Starting phenix.real_space_refine on Tue Sep 15 07:51:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v35_21028/09_2026/6v35_21028.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v35_21028/09_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_21028/09_2026/6v35_21028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v35_21028/09_2026/6v35_21028.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6v35_21028/09_2026/6v35_21028.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v35_21028/09_2026/6v35_21028.cif" model { file = "/net/cci-nas-00/data/ceres_data/6v35_21028/09_2026/6v35_21028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v35_21028/09_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): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 176 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: 63 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: 199 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: 92 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: 130 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: 63 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: 153 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: 92 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: 7.35, per 1000 atoms: 0.20 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: 2.78 Conformation dependent library (CDL) restraints added in 1.2 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: 0.97 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: 7.38 Time building geometry restraints manager: 3.60 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 - 23.36: 21232 23.36 - 46.72: 560 46.72 - 70.09: 132 70.09 - 93.45: 44 93.45 - 116.81: 8 Dihedral angle restraints: 21976 sinusoidal: 8932 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 21973 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: 1.770 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: 0.570 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 30.580 Find NCS groups from input model: 1.010 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 12.367 116.811 13472 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/Z covalent geometry : bond 0.01105 / 0.59 (37300) covalent geometry : angle 1.23293 / 0.68 (50504) SS BOND : bond 0.00514 / 0.30 ( 16) SS BOND : angle 0.75239 / 0.44 ( 32) hydrogen bonds : bond 0.20858 / 13.18 ( 1448) hydrogen bonds : angle 8.37568 / 5.98 ( 4056) Misc. bond : bond 0.00278 / 0.15 ( 8) link_NAG-ASN : bond 0.01787 / 0.95 ( 8) link_NAG-ASN : angle 6.99993 / 4.08 ( 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 : 1.313 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: 0.2189 time to fit residues: 310.8013 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 : 1.211 ------------------------------------------------------------------------------- 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... ** 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 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: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.087438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068396 restraints weight = 116841.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070654 restraints weight = 55196.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.072193 restraints weight = 34754.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073199 restraints weight = 25937.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073764 restraints weight = 21473.328| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37332 Z= 0.150 Angle : 0.649 11.935 50560 Z= 0.328 Chirality : 0.046 0.468 5756 Planarity : 0.005 0.046 6240 Dihedral : 10.823 133.803 5268 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.52 % Allowed : 9.15 % Favored : 88.34 % 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: -1.65 (0.12), residues: 4408 helix: -0.38 (0.11), residues: 1980 sheet: -1.60 (0.20), residues: 632 loop : -1.59 (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/Z covalent geometry : bond 0.00335 / 0.15 (37300) covalent geometry : angle 0.63875 / 0.33 (50504) SS BOND : bond 0.00285 / 0.20 ( 16) SS BOND : angle 0.90807 / 0.57 ( 32) hydrogen bonds : bond 0.04136 / 2.67 ( 1448) hydrogen bonds : angle 5.14238 / 3.70 ( 4056) Misc. bond : bond 0.00052 / 0.03 ( 8) link_NAG-ASN : bond 0.01600 / 0.84 ( 8) link_NAG-ASN : angle 5.30736 / 3.12 ( 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 643 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 544 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9444 (tp) cc_final: 0.9158 (tp) REVERT: A 38 PHE cc_start: 0.9156 (m-10) cc_final: 0.8886 (m-80) REVERT: A 48 TYR cc_start: 0.8626 (m-80) cc_final: 0.8197 (m-10) REVERT: A 118 LEU cc_start: 0.9349 (tp) cc_final: 0.9061 (pp) REVERT: A 153 ASP cc_start: 0.8552 (t0) cc_final: 0.7898 (t0) REVERT: A 157 ASN cc_start: 0.9217 (m-40) cc_final: 0.8503 (m110) REVERT: A 162 LEU cc_start: 0.9420 (mt) cc_final: 0.9031 (pp) REVERT: A 282 MET cc_start: 0.8857 (tpp) cc_final: 0.8622 (tpp) REVERT: A 285 MET cc_start: 0.8428 (mmm) cc_final: 0.8208 (mmm) REVERT: A 561 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8341 (pp) REVERT: A 900 ASP cc_start: 0.8604 (p0) cc_final: 0.8290 (p0) REVERT: E 2015 ASP cc_start: 0.8918 (t70) cc_final: 0.8667 (t0) REVERT: E 2016 LYS cc_start: 0.9079 (ttmt) cc_final: 0.8494 (tptt) REVERT: E 2046 ASP cc_start: 0.8747 (t70) cc_final: 0.8456 (t70) REVERT: E 2077 ARG cc_start: 0.8942 (mmt90) cc_final: 0.8600 (mmm160) REVERT: E 2163 ARG cc_start: 0.8260 (mtt-85) cc_final: 0.7373 (mmm160) REVERT: B 118 LEU cc_start: 0.9266 (tp) cc_final: 0.8980 (pp) REVERT: B 153 ASP cc_start: 0.8569 (t0) cc_final: 0.7940 (t0) REVERT: B 157 ASN cc_start: 0.9198 (m-40) cc_final: 0.8540 (m110) REVERT: B 162 LEU cc_start: 0.9463 (mm) cc_final: 0.9245 (mm) REVERT: B 182 ASN cc_start: 0.7515 (t160) cc_final: 0.7094 (t0) REVERT: B 282 MET cc_start: 0.8862 (tpp) cc_final: 0.8610 (tpp) REVERT: B 285 MET cc_start: 0.8345 (mmm) cc_final: 0.8110 (mmm) REVERT: B 362 ASP cc_start: 0.8260 (t0) cc_final: 0.7685 (t0) REVERT: B 460 MET cc_start: 0.8919 (mmm) cc_final: 0.8601 (mmm) REVERT: B 561 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8478 (pp) REVERT: B 900 ASP cc_start: 0.8701 (p0) cc_final: 0.8471 (p0) REVERT: F 2015 ASP cc_start: 0.8918 (t70) cc_final: 0.8653 (t0) REVERT: F 2016 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8423 (tptt) REVERT: F 2046 ASP cc_start: 0.8730 (t70) cc_final: 0.8405 (t70) REVERT: F 2077 ARG cc_start: 0.8951 (mmt90) cc_final: 0.8597 (mmm160) REVERT: F 2163 ARG cc_start: 0.8204 (mtt-85) cc_final: 0.7387 (mmm160) REVERT: C 26 LEU cc_start: 0.9445 (tp) cc_final: 0.9158 (tp) REVERT: C 38 PHE cc_start: 0.9166 (m-10) cc_final: 0.8852 (m-80) REVERT: C 48 TYR cc_start: 0.8602 (m-80) cc_final: 0.8174 (m-10) REVERT: C 118 LEU cc_start: 0.9346 (tp) cc_final: 0.9061 (pp) REVERT: C 153 ASP cc_start: 0.8555 (t0) cc_final: 0.7911 (t0) REVERT: C 157 ASN cc_start: 0.9206 (m-40) cc_final: 0.8498 (m110) REVERT: C 162 LEU cc_start: 0.9418 (mt) cc_final: 0.9001 (pp) REVERT: C 282 MET cc_start: 0.8844 (tpp) cc_final: 0.8605 (tpp) REVERT: C 285 MET cc_start: 0.8435 (mmm) cc_final: 0.8213 (mmm) REVERT: C 362 ASP cc_start: 0.8227 (t0) cc_final: 0.7662 (t0) REVERT: C 561 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8328 (pp) REVERT: C 1053 MET cc_start: 0.8495 (mtp) cc_final: 0.8268 (mtp) REVERT: G 2015 ASP cc_start: 0.8961 (t70) cc_final: 0.8683 (t0) REVERT: G 2016 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8507 (tptt) REVERT: G 2077 ARG cc_start: 0.8934 (mmt90) cc_final: 0.8598 (mmm160) REVERT: G 2163 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.7918 (mtt-85) REVERT: D 118 LEU cc_start: 0.9302 (tp) cc_final: 0.8924 (pp) REVERT: D 153 ASP cc_start: 0.8500 (t0) cc_final: 0.7903 (t0) REVERT: D 157 ASN cc_start: 0.9109 (m-40) cc_final: 0.8317 (m110) REVERT: D 276 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8059 (mm-30) REVERT: D 285 MET cc_start: 0.8455 (mmm) cc_final: 0.7947 (mmm) REVERT: D 303 PHE cc_start: 0.8100 (t80) cc_final: 0.7873 (t80) REVERT: D 307 PHE cc_start: 0.8091 (t80) cc_final: 0.7669 (t80) REVERT: D 362 ASP cc_start: 0.8309 (t0) cc_final: 0.7708 (t0) REVERT: D 460 MET cc_start: 0.8962 (mmm) cc_final: 0.8587 (mmm) REVERT: D 561 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8500 (pp) REVERT: D 900 ASP cc_start: 0.8556 (p0) cc_final: 0.8329 (p0) REVERT: H 2015 ASP cc_start: 0.8924 (t70) cc_final: 0.8684 (t0) REVERT: H 2016 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8278 (tptt) REVERT: H 2046 ASP cc_start: 0.8756 (t70) cc_final: 0.8511 (t70) REVERT: H 2077 ARG cc_start: 0.8869 (mmt90) cc_final: 0.8560 (mmm160) REVERT: H 2115 TYR cc_start: 0.9286 (t80) cc_final: 0.9035 (t80) REVERT: H 2141 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.7956 (tt) REVERT: H 2163 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7689 (mtp180) outliers start: 99 outliers final: 40 residues processed: 616 average time/residue: 0.1961 time to fit residues: 204.5307 Evaluate side-chains 460 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 415 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 739 MET 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: 0.6980 chunk 376 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 337 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 418 optimal weight: 0.2980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 143 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.086086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.066932 restraints weight = 117140.