 % Favored : 85.65 % 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: -0.65 (0.13), residues: 4408 helix: 0.71 (0.12), residues: 2020 sheet: -1.52 (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 0.035 0.001 TRP E2176 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00313 (37300) covalent geometry : angle 0.56883 (50504) SS BOND : bond 0.00165 ( 16) SS BOND : angle 0.51581 ( 32) hydrogen bonds : bond 0.03292 ( 1448) hydrogen bonds : angle 4.46818 ( 4056) Misc. bond : bond 0.00051 ( 8) link_NAG-ASN : bond 0.01368 ( 8) link_NAG-ASN : angle 4.00871 ( 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 539 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 444 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8726 (mmm) cc_final: 0.8299 (mmm) REVERT: A 118 LEU cc_start: 0.9314 (tp) cc_final: 0.9046 (pp) REVERT: A 153 ASP cc_start: 0.8558 (t0) cc_final: 0.8161 (t70) REVERT: A 162 LEU cc_start: 0.9413 (mm) cc_final: 0.9075 (pp) REVERT: A 182 ASN cc_start: 0.7250 (t160) cc_final: 0.6993 (t0) REVERT: A 213 ARG cc_start: 0.9125 (ttt90) cc_final: 0.8858 (tpp80) REVERT: A 285 MET cc_start: 0.8531 (mmm) cc_final: 0.7978 (mmm) REVERT: A 303 PHE cc_start: 0.8189 (t80) cc_final: 0.7966 (t80) REVERT: A 307 PHE cc_start: 0.8131 (t80) cc_final: 0.7750 (t80) REVERT: A 362 ASP cc_start: 0.8364 (t0) cc_final: 0.7796 (t0) REVERT: A 561 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8380 (pp) REVERT: A 715 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.7897 (pp) REVERT: A 1053 MET cc_start: 0.8614 (mtp) cc_final: 0.8380 (mtm) REVERT: E 2015 ASP cc_start: 0.8910 (t70) cc_final: 0.8678 (t0) REVERT: E 2016 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8510 (tptt) REVERT: E 2046 ASP cc_start: 0.8784 (t70) cc_final: 0.8532 (t70) REVERT: E 2077 ARG cc_start: 0.8904 (mmt90) cc_final: 0.8458 (mmm160) REVERT: E 2120 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8419 (mptt) REVERT: E 2163 ARG cc_start: 0.8189 (mtt-85) cc_final: 0.7300 (mmm160) REVERT: B 118 LEU cc_start: 0.9253 (tp) cc_final: 0.8998 (pp) REVERT: B 162 LEU cc_start: 0.9417 (mm) cc_final: 0.8957 (pp) REVERT: B 214 LEU cc_start: 0.9544 (mt) cc_final: 0.9045 (mt) REVERT: B 362 ASP cc_start: 0.8395 (t0) cc_final: 0.7941 (t0) REVERT: B 601 ASP cc_start: 0.7481 (p0) cc_final: 0.6672 (p0) REVERT: B 715 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.7895 (pp) REVERT: F 2015 ASP cc_start: 0.8926 (t70) cc_final: 0.8620 (t0) REVERT: F 2016 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8360 (tptt) REVERT: F 2046 ASP cc_start: 0.8735 (t70) cc_final: 0.8459 (t70) REVERT: F 2077 ARG cc_start: 0.8894 (mmt90) cc_final: 0.8456 (mmm160) REVERT: F 2120 LYS cc_start: 0.8737 (mmtm) cc_final: 0.8457 (mptt) REVERT: F 2163 ARG cc_start: 0.8194 (mtt-85) cc_final: 0.7328 (mmm160) REVERT: C 21 MET cc_start: 0.8728 (mmm) cc_final: 0.8300 (mmm) REVERT: C 118 LEU cc_start: 0.9311 (tp) cc_final: 0.9044 (pp) REVERT: C 153 ASP cc_start: 0.8568 (t0) cc_final: 0.8171 (t70) REVERT: C 162 LEU cc_start: 0.9409 (mm) cc_final: 0.9069 (pp) REVERT: C 285 MET cc_start: 0.8535 (mmm) cc_final: 0.7987 (mmm) REVERT: C 303 PHE cc_start: 0.8184 (t80) cc_final: 0.7967 (t80) REVERT: C 307 PHE cc_start: 0.8111 (t80) cc_final: 0.7723 (t80) REVERT: C 362 ASP cc_start: 0.8392 (t0) cc_final: 0.7809 (t0) REVERT: C 561 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8400 (pp) REVERT: C 715 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7883 (pp) REVERT: C 739 MET cc_start: 0.8458 (mtp) cc_final: 0.8042 (mtp) REVERT: C 878 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8850 (mp) REVERT: G 2015 ASP cc_start: 0.8927 (t70) cc_final: 0.8673 (t0) REVERT: G 2016 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8528 (tptt) REVERT: G 2046 ASP cc_start: 0.8780 (t70) cc_final: 0.8522 (t70) REVERT: G 2077 ARG cc_start: 0.8907 (mmt90) cc_final: 0.8465 (mmm160) REVERT: G 2163 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7228 (mmm160) REVERT: D 30 MET cc_start: 0.8592 (mmm) cc_final: 0.8338 (mmm) REVERT: D 118 LEU cc_start: 0.9226 (tp) cc_final: 0.8871 (pp) REVERT: D 153 ASP cc_start: 0.8677 (t0) cc_final: 0.8004 (t0) REVERT: D 157 ASN cc_start: 0.9195 (m-40) cc_final: 0.8385 (m110) REVERT: D 162 LEU cc_start: 0.9403 (mm) cc_final: 0.9160 (mm) REVERT: D 285 MET cc_start: 0.8519 (mmm) cc_final: 0.7958 (mmm) REVERT: D 303 PHE cc_start: 0.8172 (t80) cc_final: 0.7947 (t80) REVERT: D 306 PHE cc_start: 0.8638 (t80) cc_final: 0.8437 (t80) REVERT: D 307 PHE cc_start: 0.8135 (t80) cc_final: 0.7718 (t80) REVERT: D 442 MET cc_start: 0.8918 (tpp) cc_final: 0.8646 (tpp) REVERT: D 601 ASP cc_start: 0.7534 (p0) cc_final: 0.6811 (p0) REVERT: D 627 LYS cc_start: 0.8325 (tptt) cc_final: 0.7957 (tppt) REVERT: D 715 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8066 (pp) REVERT: D 878 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8887 (mp) REVERT: D 900 ASP cc_start: 0.8663 (p0) cc_final: 0.8409 (p0) REVERT: H 2015 ASP cc_start: 0.8900 (t70) cc_final: 0.8579 (t0) REVERT: H 2016 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8357 (tptt) REVERT: H 2077 ARG cc_start: 0.8904 (mmt90) cc_final: 0.8471 (mmm160) REVERT: H 2115 TYR cc_start: 0.9350 (t80) cc_final: 0.9147 (t80) REVERT: H 2141 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8010 (tt) REVERT: H 2163 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7826 (mtp180) outliers start: 95 outliers final: 51 residues processed: 516 average time/residue: 0.2099 time to fit residues: 183.6283 Evaluate side-chains 469 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 409 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 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 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 181 VAL 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 617 ASP 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: 0.9990 chunk 129 optimal weight: 0.6980 chunk 424 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 118 optimal weight: 0.0970 chunk 347 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 182 ASN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 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 = 0.3533 r_free = 0.3533 target = 0.087264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068357 restraints weight = 117255.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.070705 restraints weight = 54520.