Starting phenix.real_space_refine on Sat Feb 7 13:37:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7y_70211/02_2026/9o7y_70211.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7y_70211/02_2026/9o7y_70211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o7y_70211/02_2026/9o7y_70211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7y_70211/02_2026/9o7y_70211.map" model { file = "/net/cci-nas-00/data/ceres_data/9o7y_70211/02_2026/9o7y_70211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7y_70211/02_2026/9o7y_70211.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 236 5.16 5 C 21373 2.51 5 N 5431 2.21 5 O 5635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32675 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 7903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1049, 7893 Classifications: {'peptide': 1049} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 1006} Chain breaks: 8 Unresolved non-hydrogen bonds: 643 Unresolved non-hydrogen angles: 791 Unresolved non-hydrogen dihedrals: 536 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 17, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 4, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 403 Conformer: "B" Number of residues, atoms: 1049, 7893 Classifications: {'peptide': 1049} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 1006} Chain breaks: 8 Unresolved non-hydrogen bonds: 643 Unresolved non-hydrogen angles: 791 Unresolved non-hydrogen dihedrals: 536 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 17, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 4, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 403 bond proxies already assigned to first conformer: 8061 Chain: "B" Number of atoms: 7907 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1049, 7897 Classifications: {'peptide': 1049} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 1006} Chain breaks: 8 Unresolved non-hydrogen bonds: 642 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 14, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 406 Conformer: "B" Number of residues, atoms: 1049, 7897 Classifications: {'peptide': 1049} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 1006} Chain breaks: 8 Unresolved non-hydrogen bonds: 642 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 14, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 406 bond proxies already assigned to first conformer: 8062 Chain: "A" Number of atoms: 8001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 7991 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1017} Chain breaks: 6 Unresolved non-hydrogen bonds: 637 Unresolved non-hydrogen angles: 787 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 14, 'TYR:plan': 5, 'ASP:plan': 13, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 402 Conformer: "B" Number of residues, atoms: 1061, 7991 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1017} Chain breaks: 6 Unresolved non-hydrogen bonds: 637 Unresolved non-hydrogen angles: 787 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 14, 'TYR:plan': 5, 'ASP:plan': 13, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 402 bond proxies already assigned to first conformer: 8161 Chain: "C" Number of atoms: 8024 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1062, 8014 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1018} Chain breaks: 6 Unresolved non-hydrogen bonds: 619 Unresolved non-hydrogen angles: 765 Unresolved non-hydrogen dihedrals: 515 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 14, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 399 Conformer: "B" Number of residues, atoms: 1062, 8014 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1018} Chain breaks: 6 Unresolved non-hydrogen bonds: 619 Unresolved non-hydrogen angles: 765 Unresolved non-hydrogen dihedrals: 515 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 14, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 399 bond proxies already assigned to first conformer: 8186 Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'Y01': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS D 674 " occ=0.35 ... (18 atoms not shown) pdb=" NE2BHIS D 674 " occ=0.65 residue: pdb=" N AHIS B 674 " occ=0.44 ... (18 atoms not shown) pdb=" NE2BHIS B 674 " occ=0.56 residue: pdb=" N AHIS A 674 " occ=0.32 ... (18 atoms not shown) pdb=" NE2BHIS A 674 " occ=0.68 residue: pdb=" N AHIS C 674 " occ=0.35 ... (18 atoms not shown) pdb=" NE2BHIS C 674 " occ=0.65 Time building chain proxies: 13.34, per 1000 atoms: 0.41 Number of scatterers: 32675 At special positions: 0 Unit cell: (134.638, 133.812, 162.722, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 236 16.00 O 5635 8.00 N 5431 7.00 C 21373 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D1044 " - pdb=" SG CYS D1061 " distance=2.03 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1061 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1061 " distance=2.03 Simple disulfide: pdb=" SG CYS C1044 " - pdb=" SG CYS C1061 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 2.9 seconds 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7966 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 14 sheets defined 67.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'D' and resid 30 through 36 Processing helix chain 'D' and resid 59 through 63 removed outlier: 4.240A pdb=" N HIS D 63 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 141 removed outlier: 3.978A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 182 removed outlier: 3.770A pdb=" N ALA D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 209 Processing helix chain 'D' and resid 227 through 231 removed outlier: 3.687A pdb=" N ILE D 231 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 removed outlier: 3.564A pdb=" N GLN D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 removed outlier: 3.694A pdb=" N SER D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 Processing helix chain 'D' and resid 353 through 368 removed outlier: 3.691A pdb=" N ASP D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 Processing helix chain 'D' and resid 405 through 418 Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 433 through 441 Processing helix chain 'D' and resid 451 through 463 removed outlier: 3.577A pdb=" N LEU D 463 " --> pdb=" O ASP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 475 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 501 through 514 Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 555 through 566 Processing helix chain 'D' and resid 613 through 625 removed outlier: 4.007A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET D 625 " --> pdb=" O TRP D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.683A pdb=" N GLN D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 662 Processing helix chain 'D' and resid 665 through 694 removed outlier: 3.620A pdb=" N SER D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 704 Processing helix chain 'D' and resid 713 through 721 Processing helix chain 'D' and resid 723 through 728 removed outlier: 3.835A pdb=" N ILE D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 740 Processing helix chain 'D' and resid 751 through 760 Processing helix chain 'D' and resid 761 through 765 Processing helix chain 'D' and resid 835 through 845 Processing helix chain 'D' and resid 847 through 854 Processing helix chain 'D' and resid 854 through 872 Processing helix chain 'D' and resid 879 through 902 Processing helix chain 'D' and resid 907 through 916 Processing helix chain 'D' and resid 918 through 940 removed outlier: 3.539A pdb=" N VAL D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D 940 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 968 removed outlier: 3.730A pdb=" N ASP D 947 " --> pdb=" O PRO D 943 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU D 964 " --> pdb=" O TYR D 960 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP D 965 " --> pdb=" O ILE D 961 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 1010 removed outlier: 3.541A pdb=" N TYR D 976 " --> pdb=" O TYR D 972 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1030 removed outlier: 3.630A