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069218 restraints weight = 53924.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.070736 restraints weight = 33680.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.071701 restraints weight = 25005.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.072224 restraints weight = 20732.376| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37332 Z= 0.154 Angle : 0.600 10.938 50560 Z= 0.301 Chirality : 0.045 0.457 5756 Planarity : 0.004 0.051 6240 Dihedral : 10.095 150.754 5250 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.69 % Allowed : 10.65 % Favored : 86.66 % 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: -0.98 (0.13), residues: 4408 helix: 0.30 (0.12), residues: 2036 sheet: -1.51 (0.20), residues: 596 loop : -1.37 (0.15), residues: 1776 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 0.053 0.002 TRP E2176 HIS 0.006 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (37300) covalent geometry : angle 0.58849 / 0.30 (50504) SS BOND : bond 0.00193 / 0.13 ( 16) SS BOND : angle 0.75188 / 0.49 ( 32) hydrogen bonds : bond 0.03514 / 2.26 ( 1448) hydrogen bonds : angle 4.66649 / 3.35 ( 4056) Misc. bond : bond 0.00066 / 0.03 ( 8) link_NAG-ASN : bond 0.01588 / 0.83 ( 8) link_NAG-ASN : angle 5.39911 / 3.16 ( 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 568 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 462 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8748 (mmm) cc_final: 0.8478 (mmm) REVERT: A 48 TYR cc_start: 0.8614 (m-80) cc_final: 0.8141 (m-10) REVERT: A 118 LEU cc_start: 0.9328 (tp) cc_final: 0.9051 (pp) REVERT: A 162 LEU cc_start: 0.9388 (mt) cc_final: 0.8997 (pp) REVERT: A 285 MET cc_start: 0.8528 (mmm) cc_final: 0.8269 (mmm) REVERT: A 303 PHE cc_start: 0.8209 (t80) cc_final: 0.7937 (t80) REVERT: A 362 ASP cc_start: 0.8343 (t0) cc_final: 0.7863 (t0) REVERT: A 561 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8346 (pp) REVERT: A 715 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.7937 (pp) REVERT: A 830 MET cc_start: 0.8461 (mtp) cc_final: 0.8209 (ttm) REVERT: E 2015 ASP cc_start: 0.8910 (t70) cc_final: 0.8668 (t0) REVERT: E 2016 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8520 (tptt) REVERT: E 2046 ASP cc_start: 0.8783 (t70) cc_final: 0.8500 (t70) REVERT: E 2077 ARG cc_start: 0.8895 (mmt90) cc_final: 0.8526 (mmm160) REVERT: E 2120 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8423 (mptt) REVERT: E 2163 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7333 (mmm160) REVERT: B 118 LEU cc_start: 0.9257 (tp) cc_final: 0.8998 (pp) REVERT: B 153 ASP cc_start: 0.8719 (t0) cc_final: 0.8005 (t0) REVERT: B 157 ASN cc_start: 0.9218 (m-40) cc_final: 0.8525 (m110) REVERT: B 162 LEU cc_start: 0.9451 (mm) cc_final: 0.9010 (pp) REVERT: B 182 ASN cc_start: 0.7651 (t160) cc_final: 0.7101 (t0) REVERT: B 282 MET cc_start: 0.8960 (tpp) cc_final: 0.8745 (tpp) REVERT: B 362 ASP cc_start: 0.8342 (t0) cc_final: 0.7735 (t0) REVERT: B 561 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8419 (pp) REVERT: B 715 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.7852 (pp) REVERT: B 900 ASP cc_start: 0.8769 (p0) cc_final: 0.8534 (p0) REVERT: F 2015 ASP cc_start: 0.8914 (t70) cc_final: 0.8624 (t0) REVERT: F 2016 LYS cc_start: 0.9059 (ttmt) cc_final: 0.8385 (tptt) REVERT: F 2077 ARG cc_start: 0.9024 (mmt90) cc_final: 0.8543 (mmm160) REVERT: F 2163 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7439 (mmm160) REVERT: C 21 MET cc_start: 0.8743 (mmm) cc_final: 0.8478 (mmm) REVERT: C 118 LEU cc_start: 0.9329 (tp) cc_final: 0.9052 (pp) REVERT: C 162 LEU cc_start: 0.9391 (mt) cc_final: 0.9143 (mm) REVERT: C 285 MET cc_start: 0.8517 (mmm) cc_final: 0.8263 (mmm) REVERT: C 303 PHE cc_start: 0.8203 (t80) cc_final: 0.7930 (t80) REVERT: C 362 ASP cc_start: 0.8369 (t0) cc_final: 0.7758 (t0) REVERT: C 561 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8380 (pp) REVERT: C 715 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.7918 (pp) REVERT: C 739 MET cc_start: 0.8432 (mtm) cc_final: 0.8048 (mtp) REVERT: C 1053 MET cc_start: 0.8673 (mtp) cc_final: 0.8464 (mtm) REVERT: G 2015 ASP cc_start: 0.8920 (t70) cc_final: 0.8666 (t0) REVERT: G 2016 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8541 (tptt) REVERT: G 2046 ASP cc_start: 0.8643 (t70) cc_final: 0.8177 (t0) REVERT: G 2077 ARG cc_start: 0.8980 (mmt90) cc_final: 0.8545 (mmm160) REVERT: G 2120 LYS cc_start: 0.8671 (mmtm) cc_final: 0.8419 (mptt) REVERT: G 2163 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7360 (mmm160) REVERT: D 39 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8941 (pt) REVERT: D 118 LEU cc_start: 0.9251 (tp) cc_final: 0.8887 (pp) REVERT: D 153 ASP cc_start: 0.8650 (t0) cc_final: 0.7993 (t0) REVERT: D 157 ASN cc_start: 0.9191 (m-40) cc_final: 0.8336 (m110) REVERT: D 162 LEU cc_start: 0.9414 (mm) cc_final: 0.9029 (pp) REVERT: D 182 ASN cc_start: 0.7649 (t160) cc_final: 0.7066 (t0) REVERT: D 285 MET cc_start: 0.8503 (mmm) cc_final: 0.8240 (mmm) REVERT: D 303 PHE cc_start: 0.8178 (t80) cc_final: 0.7883 (t80) REVERT: D 362 ASP cc_start: 0.8368 (t0) cc_final: 0.7852 (t0) REVERT: D 460 MET cc_start: 0.8912 (mmm) cc_final: 0.8692 (mmm) REVERT: D 561 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8501 (pp) REVERT: D 715 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8046 (pp) REVERT: D 900 ASP cc_start: 0.8633 (p0) cc_final: 0.8371 (p0) REVERT: H 2015 ASP cc_start: 0.8925 (t70) cc_final: 0.8622 (t0) REVERT: H 2016 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8308 (tptt) REVERT: H 2046 ASP cc_start: 0.8790 (t70) cc_final: 0.8570 (t70) REVERT: H 2077 ARG cc_start: 0.8889 (mmt90) cc_final: 0.8522 (mmm160) REVERT: H 2115 TYR cc_start: 0.9352 (t80) cc_final: 0.8947 (t80) REVERT: H 2131 MET cc_start: 0.8673 (mmt) cc_final: 0.8469 (mmp) REVERT: H 2141 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8016 (tt) REVERT: H 2163 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7765 (mtp180) REVERT: H 2166 ASP cc_start: 0.7945 (p0) cc_final: 0.7453 (p0) outliers start: 106 outliers final: 41 residues processed: 539 average time/residue: 0.2014 time to fit residues: 183.7841 Evaluate side-chains 459 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 408 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 190 VAL 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 917 VAL 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 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 920 LEU Chi-restraints excluded: chain D residue 39 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 190 VAL 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 739 MET 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 2188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 199 optimal weight: 9.9990 chunk 65 optimal weight: 0.3980 chunk 265 optimal weight: 0.9990 chunk 355 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 428 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 745 ASN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 ASN C 143 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN C 745 ASN D 143 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.086279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067042 restraints weight = 117152.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069349 restraints weight = 54815.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070873 restraints weight = 34368.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.071853 restraints weight = 25565.