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.072257 restraints weight = 33868.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073259 restraints weight = 24999.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.073900 restraints weight = 20634.121| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 37332 Z= 0.104 Angle : 0.547 10.304 50560 Z= 0.273 Chirality : 0.041 0.323 5756 Planarity : 0.003 0.048 6240 Dihedral : 10.136 127.455 5978 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.03 % Allowed : 12.98 % Favored : 84.98 % 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: -0.46 (0.13), residues: 4408 helix: 0.93 (0.12), residues: 2032 sheet: -1.59 (0.20), residues: 628 loop : -1.21 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 213 TYR 0.009 0.001 TYR G2008 PHE 0.021 0.001 PHE G2033 TRP 0.026 0.001 TRP E2176 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00234 (37300) covalent geometry : angle 0.54139 (50504) SS BOND : bond 0.00132 ( 16) SS BOND : angle 0.41387 ( 32) hydrogen bonds : bond 0.03049 ( 1448) hydrogen bonds : angle 4.28029 ( 4056) Misc. bond : bond 0.00051 ( 8) link_NAG-ASN : bond 0.01360 ( 8) link_NAG-ASN : angle 3.62864 ( 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 544 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 464 time to evaluate : 1.365 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: 0.9290 (tp) cc_final: 0.9042 (pp) REVERT: A 153 ASP cc_start: 0.8533 (t0) cc_final: 0.8070 (t0) REVERT: A 162 LEU cc_start: 0.9411 (mm) cc_final: 0.9089 (pp) REVERT: A 182 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.7047 (t0) REVERT: A 273 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8701 (p) REVERT: A 285 MET cc_start: 0.8522 (mmm) cc_final: 0.8017 (mmm) REVERT: A 303 PHE cc_start: 0.8049 (t80) cc_final: 0.7769 (t80) REVERT: A 307 PHE cc_start: 0.8036 (t80) cc_final: 0.7773 (t80) REVERT: A 362 ASP cc_start: 0.8371 (t0) cc_final: 0.7809 (t0) REVERT: A 561 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8638 (pp) REVERT: A 715 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.7809 (pp) REVERT: A 739 MET cc_start: 0.8307 (mtp) cc_final: 0.7986 (mtp) REVERT: A 900 ASP cc_start: 0.8577 (p0) cc_final: 0.8300 (p0) REVERT: E 2015 ASP cc_start: 0.8889 (t70) cc_final: 0.8663 (t0) REVERT: E 2016 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8553 (tptt) REVERT: E 2077 ARG cc_start: 0.8944 (mmt90) cc_final: 0.8524 (mmm160) REVERT: E 2163 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7845 (mtp180) REVERT: B 153 ASP cc_start: 0.8626 (t0) cc_final: 0.7866 (t0) REVERT: B 157 ASN cc_start: 0.9430 (m-40) cc_final: 0.8648 (m110) REVERT: B 159 PHE cc_start: 0.9025 (t80) cc_final: 0.8661 (t80) REVERT: B 162 LEU cc_start: 0.9426 (mm) cc_final: 0.9157 (mm) REVERT: B 273 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8642 (p) REVERT: B 276 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 306 PHE cc_start: 0.8640 (t80) cc_final: 0.8417 (t80) REVERT: B 362 ASP cc_start: 0.8364 (t0) cc_final: 0.7920 (t0) REVERT: B 715 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.7860 (pp) REVERT: B 739 MET cc_start: 0.8361 (mtp) cc_final: 0.8135 (mtp) REVERT: B 900 ASP cc_start: 0.8598 (p0) cc_final: 0.8331 (p0) REVERT: F 2015 ASP cc_start: 0.8969 (t70) cc_final: 0.8625 (t0) REVERT: F 2016 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8496 (tptt) REVERT: F 2023 PHE cc_start: 0.9095 (t80) cc_final: 0.8862 (t80) REVERT: F 2077 ARG cc_start: 0.8915 (mmt90) cc_final: 0.8540 (mmm160) REVERT: F 2163 ARG cc_start: 0.8157 (mtt-85) cc_final: 0.7896 (mtp180) REVERT: C 118 LEU cc_start: 0.9257 (tp) cc_final: 0.9027 (pp) REVERT: C 153 ASP cc_start: 0.8537 (t0) cc_final: 0.8080 (t0) REVERT: C 162 LEU cc_start: 0.9412 (mm) cc_final: 0.9093 (pp) REVERT: C 182 ASN cc_start: 0.7054 (t160) cc_final: 0.6798 (t0) REVERT: C 273 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8637 (p) REVERT: C 285 MET cc_start: 0.8555 (mmm) cc_final: 0.8073 (mmm) REVERT: C 303 PHE cc_start: 0.8112 (t80) cc_final: 0.7793 (t80) REVERT: C 307 PHE cc_start: 0.8030 (t80) cc_final: 0.7776 (t80) REVERT: C 362 ASP cc_start: 0.8372 (t0) cc_final: 0.7888 (t0) REVERT: C 561 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8552 (pp) REVERT: C 715 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.7903 (pp) REVERT: C 739 MET cc_start: 0.8424 (mtp) cc_final: 0.8043 (mtp) REVERT: C 900 ASP cc_start: 0.8610 (p0) cc_final: 0.8334 (p0) REVERT: G 2015 ASP cc_start: 0.8915 (t70) cc_final: 0.8656 (t0) REVERT: G 2016 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8522 (tptt) REVERT: G 2023 PHE cc_start: 0.9101 (t80) cc_final: 0.8838 (t80) REVERT: G 2046 ASP cc_start: 0.8682 (t70) cc_final: 0.8329 (t0) REVERT: G 2077 ARG cc_start: 0.8907 (mmt90) cc_final: 0.8488 (mmm160) REVERT: G 2131 MET cc_start: 0.8528 (mmm) cc_final: 0.8324 (mmp) REVERT: G 2163 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7806 (mtp180) REVERT: D 30 MET cc_start: 0.8640 (mmm) cc_final: 0.8440 (mmm) REVERT: D 118 LEU cc_start: 0.9233 (tp) cc_final: 0.8986 (pp) REVERT: D 153 ASP cc_start: 0.8681 (t0) cc_final: 0.8035 (t0) REVERT: D 157 ASN cc_start: 0.9135 (m-40) cc_final: 0.8362 (m110) REVERT: D 159 PHE cc_start: 0.9050 (t80) cc_final: 0.8657 (t80) REVERT: D 162 LEU cc_start: 0.9427 (mm) cc_final: 0.9175 (mm) REVERT: D 273 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8704 (p) REVERT: D 276 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8331 (mm-30) REVERT: D 285 MET cc_start: 0.8518 (mmm) cc_final: 0.8011 (mmm) REVERT: D 303 PHE cc_start: 0.8043 (t80) cc_final: 0.7725 (t80) REVERT: D 306 PHE cc_start: 0.8636 (t80) cc_final: 0.8423 (t80) REVERT: D 307 PHE cc_start: 0.8015 (t80) cc_final: 0.7777 (t80) REVERT: D 386 GLU cc_start: 0.7927 (tp30) cc_final: 0.7677 (tp30) REVERT: D 442 MET cc_start: 0.9065 (tpp) cc_final: 0.8769 (tpp) REVERT: D 715 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.7940 (pp) REVERT: D 878 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8857 (mp) REVERT: D 900 ASP cc_start: 0.8679 (p0) cc_final: 0.8435 (p0) REVERT: H 2015 ASP cc_start: 0.8924 (t70) cc_final: 0.8574 (t0) REVERT: H 2016 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8386 (tptt) REVERT: H 2023 PHE cc_start: 0.9108 (t80) cc_final: 0.8863 (t80) REVERT: H 2046 ASP cc_start: 0.8554 (t70) cc_final: 0.8170 (t0) REVERT: H 2077 ARG cc_start: 0.8881 (mmt90) cc_final: 0.8445 (mmm160) REVERT: H 2131 