pdb=" N PHE D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N MET D1026 " --> pdb=" O ASN D1022 " (cutoff:3.500A) Proline residue: D1027 - end of helix Processing helix chain 'D' and resid 1031 through 1033 No H-bonds generated for 'chain 'D' and resid 1031 through 1033' Processing helix chain 'D' and resid 1036 through 1040 removed outlier: 3.760A pdb=" N ILE D1040 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1094 removed outlier: 3.861A pdb=" N ALA D1070 " --> pdb=" O TRP D1066 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL D1084 " --> pdb=" O ASN D1080 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN D1085 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR D1094 " --> pdb=" O VAL D1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1120 removed outlier: 4.725A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1124 through 1126 No H-bonds generated for 'chain 'D' and resid 1124 through 1126' Processing helix chain 'D' and resid 1127 through 1145 removed outlier: 4.356A pdb=" N SER D1131 " --> pdb=" O LEU D1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1191 removed outlier: 3.690A pdb=" N GLU D1175 " --> pdb=" O HIS D1171 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1232 removed outlier: 3.520A pdb=" N ARG D1196 " --> pdb=" O SER D1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 59 through 63 removed outlier: 4.295A pdb=" N HIS B 63 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.747A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 182 removed outlier: 3.738A pdb=" N ALA B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.690A pdb=" N ILE B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.530A pdb=" N GLN B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.941A pdb=" N SER B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 353 through 368 removed outlier: 3.856A pdb=" N ASP B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 removed outlier: 4.282A pdb=" N LYS B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 418 Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 440 removed outlier: 3.524A pdb=" N ALA B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 501 through 514 Processing helix chain 'B' and resid 533 through 546 Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 613 through 625 removed outlier: 4.268A pdb=" N GLU B 617 " --> pdb=" O PHE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.670A pdb=" N GLN B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 662 Processing helix chain 'B' and resid 665 through 694 removed outlier: 3.679A pdb=" N SER B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 704 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 723 through 728 removed outlier: 3.845A pdb=" N ILE B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.607A pdb=" N GLY B 742 " --> pdb=" O ASP B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 760 Processing helix chain 'B' and resid 761 through 764 Processing helix chain 'B' and resid 835 through 846 Processing helix chain 'B' and resid 847 through 872 Processing helix chain 'B' and resid 879 through 902 Processing helix chain 'B' and resid 907 through 916 Processing helix chain 'B' and resid 918 through 939 removed outlier: 3.543A pdb=" N VAL B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 968 removed outlier: 3.741A pdb=" N ASP B 947 " --> pdb=" O PRO B 943 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU B 964 " --> pdb=" O TYR B 960 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP B 965 " --> pdb=" O ILE B 961 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 1010 removed outlier: 4.682A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1030 removed outlier: 3.661A pdb=" N PHE B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N MET B1026 " --> pdb=" O ASN B1022 " (cutoff:3.500A) Proline residue: B1027 - end of helix Processing helix chain 'B' and resid 1036 through 1040 removed outlier: 3.776A pdb=" N ILE B1040 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1094 removed outlier: 4.035A pdb=" N ALA B1070 " --> pdb=" O TRP B1066 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL B1084 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN B1085 " --> pdb=" O ILE B1081 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B1094 " --> pdb=" O VAL B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1120 removed outlier: 4.714A pdb=" N TYR B1111 " --> pdb=" O LYS B1107 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLN B1112 " --> pdb=" O PHE B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1124 through 1126 No H-bonds generated for 'chain 'B' and resid 1124 through 1126' Processing helix chain 'B' and resid 1127 through 1145 removed outlier: 4.343A pdb=" N SER B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1191 removed outlier: 3.714A pdb=" N GLU B1175 " --> pdb=" O HIS B1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1232 removed outlier: 3.637A pdb=" N ARG B1196 " --> pdb=" O SER B1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.967A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 181 removed outlier: 3.623A pdb=" N ALA A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.599A pdb=" N ILE A 223 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 224 " --> pdb=" O TRP A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 224' Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.731A pdb=" N ILE A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.684A pdb=" N GLN A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 4.046A pdb=" N SER A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 removed outlier: 3.527A pdb=" N TYR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.748A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 440 removed outlier: 3.510A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 501 through 514 Processing helix chain 'A' and resid 533 through 546 Processing helix chain 'A' and resid 555 through 564 Processing helix chain 'A' and resid 613 through 625 removed outlier: 3.887A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.575A pdb=" N GLN A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 662 Processing helix chain 'A' and resid 665 through 694 removed outlier: 3.558A pdb=" N SER A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 704 Processing helix chain 'A' and resid 706 through 710 removed outlier: 4.054A pdb=" N SER A 710 " --> pdb=" O LYS A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.676A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.658A pdb=" N GLY A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 761 through 767 removed outlier: 4.060A pdb=" N LEU A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 846 Processing helix chain 'A' and resid 847 through 872 Processing helix chain 'A' and resid 879 through 902 Processing helix chain 'A' and resid 907 through 916 Processing helix chain 'A' and resid 918 through 939 removed outlier: 3.537A pdb=" N VAL A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 962 removed outlier: 3.553A pdb=" N ASP A 947 " --> pdb=" O PRO A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 968 removed outlier: 4.049A pdb=" N ILE A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 1010 removed outlier: 3.532A pdb=" N MET A 978 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1030 removed outlier: 3.850A pdb=" N PHE A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N MET A1026 " --> pdb=" O ASN A1022 " (cutoff:3.500A) Proline residue: A1027 - end of helix removed outlier: 3.523A pdb=" N MET A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1033 No H-bonds generated for 'chain 'A' and resid 1031 through 1033' Processing helix chain 'A' and resid 1036 through 1040 removed outlier: 3.702A pdb=" N ILE A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1081 removed outlier: 3.720A pdb=" N ALA A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1094 Processing helix chain 'A' and resid 1094 through 1109 Processing helix chain 'A' and resid 1109 through 1119 Processing helix chain 'A' and resid 1127 through 1145 removed outlier: 4.132A pdb=" N SER A1131 " --> pdb=" O LEU