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.072420 restraints weight = 21206.830| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3510 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= 0.135 Angle : 0.578 10.832 50560 Z= 0.288 Chirality : 0.044 0.456 5756 Planarity : 0.004 0.047 6240 Dihedral : 9.633 155.895 5250 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.41 % Allowed : 11.74 % Favored : 85.85 % 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: -0.69 (0.13), residues: 4408 helix: 0.65 (0.12), residues: 2044 sheet: -1.49 (0.21), residues: 588 loop : -1.33 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 213 TYR 0.015 0.001 TYR F2008 PHE 0.016 0.001 PHE B 303 TRP 0.034 0.001 TRP E2176 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (37300) covalent geometry : angle 0.56590 / 0.29 (50504) SS BOND : bond 0.00168 / 0.10 ( 16) SS BOND : angle 0.52243 / 0.34 ( 32) hydrogen bonds : bond 0.03272 / 2.10 ( 1448) hydrogen bonds : angle 4.46551 / 3.21 ( 4056) Misc. bond : bond 0.00069 / 0.03 ( 8) link_NAG-ASN : bond 0.01596 / 0.83 ( 8) link_NAG-ASN : angle 5.34519 / 3.13 ( 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 535 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 440 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8730 (mmm) cc_final: 0.8342 (mmm) REVERT: A 48 TYR cc_start: 0.8599 (m-80) cc_final: 0.8242 (m-10) REVERT: A 118 LEU cc_start: 0.9315 (tp) cc_final: 0.9053 (pp) REVERT: A 153 ASP cc_start: 0.8553 (t0) cc_final: 0.8149 (t0) REVERT: A 162 LEU cc_start: 0.9373 (mt) cc_final: 0.8987 (pp) REVERT: A 285 MET cc_start: 0.8519 (mmm) cc_final: 0.7970 (mmm) REVERT: A 303 PHE cc_start: 0.8167 (t80) cc_final: 0.7946 (t80) REVERT: A 307 PHE cc_start: 0.8094 (t80) cc_final: 0.7686 (t80) REVERT: A 362 ASP cc_start: 0.8361 (t0) cc_final: 0.7827 (t0) REVERT: A 561 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8374 (pp) REVERT: A 715 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.7941 (pp) REVERT: A 830 MET cc_start: 0.8433 (mtp) cc_final: 0.8186 (ttm) REVERT: A 900 ASP cc_start: 0.8628 (p0) cc_final: 0.8331 (p0) REVERT: E 2015 ASP cc_start: 0.8904 (t70) cc_final: 0.8671 (t0) REVERT: E 2016 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8521 (tptt) REVERT: E 2046 ASP cc_start: 0.8774 (t70) cc_final: 0.8516 (t70) REVERT: E 2077 ARG cc_start: 0.8904 (mmt90) cc_final: 0.8483 (mmm160) REVERT: E 2163 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7294 (mmm160) REVERT: B 118 LEU cc_start: 0.9228 (tp) cc_final: 0.8988 (pp) REVERT: B 162 LEU cc_start: 0.9416 (mm) cc_final: 0.8961 (pp) REVERT: B 362 ASP cc_start: 0.8362 (t0) cc_final: 0.7821 (t0) REVERT: B 601 ASP cc_start: 0.7384 (p0) cc_final: 0.6581 (p0) REVERT: B 715 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.7856 (pp) REVERT: B 900 ASP cc_start: 0.8755 (p0) cc_final: 0.8532 (p0) REVERT: F 2015 ASP cc_start: 0.8897 (t70) cc_final: 0.8595 (t0) REVERT: F 2016 LYS cc_start: 0.9037 (ttmt) cc_final: 0.8368 (tptt) REVERT: F 2046 ASP cc_start: 0.8610 (t70) cc_final: 0.8178 (t0) REVERT: F 2077 ARG cc_start: 0.8909 (mmt90) cc_final: 0.8492 (mmm160) REVERT: F 2163 ARG cc_start: 0.8073 (mtt-85) cc_final: 0.7341 (mmm160) REVERT: F 2166 ASP cc_start: 0.8334 (p0) cc_final: 0.8029 (p0) REVERT: C 21 MET cc_start: 0.8725 (mmm) cc_final: 0.8351 (mmm) REVERT: C 118 LEU cc_start: 0.9314 (tp) cc_final: 0.9052 (pp) REVERT: C 153 ASP cc_start: 0.8537 (t0) cc_final: 0.8135 (t0) REVERT: C 162 LEU cc_start: 0.9384 (mt) cc_final: 0.8980 (pp) REVERT: C 285 MET cc_start: 0.8520 (mmm) cc_final: 0.7970 (mmm) REVERT: C 303 PHE cc_start: 0.8155 (t80) cc_final: 0.7928 (t80) REVERT: C 307 PHE cc_start: 0.8085 (t80) cc_final: 0.7680 (t80) REVERT: C 362 ASP cc_start: 0.8385 (t0) cc_final: 0.7802 (t0) REVERT: C 561 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8335 (pp) REVERT: C 715 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.7940 (pp) REVERT: C 900 ASP cc_start: 0.8628 (p0) cc_final: 0.8338 (p0) REVERT: C 1053 MET cc_start: 0.8602 (mtp) cc_final: 0.8393 (mtm) REVERT: G 2015 ASP cc_start: 0.8925 (t70) cc_final: 0.8672 (t0) REVERT: G 2016 LYS cc_start: 0.9134 (ttmt) cc_final: 0.8534 (tptt) REVERT: G 2046 ASP cc_start: 0.8659 (t70) cc_final: 0.8209 (t0) REVERT: G 2077 ARG cc_start: 0.8914 (mmt90) cc_final: 0.8502 (mmm160) REVERT: G 2163 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.7362 (mmm160) REVERT: D 30 MET cc_start: 0.8565 (mmm) cc_final: 0.8310 (mmm) REVERT: D 104 MET cc_start: 0.8585 (mtp) cc_final: 0.8243 (mtp) REVERT: D 118 LEU cc_start: 0.9241 (tp) cc_final: 0.8882 (pp) REVERT: D 153 ASP cc_start: 0.8757 (t0) cc_final: 0.8114 (t0) REVERT: D 157 ASN cc_start: 0.9216 (m-40) cc_final: 0.8413 (m110) REVERT: D 162 LEU cc_start: 0.9424 (mm) cc_final: 0.9191 (mm) REVERT: D 285 MET cc_start: 0.8500 (mmm) cc_final: 0.7931 (mmm) REVERT: D 303 PHE cc_start: 0.8183 (t80) cc_final: 0.7948 (t80) REVERT: D 307 PHE cc_start: 0.8116 (t80) cc_final: 0.7697 (t80) REVERT: D 362 ASP cc_start: 0.8369 (t0) cc_final: 0.7880 (t0) REVERT: D 442 MET cc_start: 0.8904 (tpp) cc_final: 0.8693 (tpp) REVERT: D 601 ASP cc_start: 0.7395 (p0) cc_final: 0.6516 (p0) REVERT: D 715 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8046 (pp) REVERT: D 900 ASP cc_start: 0.8660 (p0) cc_final: 0.8393 (p0) REVERT: H 2015 ASP cc_start: 0.8909 (t70) cc_final: 0.8592 (t0) REVERT: H 2016 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8387 (tptt) REVERT: H 2077 ARG cc_start: 0.8932 (mmt90) cc_final: 0.8523 (mmm160) REVERT: H 2115 TYR cc_start: 0.9325 (t80) cc_final: 0.9122 (t80) REVERT: H 2141 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8020 (tt) REVERT: H 2163 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.7760 (mtp180) outliers start: 95 outliers final: 49 residues processed: 509 average time/residue: 0.1918 time to fit residues: 167.0797 Evaluate side-chains 465 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 409 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 317 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 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 715 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU 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 715 LEU 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 2187 ILE Chi-restraints excluded: chain G residue 2188 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 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 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 Chi-restraints excluded: chain H residue 2188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 116 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 424 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 347 optimal weight: 7.9990 chunk 150 optimal weight: 0.2980 chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN A 216 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN C 745 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.086596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.067746 restraints weight = 116180.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070029 restraints weight = 53623.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.071536 restraints weight = 33351.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072521 restraints weight = 24643.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073015 restraints weight = 20340.392| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37332 Z= 0.115 Angle : 0.558 10.238 50560 Z= 0.278 Chirality : 0.044 0.457 5756 Planarity : 0.003 0.047 6240 Dihedral : 8.874 138.270 5250 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.57 % Allowed : 12.20 % Favored : 85.24 % 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: -0.41 (0.13), residues: 4408 helix: 0.95 (0.12), residues: 2020 sheet: -1.46 (0.21), residues: 604 loop : -1.22 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 213 TYR 0.010 0.001 TYR F2008 PHE 0.021 0.001 PHE G2033 TRP 0.027 0.001 TRP E2176 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (37300) covalent geometry : angle 0.54594 / 0.28 (50504) SS BOND : bond 0.00129 / 0.08 ( 16) SS BOND : angle 0.44440 / 0.29 ( 32) hydrogen bonds : bond 0.03107 / 1.98 ( 1448) hydrogen bonds : angle 4.29672 / 3.08 ( 4056) Misc. bond : bond 0.00060 / 0.03 ( 8) link_NAG-ASN : bond 0.01610 / 0.84 ( 8) link_NAG-ASN : angle 5.32467 / 3.11 ( 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 553 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 452 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8597 (m-80) cc_final: 0.8309 (m-10) REVERT: A 118 LEU cc_start: 0.9302 (tp) cc_final: 0.9049 (pp) REVERT: A 153 ASP cc_start: 0.8540 (t0) cc_final: 0.8072 (t0) REVERT: A 162 LEU