MET cc_start: 0.8637 (mmp) cc_final: 0.8121 (mmp) REVERT: H 2141 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8100 (tt) outliers start: 80 outliers final: 44 residues processed: 517 average time/residue: 0.2059 time to fit residues: 181.8591 Evaluate side-chains 478 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 421 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 273 THR 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 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 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 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 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 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 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: 8.9990 chunk 315 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 278 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 414 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 216 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** 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** D 682 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.086128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.066915 restraints weight = 118318.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069248 restraints weight = 55560.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.070776 restraints weight = 34723.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071769 restraints weight = 25785.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072359 restraints weight = 21362.777| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4068 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= 0.134 Angle : 0.568 11.383 50560 Z= 0.282 Chirality : 0.041 0.311 5756 Planarity : 0.003 0.046 6240 Dihedral : 9.680 121.322 5978 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.64 % Allowed : 13.24 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.13), residues: 4408 helix: 1.09 (0.12), residues: 2012 sheet: -1.61 (0.20), residues: 632 loop : -1.16 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.008 0.001 TYR A 48 PHE 0.023 0.001 PHE G2033 TRP 0.023 0.001 TRP E2176 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00303 (37300) covalent geometry : angle 0.56342 (50504) SS BOND : bond 0.00123 ( 16) SS BOND : angle 0.39484 ( 32) hydrogen bonds : bond 0.03092 ( 1448) hydrogen bonds : angle 4.25360 ( 4056) Misc. bond : bond 0.00050 ( 8) link_NAG-ASN : bond 0.01303 ( 8) link_NAG-ASN : angle 3.52464 ( 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 531 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 427 time to evaluate : 1.214 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: 0.8571 (t0) cc_final: 0.8082 (t0) REVERT: A 162 LEU cc_start: 0.9424 (mm) cc_final: 0.9097 (pp) REVERT: A 273 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8666 (p) REVERT: A 285 MET cc_start: 0.8545 (mmm) cc_final: 0.7994 (mmm) REVERT: A 306 PHE cc_start: 0.8599 (t80) cc_final: 0.8380 (t80) REVERT: A 307 PHE cc_start: 0.8141 (t80) cc_final: 0.7695 (t80) REVERT: A 362 ASP cc_start: 0.8391 (t0) cc_final: 0.7859 (t0) REVERT: A 459 GLN cc_start: 0.8869 (mt0) cc_final: 0.8503 (mt0) REVERT: A 561 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8570 (pp) REVERT: A 627 LYS cc_start: 0.7307 (tptt) cc_final: 0.7034 (tppt) REVERT: A 715 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.7917 (pp) REVERT: A 878 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8896 (mp) REVERT: A 924 MET cc_start: 0.8632 (mtp) cc_final: 0.8311 (ttt) REVERT: E 2015 ASP cc_start: 0.8934 (t70) cc_final: 0.8699 (t0) REVERT: E 2016 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8571 (tptt) REVERT: E 2046 ASP cc_start: 0.8652 (t70) cc_final: 0.8313 (t0) REVERT: E 2077 ARG cc_start: 0.8965 (mmt90) cc_final: 0.8471 (mmm160) REVERT: E 2163 ARG cc_start: 0.7985 (mtt-85) cc_final: 0.7700 (mtp180) REVERT: B 162 LEU cc_start: 0.9439 (mm) cc_final: 0.9172 (mm) REVERT: B 273 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8638 (p) REVERT: B 428 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8865 (mmtm) REVERT: B 575 ARG cc_start: 0.6530 (mpp-170) cc_final: 0.6197 (mpp-170) REVERT: B 715 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.7880 (pp) REVERT: F 2015 ASP cc_start: 0.8985 (t70) cc_final: 0.8629 (t0) REVERT: F 2016 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8490 (tptt) REVERT: F 2023 PHE cc_start: 0.9086 (t80) cc_final: 0.8874 (t80) REVERT: F 2024 LEU cc_start: 0.8971 (mp) cc_final: 0.8567 (tp) REVERT: F 2046 ASP cc_start: 0.8502 (t70) cc_final: 0.8105 (t0) REVERT: F 2077 ARG cc_start: 0.8902 (mmt90) cc_final: 0.8448 (mmm160) REVERT: F 2163 ARG cc_start: 0.7999 (mtt-85) cc_final: 0.7772 (mtp180) REVERT: C 153 ASP cc_start: 0.8574 (t0) cc_final: 0.8089 (t0) REVERT: C 162 LEU cc_start: 0.9419 (mm) cc_final: 0.9093 (pp) REVERT: C 273 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8616 (p) REVERT: C 285 MET cc_start: 0.8586 (mmm) cc_final: 0.8056 (mmm) REVERT: C 306 PHE cc_start: 0.8601 (t80) cc_final: 0.8377 (t80) REVERT: C 307 PHE cc_start: 0.8132 (t80) cc_final: 0.7690 (t80) REVERT: C 362 ASP cc_start: 0.8395 (t0) cc_final: 0.7933 (t0) REVERT: C 460 MET cc_start: 0.8164 (mtp) cc_final: 0.7950 (ttm) REVERT: C 561 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8578 (pp) REVERT: C 715 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.7865 (pp) REVERT: C 739 MET cc_start: 0.8467 (mtp) cc_final: 0.8071 (mtp) REVERT: C 878 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8880 (mp) REVERT: G 2015 ASP cc_start: 0.8978 (t70) cc_final: 0.8735 (t0) REVERT: G 2016 LYS cc_start: 0.9130 (ttmt) cc_final: 0.8593 (tptt) REVERT: G 2023 PHE cc_start: 0.9117 (t80) cc_final: 0.8891 (t80) REVERT: G 2024 LEU cc_start: 0.9029 (mp) cc_final: 0.8583 (tp) REVERT: G 2046 ASP cc_start: 0.8685 (t70) cc_final: 0.8467 (t70) REVERT: G 2077 ARG cc_start: 0.8954 (mmt90) cc_final: 0.8470 (mmm160) REVERT: G 2131 MET cc_start: 0.8535 (mmm) cc_final: 0.8317 (mmp) REVERT: G 2163 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7726 (mtp180) REVERT: D 30 MET cc_start: 0.8678 (mmm) cc_final: 0.8472 (mmt) REVERT: D 118 LEU cc_start: 0.9213 (tp) cc_final: 0.8865 (pp) REVERT: D 154 MET cc_start: 0.7652 (mtm) cc_final: 0.7284 (mtm) REVERT: D 162 LEU cc_start: 0.9421 (mm) cc_final: 0.9159 (mm) REVERT: D 273 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8709 (p) REVERT: D 285 MET cc_start: 0.8539 (mmm) cc_final: 0.7992 (mmm) REVERT: D 306 PHE cc_start: 0.8671 (t80) cc_final: 0.8454 (t80) REVERT: D 307 PHE cc_start: 0.8146 (t80) cc_final: 0.7641 (t80) REVERT: D 442 MET cc_start: 0.9211 (tpp) cc_final: 0.8767 (tpp) REVERT: D 715 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.7866 (pp) REVERT: D 739 MET cc_start: 0.8417 (mtp) cc_final: 0.8098 (mtp) REVERT: D 878 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8900 (mp) REVERT: D 900 ASP cc_start: 0.8626 (p0) cc_final: 0.8382 (p0) REVERT: H 2015 ASP cc_start: 0.8887 (t70) cc_final: 0.8580 (t0) REVERT: H 2016 LYS cc_start: 0.9052 (ttmt) cc_final: 0.8333 (tptt) REVERT: H 2023 PHE cc_start: 0.9071 (t80) cc_final: 0.8859 (t80) REVERT: H 2024 LEU cc_start: 0.8968 (mp) cc_final: 0.8600 (tp) REVERT: H 2046 ASP cc_start: 0.8552 (t70) cc_final: 0.8322 (t0) REVERT: H 2077 ARG cc_start: 0.8905 (mmt90) cc_final: 0.8460 (mmm160) REVERT: H 2141 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8041 (tt) outliers start: 104 outliers final: 53 residues processed: 501 average time/residue: 0.2050 time to fit residues: 175.0972 Evaluate side-chains 479 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 411 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 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 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 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 273 THR 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 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: 3.9990 chunk 334 optimal weight: 7.9990 chunk 434 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 372 optimal weight: 0.7980 chunk 368 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 216 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 216 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.068085 restraints weight = 117746.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070429 restraints weight = 55026.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.071975 restraints weight = 34219.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072957 restraints weight = 25306.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073599 restraints weight = 20959.049| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 37332 Z= 0.106 Angle : 0.556 9.802 50560 Z= 0.275 Chirality : 0.041 0.299 5756 Planarity : 0.003 0.048 6240 Dihedral : 9.152 125.212 5978 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.24 % Allowed : 13.82 % Favored : 83.94 % 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: -0.27 (0.13), residues: 4408 helix: 1.14 (0.12), residues: 2016 sheet: -1.66 (0.20), residues: 644 loop : -1.10 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 213 TYR 0.009 0.001 TYR D 48 PHE 0.024 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 0.00238 (37300) covalent geometry : angle 0.55139 (50504) SS BOND : bond 0.00100 ( 16) SS BOND : angle 0.35937 ( 32) hydrogen bonds : bond 0.03002 ( 1448) hydrogen bonds : angle 4.17277 ( 4056) Misc. bond : bond 0.00048 ( 8) link_NAG-ASN : bond 0.01321 ( 8) link_NAG-ASN : angle 3.36801 ( 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 551 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 463 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9292 (tp) cc_final: 0.8913 (pp) REVERT: A 153 ASP cc_start: 0.8626 (t0) cc_final: 0.8131 (t0) REVERT: A 162 LEU cc_start: 0.9386 (mm) cc_final: 0.9071 (pp) REVERT: A 273 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8715 (p) REVERT: A 285 MET cc_start: 0.8610 (mmm) cc_final: 0.8310 (mmm) REVERT: A 303 PHE cc_start: 0.8235 (t80) cc_final: 0.7955 (t80) REVERT: A 362 ASP cc_start: 0.8374 (t0) cc_final: 0.7846 (t0) REVERT: A 459 GLN cc_start: 0.8865 (mt0) cc_final: 0.8501 (mt0) REVERT: A 601 ASP cc_start: 0.7441 (t0) cc_final: 0.7111 (t0) REVERT: A 715 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.7954 (pp) REVERT: A 924 MET cc_start: 0.8634 (mtp) cc_final: 0.8314 (ttt) REVERT: E 2015 ASP cc_start: 0.8910 (t70) cc_final: 0.8665 (t0) REVERT: E 2016 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8522 (tptt) REVERT: E 2024 LEU cc_start: 0.8995 (mp) cc_final: 0.8571 (tp) REVERT: E 2046 ASP cc_start: 0.8635 (t70) cc_final: 0.8217 (t0) REVERT: E 2077 ARG cc_start: 0.8942 (mmt90) cc_final: 0.8453 (mmm160) REVERT: E 2131 MET cc_start: 0.8472 (mmp) cc_final: 0.8050 (mmp) REVERT: B 162 LEU cc_start: 0.9441 (mm) cc_final: 0.9173 (mm) REVERT: B 273 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8580 (p) REVERT: B 575 ARG cc_start: 0.6309 (mpp-170) cc_final: 0.6080 (mpp-170) REVERT: B 715 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.7996 (pp) REVERT: B 900 ASP cc_start: 0.8571 (p0) cc_final: 0.8329 (p0) REVERT: F 2015 ASP cc_start: 0.8819 (t70) cc_final: 0.8494 (t0) REVERT: F 2016 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8463 (tptt) REVERT: F 2023 PHE cc_start: 0.9004 (t80) cc_final: 0.8736 (t80) REVERT: F 2046 ASP cc_start: 0.8512 (t70) cc_final: 0.8159 (t0) REVERT: F 2077 ARG cc_start: 0.8896 (mmt90) cc_final: 0.8436 (mmm160) REVERT: F 2131 MET cc_start: 0.8450 (mmp) cc_final: 0.7926 (mmp) REVERT: C 118 LEU cc_start: 0.9255 (tp) cc_final: 0.8887 (pp) REVERT: C 153 ASP cc_start: 0.8634 (t0) cc_final: 0.8144 (t0) REVERT: C 162 LEU cc_start: 0.9382 (mm) cc_final: 0.9068 (pp) REVERT: C 273 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8658 (p) REVERT: C 285 MET cc_start: 0.8652 (mmm) cc_final: 0.8374 (mmm) REVERT: C 303 PHE cc_start: 0.8238 (t80) cc_final: 0.7953 (t80) REVERT: C 362 ASP cc_start: 0.8367 (t0) cc_final: 0.8047 (t0) REVERT: C 601 ASP cc_start: 0.7438 (t0) cc_final: 0.7106 (t0) REVERT: C 715 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7877 (pp) REVERT: G 2015 ASP cc_start: 0.8972 (t70) cc_final: 0.8722 (t0) REVERT: G 2016 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8421 (tptt) REVERT: G 2023 PHE cc_start: 0.9073 (t80) cc_final: 0.8868 (t80) REVERT: G 2046 ASP cc_start: 0.8653 (t70) cc_final: 0.8441 (t70) REVERT: G 2077 ARG cc_start: 0.8933 (mmt90) cc_final: 0.8447 (mmm160) REVERT: G 2131 MET cc_start: 0.8503 (mmm) cc_final: 0.8296 (mmp) REVERT: G 2163 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.7604 (mtp180) REVERT: D 30 MET cc_start: 0.8775 (mmm) cc_final: 0.8529 (mmt) REVERT: D 118 LEU cc_start: 0.9222 (tp) cc_final: 0.8973 (pp) REVERT: D 153 ASP cc_start: 0.8659 (t0) cc_final: 0.8021 (t0) REVERT: D 157 ASN cc_start: 0.9380 (m-40) cc_final: 0.8793 (m110) REVERT: D 159 PHE cc_start: 0.8965 (t80) cc_final: 0.8585 (t80) REVERT: D 273 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8725 (p) REVERT: D 285 MET cc_start: 0.8630 (mmm) cc_final: 0.8338 (mmm) REVERT: D 303 PHE cc_start: 0.8250 (t80) cc_final: 0.7937 (t80) REVERT: D 442 MET cc_start: 0.9192 (tpp) cc_final: 0.8738 (tpp) REVERT: D 627 LYS cc_start: 0.7615 (tptt) cc_final: 0.7235 (tppt) REVERT: D 715 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8139 (pp) REVERT: D 739 MET cc_start: 0.8345 (mtp) cc_final: 0.8003 (mtp) REVERT: D 878 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8873 (mp) REVERT: D 900 ASP cc_start: 0.8593 (p0) cc_final: 0.8334 (p0) REVERT: H 2015 ASP cc_start: 0.8777 (t70) cc_final: 0.8455 (t0) REVERT: H 2016 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8370 (tptt) REVERT: H 2023 PHE cc_start: 0.8992 (t80) cc_final: 0.8715 (t80) REVERT: H 2046 ASP cc_start: 0.8555 (t70) cc_final: 0.8317 (t0) REVERT: H 2077 ARG cc_start: 0.8887 (mmt90) cc_final: 0.8451 (mmm160) REVERT: H 2141 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8094 (tt) outliers start: 88 outliers final: 52 residues processed: 520 average time/residue: 0.2017 time to fit residues: 178.5614 Evaluate side-chains 484 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 422 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 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 255 LEU Chi-restraints excluded: chain B residue 273 THR 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 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 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 792 VAL 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 166 LEU Chi-restraints excluded: chain D residue 185 VAL 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 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: 0.1980 chunk 166 optimal weight: 0.3980 chunk 262 optimal weight: 0.9980 chunk 327 optimal weight: 6.9990 chunk 33 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 421 optimal weight: 8.9990 chunk 340 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.087944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068995 restraints weight = 118179.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.071356 restraints weight = 55296.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072885 restraints weight = 34481.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.073900 restraints weight = 25576.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074553 restraints weight = 21111.595| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4441 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= 0.101 Angle : 0.573 10.496 50560 Z= 0.283 Chirality : 0.041 0.287 5756 Planarity : 0.003 0.048 6240 Dihedral : 8.712 127.875 5978 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.91 % Allowed : 14.71 % Favored : 83.38 % 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: -0.21 (0.13), residues: 4408 helix: 1.17 (0.12), residues: 2020 sheet: -1.65 (0.20), residues: 644 loop : -1.03 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.010 0.001 TYR A 48 PHE 0.015 0.001 PHE B 159 TRP 0.022 0.001 TRP F2176 HIS 0.003 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00224 (37300) covalent geometry : angle 0.56870 (50504) SS BOND : bond 0.00129 ( 16) SS BOND : angle 0.38413 ( 32) hydrogen bonds : bond 0.02947 ( 1448) hydrogen bonds : angle 4.10715 ( 4056) Misc. bond : bond 0.00046 ( 8) link_NAG-ASN : bond 0.01319 ( 8) link_NAG-ASN : angle 3.27672 ( 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 519 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 444 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9263 (tp) cc_final: 0.8900 (pp) REVERT: A 153 ASP cc_start: 0.8634 (t0) cc_final: 0.8126 (t0) REVERT: A 162 LEU cc_start: 0.9423 (mm) cc_final: 0.9102 (pp) REVERT: A 273 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8583 (p) REVERT: A 285 MET cc_start: 0.8631 (mmm) cc_final: 0.8035 (mmm) REVERT: A 303 PHE cc_start: 0.8048 (t80) cc_final: 0.7826 (t80) REVERT: A 307 PHE cc_start: 0.8029 (t80) cc_final: 0.7649 (t80) REVERT: A 362 ASP cc_start: 0.8357 (t0) cc_final: 0.7924 (t0) REVERT: A 459 GLN cc_start: 0.8778 (mt0) cc_final: 0.8412 (mt0) REVERT: A 715 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8043 (pp) REVERT: A 739 MET cc_start: 0.8290 (mtm) cc_final: 0.7934 (mtp) REVERT: A 924 MET cc_start: 0.8624 (mtp) cc_final: 0.8423 (ttt) REVERT: A 1053 MET cc_start: 0.8496 (mmm) cc_final: 0.8158 (mmm) REVERT: E 2015 ASP cc_start: 0.8941 (t70) cc_final: 0.8703 (t0) REVERT: E 2016 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8414 (tptt) REVERT: E 2024 LEU cc_start: 0.8978 (mp) cc_final: 0.8541 (tp) REVERT: E 2046 ASP cc_start: 0.8604 (t70) cc_final: 0.8388 (t0) REVERT: E 2077 ARG cc_start: 0.8928 (mmt90) cc_final: 0.8436 (mmm160) REVERT: B 153 ASP cc_start: 0.8507 (t0) cc_final: 0.7752 (t0) REVERT: B 157 ASN cc_start: 0.9338 (m-40) cc_final: 0.8832 (m110) REVERT: B 159 PHE cc_start: 0.9153 (t80) cc_final: 0.8918 (t80) REVERT: B 162 LEU cc_start: 0.9454 (mm) cc_final: 0.9007 (pp) REVERT: B 273 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8556 (p) REVERT: B 307 PHE cc_start: 0.8078 (t80) cc_final: 0.7712 (t80) REVERT: B 715 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.7980 (pp) REVERT: B 739 MET cc_start: 0.8279 (mtm) cc_final: 0.7911 (mtp) REVERT: B 900 ASP cc_start: 0.8573 (p0) cc_final: 0.8317 (p0) REVERT: F 2015 ASP cc_start: 0.8734 (t70) cc_final: 0.8384 (t0) REVERT: F 2016 LYS cc_start: 0.8974 (ttmt) cc_final: 0.8458 (tptt) REVERT: F 2046 ASP cc_start: 0.8437 (t70) cc_final: 0.8207 (t0) REVERT: F 2077 ARG cc_start: 0.8860 (mmt90) cc_final: 0.8389 (mmm160) REVERT: C 30 MET cc_start: 0.8777 (mmp) cc_final: 0.8508 (mmm) REVERT: C 48 TYR cc_start: 0.8552 (m-80) cc_final: 0.8332 (m-10) REVERT: C 118 LEU cc_start: 0.9269 (tp) cc_final: 0.8901 (pp) REVERT: C 153 ASP cc_start: 0.8636 (t0) cc_final: 0.8134 (t0) REVERT: C 162 LEU cc_start: 0.9418 (mm) cc_final: 0.9096 (pp) REVERT: C 273 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8572 (p) REVERT: C 285 MET cc_start: 0.8641 (mmm) cc_final: 0.8042 (mmm) REVERT: C 303 PHE cc_start: 0.8048 (t80) cc_final: 0.7830 (t80) REVERT: C 304 MET cc_start: 0.9167 (mmm) cc_final: 0.8949 (tpt) REVERT: C 307 PHE