A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1191 removed outlier: 3.666A pdb=" N LYS A1169 " --> pdb=" O ASP A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1232 removed outlier: 3.741A pdb=" N ARG A1196 " --> pdb=" O SER A1192 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1197 " --> pdb=" O ASN A1193 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A1201 " --> pdb=" O ILE A1197 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A1202 " --> pdb=" O ARG A1198 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A1203 " --> pdb=" O VAL A1199 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET A1207 " --> pdb=" O ARG A1203 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.677A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 182 Processing helix chain 'C' and resid 192 through 209 Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.656A pdb=" N ILE C 223 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 224 " --> pdb=" O TRP C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 224' Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.670A pdb=" N ILE C 231 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.557A pdb=" N GLN C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 removed outlier: 4.050A pdb=" N SER C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 353 through 368 Processing helix chain 'C' and resid 371 through 386 Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 404 through 418 removed outlier: 3.842A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 465 through 474 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 501 through 514 Processing helix chain 'C' and resid 533 through 546 Processing helix chain 'C' and resid 555 through 564 Processing helix chain 'C' and resid 613 through 625 removed outlier: 3.905A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.568A pdb=" N PHE C 633 " --> pdb=" O LYS C 629 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 662 Processing helix chain 'C' and resid 665 through 694 removed outlier: 3.869A pdb=" N SER C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 704 Processing helix chain 'C' and resid 706 through 710 removed outlier: 4.140A pdb=" N SER C 710 " --> pdb=" O LYS C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 721 Processing helix chain 'C' and resid 723 through 728 removed outlier: 3.643A pdb=" N ILE C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 742 removed outlier: 3.742A pdb=" N GLY C 742 " --> pdb=" O ASP C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 760 Processing helix chain 'C' and resid 761 through 767 removed outlier: 4.010A pdb=" N LEU C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 846 Processing helix chain 'C' and resid 847 through 872 Processing helix chain 'C' and resid 879 through 902 Processing helix chain 'C' and resid 907 through 916 Processing helix chain 'C' and resid 918 through 939 Processing helix chain 'C' and resid 943 through 962 removed outlier: 3.509A pdb=" N TYR C 958 " --> pdb=" O VAL C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 968 removed outlier: 4.021A pdb=" N ILE C 966 " --> pdb=" O ARG C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 1010 removed outlier: 3.510A pdb=" N MET C 978 " --> pdb=" O GLY C 974 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1030 removed outlier: 3.786A pdb=" N PHE C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N MET C1026 " --> pdb=" O ASN C1022 " (cutoff:3.500A) Proline residue: C1027 - end of helix Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.743A pdb=" N ILE C1040 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1081 removed outlier: 3.784A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1094 removed outlier: 3.749A pdb=" N THR C1094 " --> pdb=" O VAL C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1094 through 1109 Processing helix chain 'C' and resid 1109 through 1120 Processing helix chain 'C' and resid 1128 through 1145 Processing helix chain 'C' and resid 1163 through 1191 Processing helix chain 'C' and resid 1192 through 1232 removed outlier: 3.736A pdb=" N ARG C1196 " --> pdb=" O SER C1192 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE C1197 " --> pdb=" O ASN C1193 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG C1198 " --> pdb=" O ASP C1194 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C1199 " --> pdb=" O GLU C1195 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C1210 " --> pdb=" O ASN C1206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.658A pdb=" N GLN D 99 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 232 through 239 removed outlier: 6.719A pdb=" N PHE D 106 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG D 237 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR D 108 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TYR D 239 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU D 110 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA D 105 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU D 261 " --> pdb=" O MET D 121 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL D 123 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP D 263 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 125 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 153 through 155 removed outlier: 6.076A pdb=" N ALA D 301 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N CYS D 329 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE D 303 " --> pdb=" O CYS D 329 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL D 326 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N PHE D 395 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL D 328 " --> pdb=" O PHE D 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.636A pdb=" N GLN B 99 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 232 through 240 removed outlier: 7.029A pdb=" N PHE B 106 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 108 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA B 105 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N PHE B 259 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET B 121 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU B 261 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 123 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP B 263 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 125 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 184 through 186 removed outlier: 6.161A pdb=" N ALA B 301 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N CYS B 329 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE B 303 " --> pdb=" O CYS B 329 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 393 " --> pdb=" O VAL B 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.515A pdb=" N GLU A 40 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 99 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 232 through 240 removed outlier: 6.695A pdb=" N PHE A 106 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR A 108 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR A 239 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU A 110 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N PHE A 259 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET A 121 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 125 through 126 removed outlier: 6.359A pdb=" N VAL A 125 " --> pdb=" O ASP A 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 184 through 186 removed outlier: 6.396A pdb=" N VAL A 326 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE A 395 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 328 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.520A pdb=" N GLU C 40 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN C 99 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 232 through 240 removed outlier: 6.686A pdb=" N PHE C 106 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N TYR C 239 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU C 110 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE C 259 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N MET C 121 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 125 through 126 removed outlier: 6.447A pdb=" N VAL C 125 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 186 removed outlier: 6.396A pdb=" N VAL C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE C 395 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL C 328 " --> pdb=" O PHE C 395 " (cutoff:3.500A) 2029 hydrogen bonds defined for protein. 