cc_start: 0.9367 (mt) cc_final: 0.8982 (pp) REVERT: A 273 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8702 (p) REVERT: A 285 MET cc_start: 0.8532 (mmm) cc_final: 0.8012 (mmm) REVERT: A 303 PHE cc_start: 0.8152 (t80) cc_final: 0.7794 (t80) REVERT: A 307 PHE cc_start: 0.8074 (t80) cc_final: 0.7789 (t80) REVERT: A 362 ASP cc_start: 0.8385 (t0) cc_final: 0.7845 (t0) REVERT: A 561 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8569 (pp) REVERT: A 715 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.7829 (pp) REVERT: A 739 MET cc_start: 0.8368 (mtp) cc_final: 0.8016 (mtp) REVERT: A 900 ASP cc_start: 0.8628 (p0) cc_final: 0.8322 (p0) REVERT: E 2015 ASP cc_start: 0.8896 (t70) cc_final: 0.8653 (t0) REVERT: E 2016 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8594 (tptt) REVERT: E 2046 ASP cc_start: 0.8740 (t70) cc_final: 0.8431 (t70) REVERT: E 2077 ARG cc_start: 0.8908 (mmt90) cc_final: 0.8480 (mmm160) REVERT: E 2163 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7238 (mmm160) REVERT: E 2166 ASP cc_start: 0.8690 (p0) cc_final: 0.8474 (p0) REVERT: B 118 LEU cc_start: 0.9225 (tp) cc_final: 0.9017 (pp) REVERT: B 157 ASN cc_start: 0.9434 (m-40) cc_final: 0.8661 (m110) REVERT: B 162 LEU cc_start: 0.9410 (mm) cc_final: 0.9138 (mm) REVERT: B 273 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8640 (p) REVERT: B 276 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8414 (mm-30) REVERT: B 303 PHE cc_start: 0.8079 (t80) cc_final: 0.7878 (t80) REVERT: B 306 PHE cc_start: 0.8557 (t80) cc_final: 0.8319 (t80) REVERT: B 362 ASP cc_start: 0.8383 (t0) cc_final: 0.7856 (t0) REVERT: B 709 GLU cc_start: 0.8347 (tt0) cc_final: 0.8127 (mt-10) REVERT: B 715 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7803 (pp) REVERT: B 739 MET cc_start: 0.8376 (mtp) cc_final: 0.8141 (mtp) REVERT: F 2015 ASP cc_start: 0.8946 (t70) cc_final: 0.8648 (t0) REVERT: F 2016 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8451 (tptt) REVERT: F 2023 PHE cc_start: 0.9116 (t80) cc_final: 0.8859 (t80) REVERT: F 2046 ASP cc_start: 0.8557 (t70) cc_final: 0.8205 (t0) REVERT: F 2077 ARG cc_start: 0.8891 (mmt90) cc_final: 0.8514 (mmm160) REVERT: F 2163 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7878 (mtp180) REVERT: C 118 LEU cc_start: 0.9295 (tp) cc_final: 0.9043 (pp) REVERT: C 153 ASP cc_start: 0.8574 (t0) cc_final: 0.8120 (t0) REVERT: C 162 LEU cc_start: 0.9383 (mt) cc_final: 0.8973 (pp) REVERT: C 273 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8616 (p) REVERT: C 276 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8412 (mm-30) REVERT: C 285 MET cc_start: 0.8535 (mmm) cc_final: 0.8032 (mmm) REVERT: C 303 PHE cc_start: 0.8200 (t80) cc_final: 0.7849 (t80) REVERT: C 307 PHE cc_start: 0.8073 (t80) cc_final: 0.7795 (t80) REVERT: C 362 ASP cc_start: 0.8391 (t0) cc_final: 0.7821 (t0) REVERT: C 460 MET cc_start: 0.8254 (mmm) cc_final: 0.7974 (ttp) REVERT: C 561 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8575 (pp) REVERT: C 715 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.7929 (pp) REVERT: C 900 ASP cc_start: 0.8719 (p0) cc_final: 0.8446 (p0) REVERT: G 2015 ASP cc_start: 0.8910 (t70) cc_final: 0.8655 (t0) REVERT: G 2016 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8539 (tptt) REVERT: G 2046 ASP cc_start: 0.8643 (t70) cc_final: 0.8291 (t0) REVERT: G 2077 ARG cc_start: 0.8937 (mmt90) cc_final: 0.8489 (mmm160) REVERT: G 2163 ARG cc_start: 0.7993 (mtt-85) cc_final: 0.7760 (mtp180) REVERT: D 104 MET cc_start: 0.8497 (mtp) cc_final: 0.8169 (mtp) REVERT: D 118 LEU cc_start: 0.9228 (tp) cc_final: 0.8948 (pp) REVERT: D 154 MET cc_start: 0.7726 (mtm) cc_final: 0.7510 (mtm) REVERT: D 162 LEU cc_start: 0.9424 (mm) cc_final: 0.9170 (mm) REVERT: D 273 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8744 (p) REVERT: D 276 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8401 (mm-30) REVERT: D 285 MET cc_start: 0.8512 (mmm) cc_final: 0.7980 (mmm) REVERT: D 303 PHE cc_start: 0.8079 (t80) cc_final: 0.7716 (t80) REVERT: D 307 PHE cc_start: 0.8048 (t80) cc_final: 0.7748 (t80) REVERT: D 362 ASP cc_start: 0.8392 (t0) cc_final: 0.7917 (t0) REVERT: D 442 MET cc_start: 0.8982 (tpp) cc_final: 0.8733 (tpp) REVERT: D 460 MET cc_start: 0.8840 (mmm) cc_final: 0.8530 (mmm) REVERT: D 715 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8003 (pp) REVERT: D 878 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8859 (mp) REVERT: D 900 ASP cc_start: 0.8643 (p0) cc_final: 0.8389 (p0) REVERT: H 2015 ASP cc_start: 0.8954 (t70) cc_final: 0.8620 (t0) REVERT: H 2016 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8395 (tptt) REVERT: H 2023 PHE cc_start: 0.9132 (t80) cc_final: 0.8869 (t80) REVERT: H 2046 ASP cc_start: 0.8564 (t70) cc_final: 0.8180 (t0) REVERT: H 2077 ARG cc_start: 0.8896 (mmt90) cc_final: 0.8478 (mmm160) REVERT: H 2141 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8105 (tt) REVERT: H 2163 ARG cc_start: 0.7878 (mtt-85) cc_final: 0.7676 (mtp180) outliers start: 101 outliers final: 63 residues processed: 527 average time/residue: 0.1974 time to fit residues: 178.0928 Evaluate side-chains 493 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 418 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2204 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 477 TRP 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 2188 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 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 917 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2157 ASP Chi-restraints excluded: chain G residue 2187 ILE Chi-restraints excluded: chain G residue 2188 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 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 Chi-restraints excluded: chain H residue 2157 ASP Chi-restraints excluded: chain H residue 2168 ILE Chi-restraints excluded: chain H residue 2188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 426 optimal weight: 2.9990 chunk 315 optimal weight: 0.0470 chunk 49 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 278 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 414 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 147 optimal weight: 0.0570 chunk 48 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 182 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.087605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068819 restraints weight = 117844.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.071137 restraints weight = 54502.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072697 restraints weight = 33827.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.073682 restraints weight = 25020.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.074324 restraints weight = 20663.770| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 37332 Z= 0.100 Angle : 0.555 10.033 50560 Z= 0.274 Chirality : 0.043 0.458 5756 Planarity : 0.003 0.047 6240 Dihedral : 8.273 122.531 5250 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.34 % Allowed : 13.24 % Favored : 84.43 % 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: -0.26 (0.13), residues: 4408 helix: 1.14 (0.12), residues: 2004 sheet: -1.40 (0.21), residues: 604 loop : -1.19 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 213 TYR 0.006 0.001 TYR F2008 PHE 0.015 0.001 PHE D 303 TRP 0.022 0.001 TRP G2176 HIS 0.004 0.001 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (37300) covalent geometry : angle 0.54287 / 0.27 (50504) SS BOND : bond 0.00122 / 0.08 ( 16) SS BOND : angle 0.37970 / 0.25 ( 32) hydrogen bonds : bond 0.02976 / 1.91 ( 1448) hydrogen bonds : angle 4.16732 / 2.99 ( 4056) Misc. bond : bond 0.00063 / 0.03 ( 8) link_NAG-ASN : bond 0.01629 / 0.84 ( 8) link_NAG-ASN : angle 5.29160 / 3.10 ( 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 568 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 476 time to evaluate : 1.484 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: 0.8618 (t0) cc_final: 0.8153 (t0) REVERT: A 159 PHE cc_start: 0.9107 (t80) cc_final: 0.8684 (t80) REVERT: A 162 LEU cc_start: 0.9365 (mt) cc_final: 0.8990 (pp) REVERT: A 273 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8659 (p) REVERT: A 285 MET cc_start: 0.8572 (mmm) cc_final: 0.8106 (mmm) REVERT: A 307 PHE cc_start: 0.8039 (t80) cc_final: 0.7645 (t80) REVERT: A 362 ASP cc_start: 0.8357 (t0) cc_final: 0.7838 (t0) REVERT: A 459 GLN cc_start: 0.8719 (mt0) cc_final: 0.8437 (mt0) REVERT: A 601 ASP cc_start: 0.7373 (t0) cc_final: 0.6943 (t0) REVERT: A 715 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.7894 (pp) REVERT: A 900 ASP cc_start: 0.8615 (p0) cc_final: 