cc_start: 0.7986 (t80) cc_final: 0.7631 (t80) REVERT: C 362 ASP cc_start: 0.8353 (t0) cc_final: 0.8037 (t0) REVERT: C 442 MET cc_start: 0.8800 (tpp) cc_final: 0.8578 (tpp) REVERT: C 715 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8065 (pp) REVERT: C 739 MET cc_start: 0.8045 (mtp) cc_final: 0.7751 (mtp) REVERT: G 2015 ASP cc_start: 0.8961 (t70) cc_final: 0.8702 (t0) REVERT: G 2016 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8437 (tptt) REVERT: G 2046 ASP cc_start: 0.8629 (t70) cc_final: 0.8395 (t70) REVERT: G 2077 ARG cc_start: 0.8913 (mmt90) cc_final: 0.8414 (mmm160) REVERT: D 30 MET cc_start: 0.8771 (mmm) cc_final: 0.8553 (mmt) REVERT: D 118 LEU cc_start: 0.9197 (tp) cc_final: 0.8928 (pp) REVERT: D 157 ASN cc_start: 0.9378 (m-40) cc_final: 0.8737 (m110) REVERT: D 159 PHE cc_start: 0.8839 (t80) cc_final: 0.8560 (t80) REVERT: D 273 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8722 (p) REVERT: D 285 MET cc_start: 0.8591 (mmm) cc_final: 0.8277 (mmm) REVERT: D 303 PHE cc_start: 0.8139 (t80) cc_final: 0.7862 (t80) REVERT: D 442 MET cc_start: 0.9131 (tpp) cc_final: 0.8684 (tpp) REVERT: D 627 LYS cc_start: 0.7574 (tptt) cc_final: 0.7217 (tppt) REVERT: D 715 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8086 (pp) REVERT: D 739 MET cc_start: 0.8267 (mtp) cc_final: 0.7898 (mtp) REVERT: D 878 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8827 (mp) REVERT: D 892 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7480 (t70) REVERT: D 900 ASP cc_start: 0.8592 (p0) cc_final: 0.8329 (p0) REVERT: H 2015 ASP cc_start: 0.8606 (t70) cc_final: 0.8269 (t0) REVERT: H 2016 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8391 (tptt) REVERT: H 2046 ASP cc_start: 0.8553 (t70) cc_final: 0.8316 (t0) REVERT: H 2077 ARG cc_start: 0.8872 (mmt90) cc_final: 0.8454 (mmm160) REVERT: H 2141 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8092 (tt) outliers start: 75 outliers final: 44 residues processed: 496 average time/residue: 0.1999 time to fit residues: 169.7276 Evaluate side-chains 478 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 423 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 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 792 VAL 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 E residue 2188 VAL Chi-restraints excluded: chain B residue 105 ILE 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 273 THR 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 920 LEU Chi-restraints excluded: chain F residue 2157 ASP 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 273 THR 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 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 273 THR 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 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: 3.9990 chunk 63 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 283 optimal weight: 0.8980 chunk 248 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 327 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 216 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2061 GLN B 182 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.087350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068353 restraints weight = 118315.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.070688 restraints weight = 55561.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072220 restraints weight = 34655.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073227 restraints weight = 25683.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073730 restraints weight = 21212.334| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4517 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= 0.116 Angle : 0.588 13.874 50560 Z= 0.292 Chirality : 0.041 0.281 5756 Planarity : 0.003 0.049 6240 Dihedral : 8.499 128.699 5978 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.73 % Allowed : 15.19 % Favored : 83.08 % 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: -0.16 (0.13), residues: 4408 helix: 1.21 (0.12), residues: 2024 sheet: -1.60 (0.20), residues: 648 loop : -1.01 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 974 TYR 0.014 0.001 TYR F2008 PHE 0.028 0.001 PHE G2033 TRP 0.021 0.001 TRP G2176 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00264 (37300) covalent geometry : angle 0.58383 (50504) SS BOND : bond 0.00116 ( 16) SS BOND : angle 0.36176 ( 32) hydrogen bonds : bond 0.02973 ( 1448) hydrogen bonds : angle 4.11844 ( 4056) Misc. bond : bond 0.00044 ( 8) link_NAG-ASN : bond 0.01280 ( 8) link_NAG-ASN : angle 3.24990 ( 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 489 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 421 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8618 (m-80) cc_final: 0.8376 (m-10) REVERT: A 118 LEU cc_start: 0.9263 (tp) cc_final: 0.8911 (pp) REVERT: A 153 ASP cc_start: 0.8665 (t0) cc_final: 0.8144 (t0) REVERT: A 162 LEU cc_start: 0.9421 (mm) cc_final: 0.9104 (pp) REVERT: A 187 PHE cc_start: 0.8614 (t80) cc_final: 0.8412 (t80) REVERT: A 273 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8663 (p) REVERT: A 285 MET cc_start: 0.8631 (mmm) cc_final: 0.8014 (mmm) REVERT: A 307 PHE cc_start: 0.8025 (t80) cc_final: 0.7607 (t80) REVERT: A 362 ASP cc_start: 0.8378 (t0) cc_final: 0.7937 (t0) REVERT: A 459 GLN cc_start: 0.8834 (mt0) cc_final: 0.8495 (mt0) REVERT: A 715 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8058 (pp) REVERT: A 739 MET cc_start: 0.8313 (mtm) cc_final: 0.7964 (mtp) REVERT: A 924 MET cc_start: 0.8665 (mtp) cc_final: 0.8380 (ttt) REVERT: A 1053 MET cc_start: 0.8551 (mmm) cc_final: 0.8178 (mmm) REVERT: E 2015 ASP cc_start: 0.8949 (t70) cc_final: 0.8699 (t0) REVERT: E 2016 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8411 (tptt) REVERT: E 2046 ASP cc_start: 0.8568 (t70) cc_final: 0.8337 (t0) REVERT: E 2077 ARG cc_start: 0.8943 (mmt90) cc_final: 0.8438 (mmm160) REVERT: B 153 ASP cc_start: 0.8519 (t0) cc_final: 0.7706 (t0) REVERT: B 157 ASN cc_start: 0.9408 (m-40) cc_final: 0.8735 (m110) REVERT: B 162 LEU cc_start: 0.9448 (mm) cc_final: 0.9002 (pp) REVERT: B 187 PHE cc_start: 0.8545 (t80) cc_final: 0.8249 (t80) REVERT: B 273 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8551 (p) REVERT: B 307 PHE cc_start: 0.8065 (t80) cc_final: 0.7822 (t80) REVERT: B 715 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.7997 (pp) REVERT: B 739 MET cc_start: 0.8306 (mtm) cc_final: 