6019 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: 7.32 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5708 1.33 - 1.45: 8475 1.45 - 1.58: 18898 1.58 - 1.71: 1 1.71 - 1.83: 396 Bond restraints: 33478 Sorted by residual: bond pdb=" N MET C1026 " pdb=" CA MET C1026 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.52e+01 bond pdb=" N LEU B1123 " pdb=" CA LEU B1123 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.14e-02 7.69e+03 1.12e+01 bond pdb=" N VAL B1122 " pdb=" CA VAL B1122 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.22e-02 6.72e+03 9.23e+00 bond pdb=" N GLN D 240 " pdb=" CA GLN D 240 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.21e-02 6.83e+03 8.72e+00 bond pdb=" N VAL D 623 " pdb=" CA VAL D 623 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 8.72e+00 ... (remaining 33473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 44686 2.92 - 5.85: 845 5.85 - 8.77: 142 8.77 - 11.70: 17 11.70 - 14.62: 6 Bond angle restraints: 45696 Sorted by residual: angle pdb=" C LEU D 744 " pdb=" N ARG D 745 " pdb=" CA ARG D 745 " ideal model delta sigma weight residual 122.87 111.28 11.59 1.44e+00 4.82e-01 6.48e+01 angle pdb=" CA PRO A1125 " pdb=" C PRO A1125 " pdb=" N PRO A1126 " ideal model delta sigma weight residual 117.93 124.86 -6.93 1.20e+00 6.94e-01 3.34e+01 angle pdb=" N ASP D 738 " pdb=" CA ASP D 738 " pdb=" C ASP D 738 " ideal model delta sigma weight residual 113.97 107.15 6.82 1.28e+00 6.10e-01 2.84e+01 angle pdb=" N GLN D 733 " pdb=" CA GLN D 733 " pdb=" C GLN D 733 " ideal model delta sigma weight residual 111.71 105.61 6.10 1.15e+00 7.56e-01 2.82e+01 angle pdb=" N MET D 734 " pdb=" CA MET D 734 " pdb=" C MET D 734 " ideal model delta sigma weight residual 112.89 106.31 6.58 1.24e+00 6.50e-01 2.81e+01 ... (remaining 45691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.52: 19487 24.52 - 49.03: 1246 49.03 - 73.55: 209 73.55 - 98.07: 8 98.07 - 122.59: 12 Dihedral angle restraints: 20962 sinusoidal: 8654 harmonic: 12308 Sorted by residual: dihedral pdb=" C ASN B 749 " pdb=" N ASN B 749 " pdb=" CA ASN B 749 " pdb=" CB ASN B 749 " ideal model delta harmonic sigma weight residual -122.60 -134.52 11.92 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" CA PHE D 854 " pdb=" C PHE D 854 " pdb=" N TYR D 855 " pdb=" CA TYR D 855 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PRO D 776 " pdb=" C PRO D 776 " pdb=" N TYR D 777 " pdb=" CA TYR D 777 " ideal model delta harmonic sigma weight residual -180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 20959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4900 0.094 - 0.188: 407 0.188 - 0.283: 26 0.283 - 0.377: 7 0.377 - 0.471: 1 Chirality restraints: 5341 Sorted by residual: chirality pdb=" CB ILE D1114 " pdb=" CA ILE D1114 " pdb=" CG1 ILE D1114 " pdb=" CG2 ILE D1114 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" CG LEU C 632 " pdb=" CB LEU C 632 " pdb=" CD1 LEU C 632 " pdb=" CD2 LEU C 632 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB THR D 215 " pdb=" CA THR D 215 " pdb=" OG1 THR D 215 " pdb=" CG2 THR D 215 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 5338 not shown) Planarity restraints: 5627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 854 " -0.044 2.00e-02 2.50e+03 4.02e-02 2.83e+01 pdb=" CG PHE B 854 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 PHE B 854 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 854 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 854 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 854 " -0.025 2.00e-02 2.50e+03 pdb=" CZ PHE B 854 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 854 " -0.040 2.00e-02 2.50e+03 3.63e-02 2.31e+01 pdb=" CG PHE D 854 " 0.082 2.00e-02 2.50e+03 pdb=" CD1 PHE D 854 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE D 854 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 854 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 854 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE D 854 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 370 " 0.027 2.00e-02 2.50e+03 3.38e-02 2.29e+01 pdb=" CG TYR D 370 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR D 370 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR D 370 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR D 370 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 370 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 370 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 370 " -0.002 2.00e-02 2.50e+03 ... (remaining 5624 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 10850 2.87 - 3.38: 32100 3.38 - 3.88: 54057 3.88 - 4.39: 61133 4.39 - 4.90: 103314 Nonbonded interactions: 261454 Sorted by model distance: nonbonded pdb=" O ASP D1187 " pdb=" OD1 ASP D1187 " model vdw 2.361 3.040 nonbonded pdb=" OD1 ASP B1165 " pdb=" N GLU B1166 " model vdw 2.430 3.120 nonbonded pdb=" C THR A1163 " pdb=" OG1 THR A1163 " model vdw 2.443 2.616 nonbonded pdb=" OD1 ASN B1093 " pdb=" ND2 ASN C1092 " model vdw 2.443 3.120 nonbonded pdb=" O LEU D 735 " pdb=" N ASP D 738 " model vdw 2.446 3.120 ... (remaining 261449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 220 or (resid 221 and (name N or name CA or nam \ e C or name O or name CB )) or resid 222 through 241 or resid 250 through 251 or \ (resid 252 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 3 through 268 or (resid 269 and (name N or name CA or name C or name O or name C \ B )) or resid 270 through 278 or (resid 279 and (name N or name CA or name C or \ name O or name CB )) or resid 280 through 394 or (resid 395 and (name N or name \ CA or name C or name O or name CB )) or resid 396 through 398 or resid 404 throu \ gh 406 or (resid 407 through 408 and (name N or name CA or name C or name O or n \ ame CB )) or resid 409 through 412 or (resid 413 and (name N or name CA or name \ C or name O or name CB )) or resid 414 through 502 or (resid 503 and (name N or \ name CA or name C or name O or name CB )) or resid 504 through 528 or (resid 529 \ and (name N or name CA or name C or name O or name CB )) or resid 530 through 6 \ 49 or (resid 650 and (name N or name CA or name C or name O or name CB )) or res \ id 651 through 673 or resid 675 through 744 or (resid 745 and (name N or name CA \ or name C or name O or name CB )) or resid 746 or (resid 747 through 748 and (n \ ame N or name CA or name C or name O or name CB )) or resid 749 through 875 or ( \ resid 876 and (name N or name CA or name C or name O or name CB )) or resid 877 \ through 986 or (resid 987 and (name N or name CA or name C or name O or name CB \ )) or resid 988 through 1048 or resid 1057 through 1161 or (resid 1162 and (name \ N or name CA or name C or name O or name CB )) or resid 1163 through 1406)) selection = (chain 'B' and (resid 30 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 133 or (resid 134 and (name N or n \ ame CA or name C or name O or name CB )) or resid 135 through 145 or (resid 146 \ and (name N or name CA or name C or name O or name CB )) or resid 147 through 25 \ 1 or (resid 252 and (name N or name CA or name C or name O or name CB )) or resi \ d 253 through 268 or (resid 269 and (name N or name CA or name C or name O or na \ me CB )) or resid 270 through 369 or (resid 370 and (name N or name CA or name C \ or name O or name CB )) or resid 371 through 396 or (resid 397 and (name N or n \ ame CA or name C or name O or name CB )) or resid 398 through 502 or (resid 503 \ and (name N or name CA or name C or name O or name CB )) or resid 504 through 67 \ 3 or resid 675 through 744 or (resid 745 and (name N or name CA or name C or nam \ e O or name CB )) or resid 746 or (resid 747 through 748 and (name N or name CA \ or name C or name O or name CB )) or resid 749 through 875 or (resid 876 and (na \ me N or name CA or name C or name O or name