0.8305 (p0) REVERT: E 2015 ASP cc_start: 0.8912 (t70) cc_final: 0.8659 (t0) REVERT: E 2016 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8477 (tptt) REVERT: E 2046 ASP cc_start: 0.8704 (t70) cc_final: 0.8366 (t0) REVERT: E 2077 ARG cc_start: 0.8916 (mmt90) cc_final: 0.8501 (mmm160) REVERT: E 2131 MET cc_start: 0.8493 (mmp) cc_final: 0.8116 (mmp) REVERT: E 2163 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7841 (mtp180) REVERT: B 153 ASP cc_start: 0.8575 (t0) cc_final: 0.7869 (t0) REVERT: B 157 ASN cc_start: 0.9446 (m-40) cc_final: 0.8755 (m110) REVERT: B 159 PHE cc_start: 0.8950 (t80) cc_final: 0.8586 (t80) REVERT: B 162 LEU cc_start: 0.9423 (mm) cc_final: 0.9156 (mm) REVERT: B 273 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8615 (p) REVERT: B 276 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8380 (mm-30) REVERT: B 362 ASP cc_start: 0.8390 (t0) cc_final: 0.7843 (t0) REVERT: B 715 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7779 (pp) REVERT: B 739 MET cc_start: 0.8306 (mtp) cc_final: 0.8026 (mtp) REVERT: B 900 ASP cc_start: 0.8573 (p0) cc_final: 0.8331 (p0) REVERT: F 2015 ASP cc_start: 0.8948 (t70) cc_final: 0.8596 (t0) REVERT: F 2016 LYS cc_start: 0.9002 (ttmt) cc_final: 0.8431 (tptt) REVERT: F 2046 ASP cc_start: 0.8604 (t70) cc_final: 0.8275 (t0) REVERT: F 2077 ARG cc_start: 0.8888 (mmt90) cc_final: 0.8503 (mmm160) REVERT: F 2163 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7866 (mtp180) REVERT: C 118 LEU cc_start: 0.9296 (tp) cc_final: 0.9083 (pp) REVERT: C 153 ASP cc_start: 0.8605 (t0) cc_final: 0.8126 (t0) REVERT: C 159 PHE cc_start: 0.9060 (t80) cc_final: 0.8611 (t80) REVERT: C 162 LEU cc_start: 0.9373 (mt) cc_final: 0.8982 (pp) REVERT: C 273 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8608 (p) REVERT: C 285 MET cc_start: 0.8605 (mmm) cc_final: 0.8112 (mmm) REVERT: C 307 PHE cc_start: 0.8033 (t80) cc_final: 0.7610 (t80) REVERT: C 601 ASP cc_start: 0.7335 (t0) cc_final: 0.6724 (t0) REVERT: C 715 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.7916 (pp) REVERT: C 739 MET cc_start: 0.8435 (mtm) cc_final: 0.8077 (mtp) REVERT: C 900 ASP cc_start: 0.8686 (p0) cc_final: 0.8405 (p0) REVERT: G 2015 ASP cc_start: 0.8931 (t70) cc_final: 0.8671 (t0) REVERT: G 2016 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8465 (tptt) REVERT: G 2046 ASP cc_start: 0.8691 (t70) cc_final: 0.8294 (t0) REVERT: G 2077 ARG cc_start: 0.8930 (mmt90) cc_final: 0.8513 (mmm160) REVERT: G 2131 MET cc_start: 0.8423 (mmp) cc_final: 0.8067 (mmp) REVERT: G 2163 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7698 (mtp180) REVERT: G 2168 ILE cc_start: 0.8852 (mp) cc_final: 0.8609 (tp) REVERT: D 104 MET cc_start: 0.8422 (mtp) cc_final: 0.8109 (mtp) REVERT: D 118 LEU cc_start: 0.9209 (tp) cc_final: 0.8974 (pp) REVERT: D 157 ASN cc_start: 0.9380 (m-40) cc_final: 0.8813 (m110) REVERT: D 159 PHE cc_start: 0.8960 (t80) cc_final: 0.8578 (t80) REVERT: D 273 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8676 (p) REVERT: D 285 MET cc_start: 0.8589 (mmm) cc_final: 0.8072 (mmm) REVERT: D 306 PHE cc_start: 0.8512 (t80) cc_final: 0.8260 (t80) REVERT: D 307 PHE cc_start: 0.8047 (t80) cc_final: 0.7606 (t80) REVERT: D 442 MET cc_start: 0.9199 (tpp) cc_final: 0.8801 (tpp) REVERT: D 715 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8048 (pp) REVERT: D 900 ASP cc_start: 0.8673 (p0) cc_final: 0.8424 (p0) REVERT: H 2015 ASP cc_start: 0.8870 (t70) cc_final: 0.8564 (t0) REVERT: H 2016 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8329 (tptt) REVERT: H 2024 LEU cc_start: 0.8979 (mp) cc_final: 0.8613 (tp) REVERT: H 2046 ASP cc_start: 0.8529 (t70) cc_final: 0.8135 (t0) REVERT: H 2077 ARG cc_start: 0.8865 (mmt90) cc_final: 0.8471 (mmm160) REVERT: H 2120 LYS cc_start: 0.8223 (mmtm) cc_final: 0.7912 (mptt) REVERT: H 2141 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8069 (tt) outliers start: 92 outliers final: 52 residues processed: 537 average time/residue: 0.2133 time to fit residues: 195.7558 Evaluate side-chains 491 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 430 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 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 227 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 477 TRP 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 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2157 ASP 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 158 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 317 SER 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 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: 0.9990 chunk 334 optimal weight: 6.9990 chunk 434 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 372 optimal weight: 10.0000 chunk 368 optimal weight: 0.4980 chunk 221 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 182 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.087447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068586 restraints weight = 118486.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.070871 restraints weight = 55115.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072404 restraints weight = 34397.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073383 restraints weight = 25614.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.073979 restraints weight = 21240.992| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4151 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 : 0.578 12.451 50560 Z= 0.282 Chirality : 0.044 0.456 5756 Planarity : 0.003 0.047 6240 Dihedral : 7.943 114.380 5250 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.03 % Allowed : 13.80 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 4408 helix: 1.16 (0.12), residues: 2024 sheet: -1.40 (0.21), residues: 604 loop : -1.14 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 976 TYR 0.017 0.001 TYR A 48 PHE 0.034 0.001 PHE F2023 TRP 0.047 0.001 TRP G2176 HIS 0.004 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (37300) covalent geometry : angle 0.56731 / 0.28 (50504) SS BOND : bond 0.00106 / 0.07 ( 16) SS BOND : angle 0.37750 / 0.25 ( 32) hydrogen bonds : bond 0.02991 / 1.92 ( 1448) hydrogen bonds : angle 4.13963 / 2.96 ( 4056) Misc. bond : bond 0.00061 / 0.03 ( 8) link_NAG-ASN : bond 0.01601 / 0.83 ( 8) link_NAG-ASN : angle 5.23452 / 3.06 ( 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 534 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 454 time to evaluate : 1.264 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: A 153 ASP cc_start: 0.8633 (t0) cc_final: 0.8142 (t0) REVERT: A 162 LEU cc_start: 0.9371 (mt) cc_final: 0.9002 (pp) REVERT: A 273 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8696 (p) REVERT: A 285 MET cc_start: 0.8580 (mmm) cc_final: 0.8265 (mmm) REVERT: A 303 PHE cc_start: 0.8185 (t80) cc_final: 0.7918 (t80) REVERT: A 362 ASP cc_start: 0.8365 (t0) cc_final: 0.7845 (t0) REVERT: A 459 GLN cc_start: 0.8858 (mt0) cc_final: 0.8534 (mt0) REVERT: A 715 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.7993 (pp) REVERT: A 739 MET cc_start: 0.8138 (mtp) cc_final: 0.7810 (mtp) REVERT: A 900 ASP cc_start: 0.8474 (p0) cc_final: 0.8138 (p0) REVERT: E 2015 ASP cc_start: 0.8888 (t70) cc_final: 0.8624 (t0) REVERT: E 2016 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8435 (tptt) REVERT: E 2046 ASP cc_start: 0.8699 (t70) cc_final: 0.8358 (t0) REVERT: E 2077 ARG cc_start: 0.8933 (mmt90) cc_final: 0.8501 (mmm160) REVERT: E 2131 MET cc_start: 0.8466 (mmp) cc_final: 0.8055 (mmp) REVERT: E 2163 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.7785 (mtp180) REVERT: B 162 LEU cc_start: 0.9430 (mm) cc_final: 0.9166 (mm) REVERT: B 273 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8602 (p) REVERT: B 303 PHE cc_start: 0.8110 (t80) cc_final: 0.7873 (t80) REVERT: B 362 ASP cc_start: 0.8374 (t0) cc_final: 0.7854 (t0) REVERT: B 715 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.7950 (pp) REVERT: B 819 GLU cc_start: 0.7545 (mp0) cc_final: 0.7322 (mp0) REVERT: B 900 ASP cc_start: 0.8579 (p0) cc_final: 0.8321 (p0) REVERT: F 2015 ASP cc_start: 0.8856 (t70) cc_final: 0.8547 (t0) REVERT: F 2016 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8422 (tptt) REVERT: F 2046 ASP cc_start: 0.8611 (t70) cc_final: 0.8287 (t0) REVERT: F 2077 ARG cc_start: 0.8895 (mmt90) cc_final: 0.8482 (mmm160) REVERT: F 2131 MET cc_start: 0.8574 (mmp) cc_final: 0.8099 (mmp) REVERT: F 2176 TRP cc_start: 0.8860 (m100) cc_final: 0.8620 (m100) REVERT: C 48 TYR cc_start: 0.8585 (m-80) cc_final: 0.8376 (m-10) REVERT: C 153 ASP cc_start: 0.8639 (t0) cc_final: 0.8148 (t0) REVERT: C 162 LEU cc_start: 0.9371 (mt) cc_final: 0.8985 (pp) REVERT: C 273 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8637 (p) REVERT: C 285 MET cc_start: 0.8638 (mmm) cc_final: 0.8343 (mmm) REVERT: C 303 PHE cc_start: 0.8186 (t80) cc_final: 0.7918 (t80) REVERT: C 715 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8014 (pp) REVERT: C 739 MET cc_start: 0.8436 (mtm) cc_final: 0.8060 (mtp) REVERT: G 2015 ASP cc_start: 0.8973 (t70) cc_final: 0.8726 (t0) REVERT: G 2016 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8439 (tptt) REVERT: G 2046 ASP cc_start: 0.8684 (t70) cc_final: 0.8282 (t0) REVERT: G 2077 ARG cc_start: 0.8921 (mmt90) cc_final: 0.8480 (mmm160) REVERT: G 2163 ARG cc_start: 0.7753 (mtt-85) cc_final: 0.7504 (mtp180) REVERT: D 118 LEU cc_start: 0.9207 (tp) cc_final: 0.8944 (pp) REVERT: D 153 ASP cc_start: 0.8653 (t0) cc_final: 0.7994 (t0) REVERT: D 157 ASN cc_start: 0.9337 (m-40) cc_final: 0.8613 (m110) REVERT: D 159 PHE cc_start: 0.8840 (t80) cc_final: 0.8572 (t80) REVERT: D 187 PHE cc_start: 0.8674 (t80) cc_final: 0.8300 (t80) REVERT: D 273 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8678 (p) REVERT: D 282 MET cc_start: 0.8830 (tpp) cc_final: 0.8582 (tpp) REVERT: D 285 MET cc_start: 0.8597 (mmm) cc_final: 0.8267 (mmm) REVERT: D 303 PHE cc_start: 0.8254 (t80) cc_final: 0.7935 (t80) REVERT: D 442 MET cc_start: 0.9195 (tpp) cc_final: 0.8834 (tpp) REVERT: D 715 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.7940 (pp) REVERT: D 739 MET cc_start: 0.8372 (mtm) cc_final: 0.7994 (mtp) REVERT: D 900 ASP cc_start: 0.8659 (p0) cc_final: 0.8419 (p0) REVERT: H 2015 ASP cc_start: 0.8758 (t70) cc_final: 0.8440 (t0) REVERT: H 2016 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8398 (tptt) REVERT: H 2046 ASP cc_start: 0.8481 (t70) cc_final: 0.8235 (t0) REVERT: H 2077 ARG cc_start: 0.8867 (mmt90) cc_final: 0.8439 (mmm160) REVERT: H 2120 LYS cc_start: 0.8415 (mmtm) cc_final: 0.8039 (mptt) REVERT: H 2141 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8095 (tt) REVERT: H 2176 TRP cc_start: 0.8764 (m100) cc_final: 0.8511 (m100) outliers start: 80 outliers final: 53 residues processed: 503 average time/residue: 0.2049 time to fit residues: 175.4036 Evaluate side-chains 483 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 421 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 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 227 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 477 TRP 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 2157 ASP 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 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain G residue 2157 ASP 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 317 SER 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 705 LEU Chi-restraints excluded: chain D residue 715 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 26 optimal weight: 4.9990 chunk 166 optimal weight: 0.0370 chunk 262 optimal weight: 0.5980 chunk 327 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 421 optimal weight: 8.9990 chunk 340 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.086677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067756 restraints weight = 118391.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.070069 restraints weight = 55053.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071567 restraints weight = 34408.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072551 restraints weight = 25569.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073093 restraints weight = 21179.651| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37332 Z= 0.128 Angle : 0.598 10.794 50560 Z= 0.295 Chirality : 0.044 0.453 5756 Planarity : 0.003 0.048 6240 Dihedral : 7.783 106.497 5250 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.03 % Allowed : 14.28 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4408 helix: 1.13 (0.12), residues: 2052 sheet: -1.45 (0.21), residues: 600 loop : -1.06 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 976 TYR 0.014 0.001 TYR F2008 PHE 0.040 0.001 PHE E2023 TRP 0.046 0.001 TRP G2176 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (37300) covalent geometry : angle 0.58777 / 0.29 (50504) SS BOND : bond 0.00108 / 0.07 ( 16) SS BOND : angle 0.39310 / 0.26 ( 32) hydrogen bonds : bond 0.03050 / 1.96 ( 1448) hydrogen bonds : angle 4.15003 / 2.97 ( 4056) Misc. bond : bond 0.00066 / 0.03 ( 8) link_NAG-ASN : bond 0.01556 / 0.81 ( 8) link_NAG-ASN : angle 5.19511 / 3.03 ( 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 515 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 435 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8672 (t0) cc_final: 0.8166 (t0) REVERT: A 162 LEU cc_start: 0.9371 (mt) cc_final: 0.9016 (pp) REVERT: A 273 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8698 (p) REVERT: A 285 MET cc_start: 0.8594 (mmm) cc_final: 0.8274 (mmm) REVERT: A 303 PHE cc_start: 0.8268 (t80) cc_final: 0.7932 (t80) REVERT: A 362 ASP cc_start: 0.8397 (t0) cc_final: 0.7878 (t0) REVERT: A 459 GLN cc_start: 0.8976 (mt0) cc_final: 0.8630 (mt0) REVERT: A 715 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8010 (pp) REVERT: E 2015 ASP cc_start: 0.8945 (t70) cc_final: 0.8691 (t0) REVERT: E 2016 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8436 (tptt) REVERT: E 2046 ASP cc_start: 0.8706 (t70) cc_final: 0.8347 (t0) REVERT: E 2077 ARG cc_start: 0.8944 (mmt90) cc_final: 0.8460 (mmm160) REVERT: E 2120 LYS cc_start: 0.8830 (mmtm) cc_final: 0.8617 (mmtm) REVERT: E 2131 MET cc_start: 0.8465 (mmp) cc_final: 0.7928 (mmp) REVERT: E 2163 ARG cc_start: 0.7869 (mtt-85) cc_final: 0.7611 (mtp180) REVERT: B 162 LEU cc_start: 0.9437 (mm) cc_final: 0.9173 (mm) REVERT: B 273 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 276 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8388 (mm-30) REVERT: B 303 PHE cc_start: 0.8183 (t80) cc_final: 0.7932 (t80) REVERT: B 362 ASP cc_start: 0.8404 (t0) cc_final: 0.7861 (t0) REVERT: B 715 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.7970 (pp) REVERT: B 739 MET cc_start: 0.8107 (mtp) cc_final: 0.7782 (mtp) REVERT: B 819 GLU cc_start: 0.7570 (mp0) cc_final: 0.7274 (mp0) REVERT: F 2015 ASP cc_start: 0.8791 (t70) cc_final: 0.8464 (t0) REVERT: F 2016 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8487 (tptt) REVERT: F 2046 ASP cc_start: 0.8497 (t70) cc_final: 0.8255 (t0) REVERT: F 2077 ARG cc_start: 0.8874 (mmt90) cc_final: 0.8417 (mmm160) REVERT: F 2178 LEU cc_start: 0.9316 (tp) cc_final: 0.9051 (mp) REVERT: C 48 TYR cc_start: 0.8591 (m-80) cc_final: 0.8341 (m-10) REVERT: C 118 LEU cc_start: 0.9274 (tp) cc_final: 0.8911 (pp) REVERT: C 153 ASP cc_start: 0.8665 (t0) cc_final: 0.8153 (t0) REVERT: C 162 LEU cc_start: 0.9369 (mt) cc_final: 0.9007 (pp) REVERT: C 273 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8620 (p) REVERT: C 285 MET cc_start: 0.8599 (mmm) cc_final: 0.8309 (mmm) REVERT: C 303 PHE cc_start: 0.8234 (t80) cc_final: 0.7936 (t80) REVERT: C 715 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.7867 (pp) REVERT: C 739 MET cc_start: 0.8413 (mtm) cc_final: 0.8013 (mtp) REVERT: G 2015 ASP cc_start: 0.8966 (t70) cc_final: 0.8698 (t0) REVERT: G 2016 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8447 (tptt) REVERT: G 2046 ASP cc_start: 0.8649 (t70) cc_final: 0.8370 (t0) REVERT: G 2077 ARG cc_start: 0.8949 (mmt90) cc_final: 0.8462 (mmm160) REVERT: G 2120 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8628 (mmtm) REVERT: D 118 LEU cc_start: 0.9179 (tp) cc_final: 0.8915 (pp) REVERT: D 157 ASN cc_start: 0.9433 (m-40) cc_final: 0.8723 (m110) REVERT: D 273 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8640 (p) REVERT: D 285 MET cc_start: 0.8571 (mmm) cc_final: 0.8231 (mmm) REVERT: D 303 PHE cc_start: 0.8207 (t80) cc_final: 0.7940 (t80) REVERT: D 442 MET cc_start: 0.9208 (tpp) cc_final: 0.8684 (tpp) REVERT: D 460 MET cc_start: 0.8088 (mtp) cc_final: 0.7796 (ttt) REVERT: D 626 LYS cc_start: 0.8471 (mmmt) cc_final: 0.7880 (mmmt) REVERT: D 715 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8007 (pp) REVERT: D 739 MET cc_start: 0.8408 (mtm) cc_final: 0.8038 (mtp) REVERT: D 819 GLU cc_start: 0.7746 (mp0) cc_final: 0.7506 (mp0) REVERT: D 878 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8879 (mp) REVERT: D 892 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7461 (t70) REVERT: D 900 ASP cc_start: 0.8624 (p0) cc_final: 0.8364 (p0) REVERT: H 2015 ASP cc_start: 0.8770 (t70) cc_final: 0.8439 (t0) REVERT: H 2016 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8361 (tptt) REVERT: H 2024 LEU cc_start: 0.8947 (mp) cc_final: 0.8504 (tp) REVERT: H 2046 ASP cc_start: 