0.7949 (mtp) REVERT: B 819 GLU cc_start: 0.7617 (mp0) cc_final: 0.7406 (mp0) REVERT: F 2015 ASP cc_start: 0.8647 (t70) cc_final: 0.8344 (t0) REVERT: F 2016 LYS cc_start: 0.8985 (ttmt) cc_final: 0.8458 (tptt) REVERT: F 2046 ASP cc_start: 0.8391 (t70) cc_final: 0.8154 (t0) REVERT: F 2077 ARG cc_start: 0.8880 (mmt90) cc_final: 0.8402 (mmm160) REVERT: C 48 TYR cc_start: 0.8562 (m-80) cc_final: 0.8309 (m-10) REVERT: C 118 LEU cc_start: 0.9269 (tp) cc_final: 0.8901 (pp) REVERT: C 153 ASP cc_start: 0.8671 (t0) cc_final: 0.8154 (t0) REVERT: C 162 LEU cc_start: 0.9417 (mm) cc_final: 0.9101 (pp) REVERT: C 273 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8644 (p) REVERT: C 285 MET cc_start: 0.8632 (mmm) cc_final: 0.8002 (mmm) REVERT: C 303 PHE cc_start: 0.8125 (t80) cc_final: 0.7855 (t80) REVERT: C 304 MET cc_start: 0.9183 (mmm) cc_final: 0.8968 (tpt) REVERT: C 307 PHE cc_start: 0.8016 (t80) cc_final: 0.7614 (t80) REVERT: C 362 ASP cc_start: 0.8378 (t0) cc_final: 0.8044 (t0) REVERT: C 442 MET cc_start: 0.8930 (tpp) cc_final: 0.8645 (tpp) REVERT: C 459 GLN cc_start: 0.8769 (mt0) cc_final: 0.8457 (mt0) REVERT: C 715 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8065 (pp) REVERT: C 878 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8884 (mp) REVERT: G 2015 ASP cc_start: 0.8956 (t70) cc_final: 0.8647 (t0) REVERT: G 2016 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8439 (tptt) REVERT: G 2077 ARG cc_start: 0.8923 (mmt90) cc_final: 0.8413 (mmm160) REVERT: D 30 MET cc_start: 0.8673 (mmm) cc_final: 0.8466 (mmt) REVERT: D 118 LEU cc_start: 0.9196 (tp) cc_final: 0.8936 (pp) REVERT: D 153 ASP cc_start: 0.8797 (t0) cc_final: 0.8141 (t0) REVERT: D 157 ASN cc_start: 0.9406 (m-40) cc_final: 0.8800 (m110) REVERT: D 273 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8631 (p) REVERT: D 285 MET cc_start: 0.8587 (mmm) cc_final: 0.8286 (mmm) REVERT: D 303 PHE cc_start: 0.8203 (t80) cc_final: 0.7926 (t80) REVERT: D 442 MET cc_start: 0.9113 (tpp) cc_final: 0.8687 (tpp) REVERT: D 627 LYS cc_start: 0.7538 (tptt) cc_final: 0.7163 (tppt) REVERT: D 715 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8056 (pp) REVERT: D 739 MET cc_start: 0.8328 (mtp) cc_final: 0.7945 (mtp) REVERT: D 878 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8906 (mp) REVERT: D 892 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7465 (t70) REVERT: D 1053 MET cc_start: 0.8571 (mmm) cc_final: 0.8229 (mmm) REVERT: H 2015 ASP cc_start: 0.8560 (t70) cc_final: 0.8277 (t0) REVERT: H 2016 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8350 (tptt) REVERT: H 2046 ASP cc_start: 0.8530 (t70) cc_final: 0.8294 (t0) REVERT: H 2077 ARG cc_start: 0.8878 (mmt90) cc_final: 0.8457 (mmm160) REVERT: H 2141 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8122 (tt) outliers start: 68 outliers final: 50 residues processed: 468 average time/residue: 0.1933 time to fit residues: 155.4230 Evaluate side-chains 469 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 407 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 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 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 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 185 VAL Chi-restraints excluded: chain B residue 227 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 792 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2157 ASP 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 273 THR 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 2157 ASP Chi-restraints excluded: chain G residue 2168 ILE 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 273 THR 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 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: 10.0000 chunk 199 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 346 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 425 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** ** 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 = 0.3500 r_free = 0.3500 target = 0.085718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.066521 restraints weight = 118636.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068780 restraints weight = 55702.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070328 restraints weight = 34869.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071292 restraints weight = 25921.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.071934 restraints weight = 21545.276| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4531 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 : 0.621 12.716 50560 Z= 0.311 Chirality : 0.042 0.275 5756 Planarity : 0.003 0.048 6240 Dihedral : 8.427 128.270 5978 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.68 % Allowed : 15.42 % Favored : 82.90 % 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: -0.13 (0.13), residues: 4408 helix: 1.10 (0.12), residues: 2060 sheet: -1.44 (0.21), residues: 600 loop : -0.94 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 575 TYR 0.020 0.001 TYR H2008 PHE 0.018 0.001 PHE C 303 TRP 0.026 0.001 TRP E2176 HIS 0.007 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00363 (37300) covalent geometry : angle 0.61762 (50504) SS BOND : bond 0.00128 ( 16) SS BOND : angle 0.42948 ( 32) hydrogen bonds : bond 0.03151 ( 1448) hydrogen bonds : angle 4.20471 ( 4056) Misc. bond : bond 0.00073 ( 8) link_NAG-ASN : bond 0.01223 ( 8) link_NAG-ASN : angle 3.24857 ( 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: 66 poor density : 413 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8611 (m-80) cc_final: 0.8277 (m-10) REVERT: A 118 LEU cc_start: 0.9297 (tp) cc_final: 0.8936 (pp) REVERT: A 153 ASP cc_start: 0.8668 (t0) cc_final: 0.8446 (t0) REVERT: A 162 LEU cc_start: 0.9431 (mm) cc_final: 0.9138 (pp) REVERT: A 187 PHE cc_start: 0.8637 (t80) cc_final: 0.8340 (t80) REVERT: A 273 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8680 (p) REVERT: A 285 MET cc_start: 0.8598 (mmm) cc_final: 0.8297 (mmm) REVERT: A 303 PHE cc_start: 0.8122 (t80) cc_final: 0.7868 (t80) REVERT: A 362 ASP cc_start: 0.8434 (t0) cc_final: 0.7889 (t0) REVERT: A 459 GLN cc_start: 0.8809 (mt0) cc_final: 0.8530 (mt0) REVERT: A 627 LYS cc_start: 0.7445 (tptt) cc_final: 0.6989 (tppt) REVERT: A 715 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8183 (pp) REVERT: A 739 MET cc_start: 0.8352 (mtm) cc_final: 0.8007 (mtp) REVERT: A 878 