CB )) or resid 877 through 1048 or r \ esid 1057 through 1145 or resid 1156 through 1406)) selection = (chain 'C' and (resid 30 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 126 or (resid 127 through 128 and \ (name N or name CA or name C or name O or name CB )) or resid 129 through 133 or \ (resid 134 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 5 through 137 or (resid 138 and (name N or name CA or name C or name O or name C \ B )) or resid 139 through 145 or (resid 146 and (name N or name CA or name C or \ name O or name CB )) or resid 147 through 220 or (resid 221 and (name N or name \ CA or name C or name O or name CB )) or resid 222 through 241 or resid 250 throu \ gh 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) or \ resid 253 through 268 or (resid 269 and (name N or name CA or name C or name O \ or name CB )) or resid 270 through 369 or (resid 370 and (name N or name CA or n \ ame C or name O or name CB )) or resid 371 through 394 or (resid 395 and (name N \ or name CA or name C or name O or name CB )) or resid 396 or (resid 397 and (na \ me N or name CA or name C or name O or name CB )) or resid 398 or resid 404 thro \ ugh 406 or (resid 407 through 408 and (name N or name CA or name C or name O or \ name CB )) or resid 409 through 412 or (resid 413 and (name N or name CA or name \ C or name O or name CB )) or resid 414 through 649 or (resid 650 and (name N or \ name CA or name C or name O or name CB )) or resid 651 through 673 or resid 675 \ through 744 or (resid 745 and (name N or name CA or name C or name O or name CB \ )) or resid 746 or (resid 747 through 748 and (name N or name CA or name C or n \ ame O or name CB )) or resid 749 through 875 or (resid 876 and (name N or name C \ A or name C or name O or name CB )) or resid 877 through 986 or (resid 987 and ( \ name N or name CA or name C or name O or name CB )) or resid 988 through 1048 or \ resid 1057 through 1145 or resid 1156 through 1161 or (resid 1162 and (name N o \ r name CA or name C or name O or name CB )) or resid 1163 through 1406)) selection = (chain 'D' and (resid 30 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 126 or (resid 127 through 128 and \ (name N or name CA or name C or name O or name CB )) or resid 129 through 133 or \ (resid 134 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 5 through 145 or (resid 146 and (name N or name CA or name C or name O or name C \ B )) or resid 147 through 220 or (resid 221 and (name N or name CA or name C or \ name O or name CB )) or resid 222 through 241 or resid 250 through 369 or (resid \ 370 and (name N or name CA or name C or name O or name CB )) or resid 371 throu \ gh 396 or (resid 397 and (name N or name CA or name C or name O or name CB )) or \ resid 398 through 502 or (resid 503 and (name N or name CA or name C or name O \ or name CB )) or resid 504 through 528 or (resid 529 and (name N or name CA or n \ ame C or name O or name CB )) or resid 530 through 673 or resid 675 through 1048 \ or resid 1057 through 1145 or resid 1156 through 1406)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 39.980 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.005 0.084 33482 Z= 0.284 Angle : 0.984 14.621 45704 Z= 0.547 Chirality : 0.054 0.471 5341 Planarity : 0.008 0.113 5627 Dihedral : 15.799 122.586 12984 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.15 % Allowed : 12.50 % Favored : 86.35 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.71 % 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: -2.57 (0.11), residues: 4169 helix: -1.66 (0.08), residues: 2611 sheet: -0.72 (0.36), residues: 238 loop : -1.59 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG A1188 TYR 0.083 0.002 TYR D 370 PHE 0.090 0.003 PHE B 854 TRP 0.056 0.003 TRP B 142 HIS 0.025 0.002 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00543 (33478) covalent geometry : angle 0.98418 (45696) SS BOND : bond 0.00356 ( 4) SS BOND : angle 2.03209 ( 8) hydrogen bonds : bond 0.18659 ( 2029) hydrogen bonds : angle 7.32541 ( 6019) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 1.238 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: D 216 ILE cc_start: 0.8276 (mm) cc_final: 0.7652 (mp) REVERT: D 255 MET cc_start: 0.6868 (mmm) cc_final: 0.6294 (mmm) REVERT: D 328 VAL cc_start: 0.8558 (m) cc_final: 0.8304 (p) REVERT: D 457 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9061 (tpt) REVERT: B 121 MET cc_start: 0.5998 (mpp) cc_final: 0.5671 (mpp) REVERT: B 255 MET cc_start: 0.7203 (tpp) cc_final: 0.5987 (tpt) REVERT: B 1209 MET cc_start: 0.9018 (mtp) cc_final: 0.8613 (ttt) REVERT: A 179 MET cc_start: 0.8579 (ttp) cc_final: 0.8341 (mtp) REVERT: A 255 MET cc_start: 0.8616 (mmt) cc_final: 0.8234 (mmp) REVERT: A 329 CYS cc_start: 0.8994 (m) cc_final: 0.8638 (t) REVERT: A 334 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7645 (mtp85) REVERT: A 1120 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8260 (mtt90) REVERT: A 1172 ASP cc_start: 0.8521 (m-30) cc_final: 0.7974 (p0) REVERT: C 181 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.8007 (t) REVERT: C 273 GLU cc_start: 0.8525 (pm20) cc_final: 0.8042 (pm20) REVERT: C 415 LYS cc_start: 0.8800 (ptpp) cc_final: 0.8197 (pttm) REVERT: C 685 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8407 (mt-10) REVERT: C 854 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8779 (m-80) outliers start: 36 outliers final: 14 residues processed: 307 average time/residue: 0.1968 time to fit residues: 99.3546 Evaluate side-chains 258 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain A residue 1120 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1133 MET Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain A residue 1139 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1090 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 689 GLN D1092 ASN B 227 GLN B 955 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 955 ASN A1092 ASN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 ASN C1093 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.079158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056659 restraints weight = 303936.020| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 5.73 r_work: 0.2996 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33482 Z= 0.131 Angle : 0.581 9.967 45704 Z= 0.300 Chirality : 0.039 0.322 5341 Planarity : 0.005 0.069 5627 Dihedral : 9.584 87.463 6248 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.18 % Allowed : 13.24 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.02 (0.12), residues: 4169 helix: 0.70 (0.09), residues: 2634 sheet: -0.65 (0.34), residues: 258 loop : -1.14 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 210 TYR 0.024 0.001 TYR D 239 PHE 0.051 0.001 PHE B 854 TRP 0.023 0.001 TRP D 621 HIS 0.014 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00281 (33478) covalent geometry : angle 0.58114 (45696) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.87646 ( 8) hydrogen bonds : bond 0.04627 ( 2029) hydrogen bonds : angle 4.39239 ( 6019) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 255 MET cc_start: 0.7076 (mmm) cc_final: 0.6524 (mmm) REVERT: D 328 VAL cc_start: 0.8685 (m) cc_final: 0.8395 (p) REVERT: D 397 MET cc_start: 0.4874 (tpt) cc_final: 0.4302 (tpt) REVERT: D 935 MET cc_start: 0.9055 (tmm) cc_final: 0.8854 (ttp) REVERT: D 983 MET cc_start: 0.9283 (mmt) cc_final: 0.8867 (mmt) REVERT: D 1133 MET cc_start: 0.9007 (mpp) cc_final: 0.8580 (mpp) REVERT: B 121 MET cc_start: 0.5535 (mpp) cc_final: 0.4925 (mpp) REVERT: B 142 TRP cc_start: 0.5125 (m100) cc_final: 0.3956 (m100) REVERT: B 255 MET cc_start: 0.7100 (tpp) cc_final: 0.6197 (tpt) REVERT: B 1115 MET cc_start: 0.9363 (tpp) cc_final: 0.9129 (mpp) REVERT: B 1209 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8820 (ttt) REVERT: A 179 MET cc_start: 0.8787 (ttp) cc_final: 0.8311 (mtp) REVERT: A 255 MET cc_start: 0.8640 (mmt) cc_final: 0.8223 (mmp) REVERT: A 329 CYS cc_start: 0.8796 (m) cc_final: 0.8388 (t) REVERT: C 138 MET cc_start: 0.9079 (ttm) cc_final: 0.8800 (ttt) REVERT: C 273 GLU cc_start: 0.8474 (pm20) cc_final: 0.8016 (pm20) outliers start: 37 outliers final: 24 residues