0.8518 (t70) cc_final: 0.8270 (t0) REVERT: H 2077 ARG cc_start: 0.8900 (mmt90) cc_final: 0.8445 (mmm160) REVERT: H 2120 LYS cc_start: 0.8410 (mmtm) cc_final: 0.8028 (mptt) REVERT: H 2141 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8128 (tt) outliers start: 80 outliers final: 55 residues processed: 487 average time/residue: 0.2069 time to fit residues: 172.2562 Evaluate side-chains 486 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 420 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain 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 317 SER Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 917 VAL 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 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 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2157 ASP 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 317 SER 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 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 Chi-restraints excluded: chain H residue 2168 ILE Chi-restraints excluded: chain H residue 2187 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 1 optimal weight: 5.9990 chunk 419 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 290 optimal weight: 7.9990 chunk 283 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 327 optimal weight: 0.0170 chunk 126 optimal weight: 0.9980 overall best weight: 1.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** F2061 GLN C 459 GLN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.086985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.068081 restraints weight = 118382.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070423 restraints weight = 54994.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.071965 restraints weight = 34178.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072968 restraints weight = 25283.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.073583 restraints weight = 20872.864| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37332 Z= 0.117 Angle : 0.599 10.365 50560 Z= 0.294 Chirality : 0.044 0.453 5756 Planarity : 0.003 0.048 6240 Dihedral : 7.608 101.298 5250 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.83 % Allowed : 14.38 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 4408 helix: 1.12 (0.12), residues: 2060 sheet: -1.42 (0.21), residues: 600 loop : -1.06 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 976 TYR 0.013 0.001 TYR H2008 PHE 0.031 0.001 PHE F2023 TRP 0.036 0.001 TRP G2176 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (37300) covalent geometry : angle 0.58860 / 0.29 (50504) SS BOND : bond 0.00094 / 0.06 ( 16) SS BOND : angle 0.39491 / 0.27 ( 32) hydrogen bonds : bond 0.02995 / 1.93 ( 1448) hydrogen bonds : angle 4.12627 / 2.95 ( 4056) Misc. bond : bond 0.00067 / 0.03 ( 8) link_NAG-ASN : bond 0.01568 / 0.82 ( 8) link_NAG-ASN : angle 5.17364 / 3.02 ( 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 512 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 440 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8383 (mmm) cc_final: 0.7811 (mmm) REVERT: A 162 LEU cc_start: 0.9402 (mt) cc_final: 0.9051 (pp) REVERT: A 273 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8667 (p) REVERT: A 285 MET cc_start: 0.8590 (mmm) cc_final: 0.8273 (mmm) REVERT: A 303 PHE cc_start: 0.8143 (t80) cc_final: 0.7867 (t80) REVERT: A 362 ASP cc_start: 0.8399 (t0) cc_final: 0.7881 (t0) REVERT: A 715 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.7982 (pp) REVERT: A 739 MET cc_start: 0.8331 (mtm) cc_final: 0.7992 (mtp) REVERT: A 1053 MET cc_start: 0.8360 (mtp) cc_final: 0.8121 (mmm) REVERT: E 2015 ASP cc_start: 0.8945 (t70) cc_final: 0.8673 (t0) REVERT: E 2016 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8437 (tptt) REVERT: E 2046 ASP cc_start: 0.8698 (t70) cc_final: 0.8337 (t0) REVERT: E 2077 ARG cc_start: 0.8922 (mmt90) cc_final: 0.8428 (mmm160) REVERT: E 2120 LYS cc_start: 0.8863 (mmtm) cc_final: 0.8653 (mmtm) REVERT: B 153 ASP cc_start: 0.8512 (t0) cc_final: 0.7775 (t0) REVERT: B 157 ASN cc_start: 0.9347 (m-40) cc_final: 0.8795 (m110) REVERT: B 159 PHE cc_start: 0.9157 (t80) cc_final: 0.8931 (t80) REVERT: B 162 LEU cc_start: 0.9432 (mm) cc_final: 0.8978 (pp) REVERT: B 273 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8604 (p) REVERT: B 276 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8375 (mm-30) REVERT: B 362 ASP cc_start: 0.8416 (t0) cc_final: 0.8070 (t0) REVERT: B 459 GLN cc_start: 0.8794 (mt0) cc_final: 0.8483 (mt0) REVERT: B 715 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.7999 (pp) REVERT: B 924 MET cc_start: 0.8897 (mtp) cc_final: 0.8456 (ttt) REVERT: B 1053 MET cc_start: 0.8482 (mmm) cc_final: 0.8240 (mmm) REVERT: F 2015 ASP cc_start: 0.8758 (t70) cc_final: 0.8414 (t0) REVERT: F 2016 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8488 (tptt) REVERT: F 2046 ASP cc_start: 0.8570 (t70) cc_final: 0.8338 (t0) REVERT: F 2077 ARG cc_start: 0.8861 (mmt90) cc_final: 0.8407 (mmm160) REVERT: F 2178 LEU cc_start: 0.9300 (tp) cc_final: 0.9056 (mp) REVERT: C 48 TYR cc_start: 0.8559 (m-80) cc_final: 0.8313 (m-10) REVERT: C 118 LEU cc_start: 0.9267 (tp) cc_final: 0.8914 (pp) REVERT: C 153 ASP cc_start: 0.8662 (t0) cc_final: 0.8149 (t0) REVERT: C 162 LEU cc_start: 0.9358 (mt) cc_final: 0.9064 (pp) REVERT: C 273 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8602 (p) REVERT: C 285 MET cc_start: 0.8646 (mmm) cc_final: 0.8334 (mmm) REVERT: C 303 PHE cc_start: 0.8216 (t80) cc_final: 0.7906 (t80) REVERT: C 715 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.7965 (pp) REVERT: C 819 GLU cc_start: 0.7693 (mp0) cc_final: 0.7457 (mp0) REVERT: G 2015 ASP cc_start: 0.8924 (t70) cc_final: 0.8651 (t0) REVERT: G 2016 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8439 (tptt) REVERT: G 2046 ASP cc_start: 0.8595 (t70) cc_final: 0.8347 (t0) REVERT: G 2077 ARG cc_start: 0.8920 (mmt90) cc_final: 0.8422 (mmm160) REVERT: G 2120 LYS cc_start: 0.8868 (mmtm) cc_final: 0.8660 (mmtm) REVERT: D 118 LEU cc_start: 0.9160 (tp) cc_final: 0.8907 (pp) REVERT: D 153 ASP cc_start: 0.8675 (t0) cc_final: 0.8015 (t0) REVERT: D 157 ASN cc_start: 0.9386 (m-40) cc_final: 0.8745 (m110) REVERT: D 273 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8615 (p) REVERT: D 285 MET cc_start: 0.8562 (mmm) cc_final: 0.8222 (mmm) REVERT: D 303 PHE cc_start: 0.8210 (t80) cc_final: 0.7896 (t80) REVERT: D 442 MET cc_start: 0.9179 (tpp) cc_final: 0.8704 (tpp) REVERT: D 460 MET cc_start: 0.8130 (mtp) cc_final: 0.7889 (ttm) REVERT: D 715 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8096 (pp) REVERT: D 739 MET cc_start: 0.8392 (mtm) cc_final: 0.8019 (mtp) REVERT: D 878 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8877 (mp) REVERT: D 900 ASP cc_start: 0.8599 (p0) cc_final: 0.8343 (p0) REVERT: D 1053 MET cc_start: 0.8504 (mmm) cc_final: 0.8185 (mmm) REVERT: H 2015 ASP cc_start: 0.8710 (t70) cc_final: 0.8380 (t0) REVERT: H 2016 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8327 (tptt) REVERT: H 2024 LEU cc_start: 0.8975 (mp) cc_final: 0.8557 (tp) REVERT: H 2046 ASP cc_start: 0.8528 (t70) cc_final: 0.8286 (t0) REVERT: H 2077 ARG cc_start: 0.8883 (mmt90) cc_final: 0.8432 (mmm160) REVERT: H 2141 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8133 (tt) outliers start: 72 outliers final: 56 residues processed: 487 average time/residue: 0.2105 time to fit residues: 175.9516 Evaluate side-chains 487 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 421 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 429 TYR 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 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 317 SER 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 917 VAL 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 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 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 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 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 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 317 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 55 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 346 optimal weight: 0.1980 chunk 341 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 425 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2061 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2061 GLN C 182 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.087096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.068223 restraints weight = 118572.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070555 restraints weight = 54949.