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8941 (mp) REVERT: A 924 MET cc_start: 0.8692 (mtp) cc_final: 0.8418 (ttt) REVERT: A 1053 MET cc_start: 0.8672 (mmm) cc_final: 0.8372 (mmm) REVERT: E 2015 ASP cc_start: 0.8963 (t70) cc_final: 0.8687 (t0) REVERT: E 2016 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8435 (tptt) REVERT: E 2046 ASP cc_start: 0.8596 (t70) cc_final: 0.8372 (t0) REVERT: E 2077 ARG cc_start: 0.8978 (mmt90) cc_final: 0.8438 (mmm160) REVERT: B 153 ASP cc_start: 0.8514 (t0) cc_final: 0.7706 (t0) REVERT: B 157 ASN cc_start: 0.9395 (m-40) cc_final: 0.8785 (m110) REVERT: B 159 PHE cc_start: 0.9153 (t80) cc_final: 0.8934 (t80) REVERT: B 162 LEU cc_start: 0.9459 (mm) cc_final: 0.9023 (pp) REVERT: B 187 PHE cc_start: 0.8472 (t80) cc_final: 0.8071 (t80) REVERT: B 273 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8617 (p) REVERT: B 460 MET cc_start: 0.8606 (ttm) cc_final: 0.8377 (mtp) REVERT: B 715 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8196 (pp) REVERT: B 739 MET cc_start: 0.8348 (mtm) cc_final: 0.7990 (mtp) REVERT: B 1053 MET cc_start: 0.8535 (mmm) cc_final: 0.8224 (mmm) REVERT: F 2015 ASP cc_start: 0.8740 (t70) cc_final: 0.8383 (t0) REVERT: F 2016 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8461 (tptt) REVERT: F 2046 ASP cc_start: 0.8427 (t70) cc_final: 0.8199 (t0) REVERT: F 2077 ARG cc_start: 0.8926 (mmt90) cc_final: 0.8400 (mmm160) REVERT: C 48 TYR cc_start: 0.8550 (m-80) cc_final: 0.8239 (m-10) REVERT: C 118 LEU cc_start: 0.9264 (tp) cc_final: 0.8907 (pp) REVERT: C 153 ASP cc_start: 0.8685 (t0) cc_final: 0.8465 (t0) REVERT: C 162 LEU cc_start: 0.9427 (mm) cc_final: 0.9137 (pp) REVERT: C 186 ASP cc_start: 0.7654 (m-30) cc_final: 0.7170 (m-30) REVERT: C 273 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8660 (p) REVERT: C 285 MET cc_start: 0.8590 (mmm) cc_final: 0.8306 (mmm) REVERT: C 303 PHE cc_start: 0.8353 (t80) cc_final: 0.8021 (t80) REVERT: C 304 MET cc_start: 0.9170 (mmm) cc_final: 0.8956 (tpt) REVERT: C 362 ASP cc_start: 0.8426 (t0) cc_final: 0.8092 (t0) REVERT: C 459 GLN cc_start: 0.8901 (mt0) cc_final: 0.8531 (mt0) REVERT: C 627 LYS cc_start: 0.7451 (tptt) cc_final: 0.7058 (tppt) REVERT: C 715 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8192 (pp) REVERT: C 739 MET cc_start: 0.8318 (mtm) cc_final: 0.7988 (mtp) REVERT: C 878 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8924 (mp) REVERT: C 924 MET cc_start: 0.8641 (mtp) cc_final: 0.8321 (ttt) REVERT: G 2015 ASP cc_start: 0.8927 (t70) cc_final: 0.8620 (t0) REVERT: G 2016 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8423 (tptt) REVERT: G 2046 ASP cc_start: 0.8480 (t70) cc_final: 0.8271 (t0) REVERT: G 2077 ARG cc_start: 0.8962 (mmt90) cc_final: 0.8415 (mmm160) REVERT: D 118 LEU cc_start: 0.9165 (tp) cc_final: 0.8906 (pp) REVERT: D 273 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8721 (p) REVERT: D 285 MET cc_start: 0.8586 (mmm) cc_final: 0.8283 (mmm) REVERT: D 362 ASP cc_start: 0.8598 (t70) cc_final: 0.8375 (t0) REVERT: D 442 MET cc_start: 0.9084 (tpp) cc_final: 0.8659 (tpp) REVERT: D 627 LYS cc_start: 0.7569 (tptt) cc_final: 0.7161 (tppt) REVERT: D 715 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8323 (pp) REVERT: D 739 MET cc_start: 0.8414 (mtp) cc_final: 0.7994 (mtp) REVERT: D 878 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8933 (mp) REVERT: D 1053 MET cc_start: 0.8618 (mmm) cc_final: 0.8380 (mmm) REVERT: H 2015 ASP cc_start: 0.8614 (t70) cc_final: 0.8269 (t0) REVERT: H 2016 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8395 (tptt) REVERT: H 2046 ASP cc_start: 0.8539 (t70) cc_final: 0.8302 (t0) REVERT: H 2077 ARG cc_start: 0.8892 (mmt90) cc_final: 0.8488 (mmm160) REVERT: H 2141 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8085 (tt) outliers start: 66 outliers final: 48 residues processed: 462 average time/residue: 0.2042 time to fit residues: 161.5772 Evaluate side-chains 456 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 396 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 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 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 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 166 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 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 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 185 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 314 MET 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 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 273 THR 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 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: 0.8980 chunk 287 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 424 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 182 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN F2061 GLN C 182 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2061 GLN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.085793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.066508 restraints weight = 118260.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068808 restraints weight = 55559.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070331 restraints weight = 34805.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071315 restraints weight = 25891.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.071923 restraints weight = 21493.796| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37332 Z= 0.155 Angle : 0.630 12.277 50560 Z= 0.314 Chirality : 0.042 0.273 5756 Planarity : 0.003 0.081 6240 Dihedral : 8.223 128.306 5978 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.80 % Allowed : 15.68 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4408 helix: 1.02 (0.12), residues: 2092 sheet: -1.70 (0.20), residues: 640 loop : -0.86 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 974 TYR 0.014 0.001 TYR F2008 PHE 0.040 0.001 PHE E2023 TRP 0.023 0.001 TRP G2176 HIS 0.007 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00357 (37300) covalent geometry : angle 0.62663 (50504) SS BOND : bond 0.00130 ( 16) SS BOND : angle 0.41630 ( 32) hydrogen bonds : bond 0.03136 ( 1448) hydrogen bonds : angle 4.22228 ( 4056) Misc. bond : bond 0.00061 ( 8) link_NAG-ASN : bond 0.01211 ( 8) link_NAG-ASN : angle 3.23532 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6158.02 seconds wall clock time: 107 minutes 27.89 seconds (6447.89 seconds total)