processed: 269 average time/residue: 0.1831 time to fit residues: 84.3907 Evaluate side-chains 249 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 978 MET Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 1209 MET Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1139 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 995 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 357 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 chunk 400 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 401 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1132 HIS ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN C 693 GLN C 867 ASN C1215 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.077092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054449 restraints weight = 235520.174| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 4.52 r_work: 0.2975 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33482 Z= 0.159 Angle : 0.588 10.703 45704 Z= 0.298 Chirality : 0.040 0.407 5341 Planarity : 0.005 0.058 5627 Dihedral : 8.247 59.657 6231 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.53 % Allowed : 13.49 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 1.16 (0.13), residues: 4169 helix: 1.73 (0.10), residues: 2650 sheet: -0.63 (0.34), residues: 255 loop : -0.97 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1188 TYR 0.022 0.001 TYR D 345 PHE 0.042 0.002 PHE D 854 TRP 0.025 0.002 TRP D 621 HIS 0.015 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00358 (33478) covalent geometry : angle 0.58790 (45696) SS BOND : bond 0.00121 ( 4) SS BOND : angle 0.80538 ( 8) hydrogen bonds : bond 0.04327 ( 2029) hydrogen bonds : angle 4.06098 ( 6019) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 328 VAL cc_start: 0.9017 (m) cc_final: 0.8677 (p) REVERT: D 397 MET cc_start: 0.5211 (tpt) cc_final: 0.4883 (tpt) REVERT: D 1133 MET cc_start: 0.8984 (mpp) cc_final: 0.8523 (mpp) REVERT: B 255 MET cc_start: 0.7145 (tpp) cc_final: 0.6645 (tpp) REVERT: B 979 MET cc_start: 0.8952 (mtm) cc_final: 0.8625 (mtt) REVERT: A 179 MET cc_start: 0.8847 (ttp) cc_final: 0.7969 (mtp) REVERT: A 205 HIS cc_start: 0.8116 (t70) cc_final: 0.7312 (t70) REVERT: A 329 CYS cc_start: 0.8668 (m) cc_final: 0.8407 (t) REVERT: A 1135 MET cc_start: 0.8702 (ttm) cc_final: 0.8393 (mtp) REVERT: A 1160 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8668 (tp) REVERT: C 138 MET cc_start: 0.9085 (ttm) cc_final: 0.8830 (ttt) REVERT: C 636 GLN cc_start: 0.9112 (tt0) cc_final: 0.8650 (tm-30) outliers start: 48 outliers final: 28 residues processed: 280 average time/residue: 0.1698 time to fit residues: 81.5696 Evaluate side-chains 258 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1139 HIS Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1178 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 277 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 211 optimal weight: 50.0000 chunk 405 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 373 optimal weight: 9.9990 chunk 335 optimal weight: 30.0000 chunk 285 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 693 GLN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN C1215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.077293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.054127 restraints weight = 335153.823| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 6.07 r_work: 0.2926 rms_B_bonded: 5.68 restraints_weight: 2.0000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33482 Z= 0.144 Angle : 0.551 11.897 45704 Z= 0.281 Chirality : 0.039 0.246 5341 Planarity : 0.004 0.068 5627 Dihedral : 7.782 59.960 6226 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.12 % Allowed : 14.74 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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 (0.13), residues: 4169 helix: 2.15 (0.10), residues: 2643 sheet: -0.49 (0.34), residues: 252 loop : -0.85 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 210 TYR 0.019 0.001 TYR D 777 PHE 0.035 0.001 PHE D 854 TRP 0.019 0.001 TRP D 621 HIS 0.008 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00320 (33478) covalent geometry : angle 0.55106 (45696) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.71652 ( 8) hydrogen bonds : bond 0.03971 ( 2029) hydrogen bonds : angle 3.94060 ( 6019) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 216 ILE cc_start: 0.8224 (mm) cc_final: 0.7699 (mp) REVERT: D 255 MET cc_start: 0.7221 (mmp) cc_final: 0.6449 (mmm) REVERT: D 397 MET cc_start: 0.5693 (tpt) cc_final: 0.5199 (tpt) REVERT: D 734 MET cc_start: 0.9064 (mtp) cc_final: 0.8828 (mtm) REVERT: D 1133 MET cc_start: 0.9041 (mpp) cc_final: 0.8547 (mpp) REVERT: B 255 MET cc_start: 0.7243 (tpp) cc_final: 0.6841 (tpp) REVERT: A 179 MET cc_start: 0.8900 (ttp) cc_final: 0.8045 (mtp) REVERT: A 205 HIS cc_start: 0.8222 (t70) cc_final: 0.7472 (t70) REVERT: A 329 CYS cc_start: 0.8657 (m) cc_final: 0.8339 (t) REVERT: A 1135 MET cc_start: 0.8774 (ttm) cc_final: 0.8512 (mtp) REVERT: A 1139 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6749 (t-90) REVERT: C 138 MET cc_start: 0.9093 (ttm) cc_final: 0.8848 (ttt) REVERT: C 210 ARG cc_start: 0.6986 (mmt180) cc_final: 0.6749 (mpt180) REVERT: C 457 MET cc_start: 0.7496 (tpt) cc_final: 0.7154 (tpt) outliers start: 35 outliers final: 21 residues processed: 261 average time/residue: 0.1819 time to fit residues: 81.5519 Evaluate side-chains 242 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 1046 GLN Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1139 HIS Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 204 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 305 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 371 optimal weight: 8.9990 chunk 252 optimal weight: 0.0570 chunk 359 optimal weight: 5.9990 chunk 315 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 84 optimal weight: 0.4980 overall best weight: 3.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN C 637 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.075757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.052996 restraints weight = 235564.750| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 4.43 r_work: 0.2935 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33482 Z= 0.191 Angle : 0.589 11.812 45704 Z= 0.300 Chirality : 0.040 0.228 5341 Planarity : 0.005 0.072 5627 Dihedral : 7.685 59.832 6218 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.15 % Allowed : 14.80 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 1.69 (0.13), residues: 4169 helix: 2.15 (0.10), residues: 2662 sheet: -0.43 (0.34), residues: 252 loop : -0.81 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 210 TYR 0.029 0.001 TYR C1181 PHE 0.034 0.002 PHE B 866 TRP 0.019 0.002 TRP B 184 HIS 0.007 0.001 HIS C1132 Details of bonding type rmsd covalent geometry : bond 0.00434 (33478) covalent geometry : angle 0.58891 (45696) SS BOND : bond 0.00090 ( 4) SS BOND : angle 0.79404 ( 8) hydrogen bonds : bond 0.04336 ( 2029) hydrogen bonds : angle 4.01793 ( 6019) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 255 MET cc_start: 0.7217 (mmp) cc_final: 0.6514 (mmm) REVERT: D 397 MET cc_start: 0.5791 (tpt) cc_final: 0.4223 (ttt) REVERT: D 1133 MET cc_start: 0.8988 (mpp) cc_final: 0.8501 (mpp) REVERT: D 1209 MET cc_start: 0.9221 (mmp) cc_final: 0.8924 (mtp) REVERT: B 149 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6559 (mt) REVERT: B 255 MET cc_start: 0.7268 (tpp) cc_final: 0.6821 (tpp) REVERT: B 636 GLN cc_start: 0.9140 (tt0) cc_final: 0.8742 (tm-30) REVERT: A 179 MET cc_start: 0.8848 (ttp) cc_final: 0.8040 (mtp) REVERT: A 205 HIS cc_start: 0.8404 (t70) cc_final: 0.7446 (t70) REVERT: A 329 CYS cc_start: 0.8613 (m) cc_final: 0.8308 (t) REVERT: A 1139 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.6725 (t-90) outliers start: 36 outliers final: 23 residues processed: 260 average time/residue: 0.1853 time to fit residues: 83.2245 Evaluate side-chains 251 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 1135 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1139 HIS Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 1090 VAL Chi-restraints excluded: chain C residue 1178 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 347 optimal weight: 10.0000 chunk 399 optimal weight: 0.0270 chunk 184 optimal weight: 7.9990 chunk 405 optimal weight: 2.9990 chunk 384 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 327 optimal weight: 20.0000 chunk 270 optimal weight: 5.9990 chunk 363 optimal weight: 9.