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072057 restraints weight = 34224.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073061 restraints weight = 25452.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.073630 restraints weight = 21090.972| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37332 Z= 0.119 Angle : 0.612 10.088 50560 Z= 0.301 Chirality : 0.044 0.457 5756 Planarity : 0.003 0.047 6240 Dihedral : 7.462 94.131 5250 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.78 % Allowed : 14.74 % Favored : 83.49 % 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: -0.12 (0.13), residues: 4408 helix: 1.16 (0.12), residues: 2036 sheet: -1.43 (0.20), residues: 616 loop : -0.98 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 976 TYR 0.015 0.001 TYR G2008 PHE 0.030 0.001 PHE F2023 TRP 0.036 0.001 TRP G2176 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (37300) covalent geometry : angle 0.60228 / 0.30 (50504) SS BOND : bond 0.00097 / 0.06 ( 16) SS BOND : angle 0.40277 / 0.27 ( 32) hydrogen bonds : bond 0.02976 / 1.92 ( 1448) hydrogen bonds : angle 4.12598 / 2.95 ( 4056) Misc. bond : bond 0.00067 / 0.03 ( 8) link_NAG-ASN : bond 0.01567 / 0.81 ( 8) link_NAG-ASN : angle 5.17491 / 3.02 ( 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 501 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 431 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8360 (mmm) cc_final: 0.7844 (mmm) REVERT: A 30 MET cc_start: 0.8836 (mmp) cc_final: 0.8563 (mmm) REVERT: A 273 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8670 (p) REVERT: A 285 MET cc_start: 0.8604 (mmm) cc_final: 0.8280 (mmm) REVERT: A 303 PHE cc_start: 0.8095 (t80) cc_final: 0.7849 (t80) REVERT: A 362 ASP cc_start: 0.8398 (t0) cc_final: 0.7886 (t0) REVERT: A 715 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8080 (pp) REVERT: A 739 MET cc_start: 0.8333 (mtm) cc_final: 0.7987 (mtp) REVERT: E 2015 ASP cc_start: 0.8874 (t70) cc_final: 0.8592 (t0) REVERT: E 2016 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8429 (tptt) REVERT: E 2046 ASP cc_start: 0.8677 (t70) cc_final: 0.8368 (t0) REVERT: E 2077 ARG cc_start: 0.8923 (mmt90) cc_final: 0.8424 (mmm160) REVERT: E 2120 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8614 (mmtm) REVERT: E 2178 LEU cc_start: 0.9288 (tp) cc_final: 0.9034 (mp) REVERT: B 153 ASP cc_start: 0.8523 (t0) cc_final: 0.7758 (t0) REVERT: B 157 ASN cc_start: 0.9296 (m-40) cc_final: 0.8746 (m110) REVERT: B 159 PHE cc_start: 0.9136 (t80) cc_final: 0.8935 (t80) REVERT: B 162 LEU cc_start: 0.9445 (mm) cc_final: 0.9009 (pp) REVERT: B 273 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8610 (p) REVERT: B 276 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 303 PHE cc_start: 0.8280 (t80) cc_final: 0.8021 (t80) REVERT: B 362 ASP cc_start: 0.8447 (t0) cc_final: 0.8067 (t0) REVERT: B 715 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.7967 (pp) REVERT: B 739 MET cc_start: 0.8291 (mtm) cc_final: 0.7936 (mtp) REVERT: B 924 MET cc_start: 0.8891 (mtp) cc_final: 0.8486 (ttt) REVERT: B 1053 MET cc_start: 0.8522 (mmm) cc_final: 0.8176 (mmm) REVERT: F 2015 ASP cc_start: 0.8730 (t70) cc_final: 0.8381 (t0) REVERT: F 2016 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8485 (tptt) REVERT: F 2046 ASP cc_start: 0.8559 (t70) cc_final: 0.8326 (t0) REVERT: F 2077 ARG cc_start: 0.8872 (mmt90) cc_final: 0.8407 (mmm160) REVERT: F 2178 LEU cc_start: 0.9297 (tp) cc_final: 0.9054 (mp) REVERT: C 48 TYR cc_start: 0.8564 (m-80) cc_final: 0.8316 (m-10) REVERT: C 118 LEU cc_start: 0.9267 (tp) cc_final: 0.8912 (pp) REVERT: C 153 ASP cc_start: 0.8696 (t0) cc_final: 0.8185 (t0) REVERT: C 273 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8604 (p) REVERT: C 285 MET cc_start: 0.8643 (mmm) cc_final: 0.8333 (mmm) REVERT: C 303 PHE cc_start: 0.8105 (t80) cc_final: 0.7840 (t80) REVERT: C 715 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.7938 (pp) REVERT: C 739 MET cc_start: 0.8305 (mtm) cc_final: 0.7970 (mtp) REVERT: C 819 GLU cc_start: 0.7627 (mp0) cc_final: 0.7361 (mp0) REVERT: G 2015 ASP cc_start: 0.8892 (t70) cc_final: 0.8582 (t0) REVERT: G 2016 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8480 (tptt) REVERT: G 2046 ASP cc_start: 0.8585 (t70) cc_final: 0.8335 (t0) REVERT: G 2077 ARG cc_start: 0.8924 (mmt90) cc_final: 0.8423 (mmm160) REVERT: G 2120 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8618 (mmtm) REVERT: D 118 LEU cc_start: 0.9152 (tp) cc_final: 0.8904 (pp) REVERT: D 153 ASP cc_start: 0.8629 (t0) cc_final: 0.7992 (t0) REVERT: D 157 ASN cc_start: 0.9371 (m-40) cc_final: 0.8701 (m110) REVERT: D 273 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8621 (p) REVERT: D 285 MET cc_start: 0.8552 (mmm) cc_final: 0.8215 (mmm) REVERT: D 303 PHE cc_start: 0.8105 (t80) cc_final: 0.7860 (t80) REVERT: D 442 MET cc_start: 0.9161 (tpp) cc_final: 0.8681 (tpp) REVERT: D 459 GLN cc_start: 0.9088 (mt0) cc_final: 0.8883 (mt0) REVERT: D 460 MET cc_start: 0.8110 (mtp) cc_final: 0.7791 (ttt) REVERT: D 627 LYS cc_start: 0.6219 (tppt) cc_final: 0.5951 (mmmt) REVERT: D 715 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8081 (pp) REVERT: D 739 MET cc_start: 0.8400 (mtm) cc_final: 0.8013 (mtp) REVERT: D 878 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8861 (mp) REVERT: D 924 MET cc_start: 0.8697 (mtp) cc_final: 0.8424 (ttp) REVERT: H 2015 ASP cc_start: 0.8676 (t70) cc_final: 0.8326 (t0) REVERT: H 2016 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8373 (tptt) REVERT: H 2024 LEU cc_start: 0.8980 (mp) cc_final: 0.8575 (tp) REVERT: H 2046 ASP cc_start: 0.8545 (t70) cc_final: 0.8301 (t0) REVERT: H 2077 ARG cc_start: 0.8890 (mmt90) cc_final: 0.8432 (mmm160) REVERT: H 2141 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8152 (tt) outliers start: 70 outliers final: 54 residues processed: 476 average time/residue: 0.2062 time to fit residues: 168.6929 Evaluate side-chains 477 residues out of total 3944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 413 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 429 TYR 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 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 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 792 VAL Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2157 ASP 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 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 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 2157 ASP 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 317 SER 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 920 LEU Chi-restraints excluded: chain H residue 2141 ILE Chi-restraints excluded: chain H residue 2157 ASP Chi-restraints excluded: chain H residue 2187 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 172 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 94 optimal weight: 0.4980 chunk 213 optimal weight: 7.9990 chunk 424 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** 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 182 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.086749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067802 restraints weight = 118337.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070107 restraints weight = 55099.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071654 restraints weight = 34382.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072639 restraints weight = 25540.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073225 restraints weight = 21171.917| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37332 Z= 0.128 Angle : 0.615 11.247 50560 Z= 0.302 Chirality : 0.044 0.456 5756 Planarity : 0.004 0.080 6240 Dihedral : 7.386 86.417 5250 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.65 % Allowed : 14.94 % Favored : 83.41 % 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: -0.10 (0.13), residues: 4408 helix: 1.16 (0.12), residues: 2052 sheet: -1.43 (0.20), residues: 616 loop : -0.95 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 976 TYR 0.014 0.001 TYR F2008 PHE 0.029 0.001 PHE F2023 TRP 0.034 0.001 TRP G2176 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (37300) covalent geometry : angle 0.60456 / 0.30 (50504) SS BOND : bond 0.00096 / 0.06 ( 16) SS BOND : angle 0.40506 / 0.27 ( 32) hydrogen bonds : bond 0.02981 / 1.92 ( 1448) hydrogen bonds : angle 4.12596 / 2.95 ( 4056) Misc. bond : bond 0.00071 / 0.04 ( 8) link_NAG-ASN : bond 0.01549 / 0.81 ( 8) link_NAG-ASN : angle 5.15885 / 3.01 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6163.91 seconds wall clock time: 107 minutes 43.95 seconds (6463.95 seconds total)