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 716 GLN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** 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 = 0.3714 r_free = 0.3714 target = 0.074901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.052014 restraints weight = 274017.485| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 5.27 r_work: 0.2872 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33482 Z= 0.216 Angle : 0.615 17.570 45704 Z= 0.310 Chirality : 0.041 0.186 5341 Planarity : 0.004 0.051 5627 Dihedral : 7.665 59.718 6218 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.24 % Allowed : 14.99 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 1.68 (0.13), residues: 4169 helix: 2.15 (0.10), residues: 2658 sheet: -0.32 (0.33), residues: 251 loop : -0.86 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1198 TYR 0.017 0.001 TYR B 958 PHE 0.033 0.002 PHE B 866 TRP 0.025 0.002 TRP D 621 HIS 0.007 0.001 HIS D 616 Details of bonding type rmsd covalent geometry : bond 0.00489 (33478) covalent geometry : angle 0.61478 (45696) SS BOND : bond 0.00084 ( 4) SS BOND : angle 0.81116 ( 8) hydrogen bonds : bond 0.04394 ( 2029) hydrogen bonds : angle 4.07856 ( 6019) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 255 MET cc_start: 0.7315 (mmp) cc_final: 0.6911 (mmm) REVERT: D 397 MET cc_start: 0.6096 (tpt) cc_final: 0.4831 (ttt) REVERT: D 1133 MET cc_start: 0.9055 (mpp) cc_final: 0.8602 (mpp) REVERT: D 1209 MET cc_start: 0.9271 (mmp) cc_final: 0.8981 (mtp) REVERT: B 149 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7186 (mp) REVERT: B 255 MET cc_start: 0.7407 (tpp) cc_final: 0.6836 (tpp) REVERT: B 746 MET cc_start: 0.7687 (ttt) cc_final: 0.7118 (mtp) REVERT: A 179 MET cc_start: 0.8821 (ttp) cc_final: 0.7988 (mtp) REVERT: A 205 HIS cc_start: 0.8510 (t70) cc_final: 0.7335 (t70) REVERT: A 329 CYS cc_start: 0.8661 (m) cc_final: 0.8289 (t) REVERT: A 935 MET cc_start: 0.8819 (tmm) cc_final: 0.8596 (tmm) REVERT: A 1139 HIS cc_start: 0.7287 (OUTLIER) cc_final: 0.6306 (t-90) REVERT: C 138 MET cc_start: 0.8958 (ttm) cc_final: 0.8736 (ttt) REVERT: C 699 MET cc_start: 0.8833 (mmm) cc_final: 0.8598 (mmm) outliers start: 39 outliers final: 30 residues processed: 255 average time/residue: 0.1828 time to fit residues: 80.5816 Evaluate side-chains 251 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 979 MET Chi-restraints excluded: chain D residue 1135 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 1046 GLN Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1139 HIS Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 1090 VAL Chi-restraints excluded: chain C residue 1178 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 302 optimal weight: 7.9990 chunk 225 optimal weight: 30.0000 chunk 396 optimal weight: 0.7980 chunk 220 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 296 optimal weight: 7.9990 chunk 409 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.075562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.052695 restraints weight = 319870.584| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 5.84 r_work: 0.2880 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33482 Z= 0.144 Angle : 0.557 14.257 45704 Z= 0.280 Chirality : 0.039 0.202 5341 Planarity : 0.004 0.051 5627 Dihedral : 7.385 58.277 6218 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.18 % Allowed : 14.93 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 1.91 (0.13), residues: 4169 helix: 2.34 (0.10), residues: 2658 sheet: -0.28 (0.34), residues: 253 loop : -0.79 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1188 TYR 0.018 0.001 TYR B 958 PHE 0.029 0.001 PHE B 170 TRP 0.026 0.001 TRP D 621 HIS 0.006 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00326 (33478) covalent geometry : angle 0.55684 (45696) SS BOND : bond 0.00087 ( 4) SS BOND : angle 0.68796 ( 8) hydrogen bonds : bond 0.04080 ( 2029) hydrogen bonds : angle 3.95205 ( 6019) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: D 255 MET cc_start: 0.7328 (mmp) cc_final: 0.6957 (mmm) REVERT: D 397 MET cc_start: 0.6320 (tpt) cc_final: 0.4953 (ttt) REVERT: D 1133 MET cc_start: 0.9064 (mpp) cc_final: 0.8591 (mpp) REVERT: D 1209 MET cc_start: 0.9303 (mmp) cc_final: 0.9017 (mtp) REVERT: B 255 MET cc_start: 0.7437 (tpp) cc_final: 0.6493 (tpt) REVERT: A 179 MET cc_start: 0.8822 (ttp) cc_final: 0.8053 (mtp) REVERT: A 205 HIS cc_start: 0.8549 (t70) cc_final: 0.7541 (t70) REVERT: A 329 CYS cc_start: 0.8645 (m) cc_final: 0.8307 (t) REVERT: A 386 MET cc_start: 0.2610 (tpt) cc_final: 0.2212 (mmt) REVERT: A 935 MET cc_start: 0.8888 (tmm) cc_final: 0.8619 (tmm) REVERT: A 1135 MET cc_start: 0.8741 (ttm) cc_final: 0.8475 (mtp) REVERT: A 1139 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6253 (t-90) REVERT: C 138 MET cc_start: 0.8968 (ttm) cc_final: 0.8741 (ttt) REVERT: C 429 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8433 (mt) REVERT: C 699 MET cc_start: 0.8815 (mmm) cc_final: 0.8588 (mmm) outliers start: 37 outliers final: 29 residues processed: 247 average time/residue: 0.1929 time to fit residues: 81.7701 Evaluate side-chains 246 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 979 MET Chi-restraints excluded: chain D residue 1135 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 1046 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 HIS Chi-restraints excluded: chain A residue 1183 ARG Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 1178 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 65 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 360 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 290 optimal weight: 0.9980 chunk 118 optimal weight: 50.0000 chunk 119 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 227 GLN B 749 ASN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.074820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.051802 restraints weight = 298979.763| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 5.60 r_work: 0.2865 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33482 Z= 0.182 Angle : 0.596 14.123 45704 Z= 0.299 Chirality : 0.040 0.188 5341 Planarity : 0.004 0.051 5627 Dihedral : 7.348 59.461 6218 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.21 % Allowed : 15.09 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 1.87 (0.13), residues: 4169 helix: 2.29 (0.10), residues: 2667 sheet: -0.16 (0.34), residues: 252 loop : -0.80 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1183 TYR 0.018 0.001 TYR D 777 PHE 0.032 0.002 PHE B 170 TRP 0.024 0.001 TRP D 621 HIS 0.011 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00415 (33478) covalent geometry : angle 0.59580 (45696) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.75385 ( 8) hydrogen bonds : bond 0.04237 ( 2029) hydrogen bonds : angle 4.00010 ( 6019) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: D 255 MET cc_start: 0.7238 (mmp) cc_final: 0.6863 (mmm) REVERT: D 397 MET cc_start: 0.6506 (tpt) cc_final: 0.5404 (ttt) REVERT: D 1133 MET cc_start: 0.9067 (mpp) cc_final: 0.8612 (mpp) REVERT: D 1209 MET cc_start: 0.9298 (mmp) cc_final: 0.9022 (mtp) REVERT: B 255 MET cc_start: 0.7576 (tpp) cc_final: 0.7033 (tpp) REVERT: B 746 MET cc_start: 0.7597 (ttt) cc_final: 0.7068 (mtp) REVERT: A 179 MET cc_start: 0.8796 (ttp) cc_final: 0.8038 (mtp) REVERT: A 205 HIS cc_start: 0.8617 (t70) cc_final: 0.7824 (t70) REVERT: A 329 CYS cc_start: 0.8645 (m) cc_final: 0.8272 (t) REVERT: A 386 MET cc_start: 0.2772 (tpt) cc_final: 0.2548 (mmt) REVERT: A 1139 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6252 (t-90) REVERT: C 138 MET cc_start: 0.8960 (ttm) cc_final: 0.8712 (ttt) REVERT: C 397 MET cc_start: 0.8450 (tpt) cc_final: 0.8145 (tpt) REVERT: C 429 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8448 (mt) outliers start: 38 outliers final: 33 residues processed: 248 average time/residue: 0.1859 time to fit residues: 79.3925 Evaluate side-chains 250 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 979 MET Chi-restraints excluded: chain D residue 1135 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1046 GLN Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 HIS Chi-restraints excluded: chain A residue 1183 ARG Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 1178 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 255 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 chunk 118 optimal weight: 40.0000 chunk 231 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 412 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 325 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN ** C 440 GLN ** 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 = 0.3680 r_free = 0.3680 target = 0.073853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.050693 restraints weight = 289903.998| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 5.30 r_work: 0.2837 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 33482 Z= 0.238 Angle : 0.648 13.200 45704 Z= 0.325 Chirality : 0.042 0.194 5341 Planarity : 0.005 0.050 5627 Dihedral : 7.513 59.887 6218 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 1.31 % Allowed : 15.09 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 1.73 (0.13), residues: 4169 helix: 2.18 (0.10), residues: 2665 sheet: -0.34 (0.34), residues: 253 loop : -0.84 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1198 TYR 0.017 0.002 TYR B 958 PHE 0.033 0.002 PHE B 866 TRP 0.071 0.002 TRP B 184 HIS 0.008 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00540 (33478) covalent geometry : angle 0.64806 (45696) SS BOND : bond 0.00091 ( 4) SS BOND : angle 0.85293 ( 8) hydrogen bonds : bond 0.04526 ( 2029) hydrogen bonds : angle 4.16846 ( 6019) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 255 MET cc_start: 0.7163 (mmp) cc_final: 0.6777 (mmm) REVERT: D 397 MET cc_start: 0.6475 (tpt) cc_final: 0.5724 (ttt) REVERT: D 1133 MET cc_start: 0.9058 (mpp) cc_final: 0.8598 (mpp) REVERT: D 1209 MET cc_start: 0.9258 (mmp) cc_final: 0.9013 (mtp) REVERT: B 239 TYR cc_start: 0.6451 (t80) cc_final: 0.6197 (t80) REVERT: B 255 MET cc_start: 0.7585 (tpp) cc_final: 0.7310 (tpp) REVERT: B 636 GLN cc_start: 0.9228 (tt0) cc_final: 0.8777 (tm-30) REVERT: A 205 HIS cc_start: 0.8657 (t70) cc_final: 0.8377 (t70) REVERT: A 329 CYS cc_start: 0.8639 (m) cc_final: 0.8223 (t) REVERT: A 1139 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.6330 (t-90) REVERT: A 1214 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8780 (m) REVERT: C 138 MET cc_start: 0.8954 (ttm) cc_final: 0.8725 (ttt) REVERT: C 397 MET cc_start: 0.8329 (tpt) cc_final: 0.8020 (tpt) REVERT: C 429 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8508 (mt) outliers start: 41 outliers final: 35 residues processed: 254 average time/residue: 0.1848 time to fit residues: 80.9073 Evaluate side-chains 258 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 979 MET Chi-restraints excluded: chain D residue 1026 MET Chi-restraints excluded: chain D residue 1135 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1046 GLN Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 HIS Chi-restraints excluded: chain A residue 1183 ARG Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 1178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 1 optimal weight: 0.8980 chunk 371 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 372 optimal weight: 0.8980 chunk 325 optimal weight: 8.9990 chunk 376 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 264 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.075460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.052827 restraints weight = 236484.740| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 4.69 r_work: 0.2921 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33482 Z= 0.124 Angle : 0.559 14.456 45704 Z= 0.280 Chirality : 0.039 0.235 5341 Planarity : 0.004 0.060 5627 Dihedral : 7.173 59.484 6218 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.06 % Favored : 96.92 % Rotamer: Outliers : 1.21 % Allowed : 15.34 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 1.98 (0.14), residues: 4169 helix: 2.39 (0.10), residues: 2661 sheet: -0.15 (0.34), residues: 250 loop : -0.79 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 210 TYR 0.020 0.001 TYR D 777 PHE 0.033 0.001 PHE B 170 TRP 0.062 0.002 TRP B 184 HIS 0.006 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00274 (33478) covalent geometry : angle 0.55870 (45696) SS BOND : bond 0.00097 ( 4) SS BOND : angle 0.68584 ( 8) hydrogen bonds : bond 0.04039 ( 2029) hydrogen bonds : angle 3.95150 ( 6019) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 255 MET cc_start: 0.7155 (mmp) cc_final: 0.6786 (mmm) REVERT: D 397 MET cc_start: 0.6625 (tpt) cc_final: 0.5752 (ttt) REVERT: D 1133 MET cc_start: 0.9035 (mpp) cc_final: 0.8571 (mpp) REVERT: D 1209 MET cc_start: 0.9244 (mmp) cc_final: 0.8992 (mtp) REVERT: B 239 TYR cc_start: 0.6423 (t80) cc_final: 0.6202 (t80) REVERT: B 255 MET cc_start: 0.7476 (tpp) cc_final: 0.6677 (tpt) REVERT: B 636 GLN cc_start: 0.9198 (tt0) cc_final: 0.8824 (tm-30) REVERT: A 205 HIS cc_start: 0.8596 (t70) cc_final: 0.8316 (t70) REVERT: A 329 CYS cc_start: 0.8560 (m) cc_final: 0.8179 (t) REVERT: A 1135 MET cc_start: 0.8762 (ttm) cc_final: 0.8481 (mtp) REVERT: A 1139 HIS cc_start: 0.7158 (OUTLIER) cc_final: 0.6147 (t-90) REVERT: A 1160 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8661 (mp) REVERT: A 1214 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8734 (m) REVERT: C 121 MET cc_start: 0.7820 (ptp) cc_final: 0.7593 (ppp) REVERT: C 138 MET cc_start: 0.9008 (ttm) cc_final: 0.8793 (ttt) REVERT: C 397 MET cc_start: 0.8351 (tpt) cc_final: 0.8033 (tpt) REVERT: C 429 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8422 (mt) outliers start: 38 outliers final: 31 residues processed: 247 average time/residue: 0.1820 time to fit residues: 77.3757 Evaluate side-chains 252 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 746 MET Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 897 MET Chi-restraints excluded: chain D residue 1026 MET Chi-restraints excluded: chain D residue 1135 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1046 GLN Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1139 HIS Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1183 ARG Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 1178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 378 optimal weight: 7.9990 chunk 2 optimal weight: 0.0030 chunk 11 optimal weight: 5.9990 chunk 296 optimal weight: 0.8980 chunk 289 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 269 optimal weight: 8.9990 chunk 351 optimal weight: 0.9990 chunk 402 optimal weight: 5.9990 chunk 305 optimal weight: 20.0000 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** 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 = 0.3741 r_free = 0.3741 target = 0.076225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.053615 restraints weight = 256421.542| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 5.03 r_work: 0.2939 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 33482 Z= 0.108 Angle : 0.538 13.328 45704 Z= 0.269 Chirality : 0.038 0.191 5341 Planarity : 0.004 0.067 5627 Dihedral : 6.906 59.781 6218 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.68 % Rotamer: Outliers : 0.86 % Allowed : 15.63 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 2.12 (0.14), residues: 4169 helix: 2.48 (0.10), residues: 2670 sheet: -0.12 (0.34), residues: 254 loop : -0.70 (0.19), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1188 TYR 0.054 0.001 TYR B 370 PHE 0.032 0.001 PHE B 170 TRP 0.046 0.001 TRP B 184 HIS 0.006 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00233 (33478) covalent geometry : angle 0.53771 (45696) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.64760 ( 8) hydrogen bonds : bond 0.03751 ( 2029) hydrogen bonds : angle 3.82277 ( 6019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9479.85 seconds wall clock time: 162 minutes 55.07 seconds (9775.07 seconds total)