Starting phenix.real_space_refine on Sat Feb 7 13:45:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7z_70212/02_2026/9o7z_70212.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7z_70212/02_2026/9o7z_70212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o7z_70212/02_2026/9o7z_70212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7z_70212/02_2026/9o7z_70212.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o7z_70212/02_2026/9o7z_70212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7z_70212/02_2026/9o7z_70212.map" } resolution = 3.6 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 237 5.16 5 C 21378 2.51 5 N 5441 2.21 5 O 5648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 32704 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7952 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1056, 7942 Classifications: {'peptide': 1056} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1012} Chain breaks: 7 Unresolved non-hydrogen bonds: 646 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 14, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 394 Conformer: "B" Number of residues, atoms: 1056, 7942 Classifications: {'peptide': 1056} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1012} Chain breaks: 7 Unresolved non-hydrogen bonds: 646 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 14, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 394 bond proxies already assigned to first conformer: 8112 Chain: "D" Number of atoms: 7942 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 7932 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1013} Chain breaks: 7 Unresolved non-hydrogen bonds: 664 Unresolved non-hydrogen angles: 821 Unresolved non-hydrogen dihedrals: 551 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 15, 'TYR:plan': 4, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 403 Conformer: "B" Number of residues, atoms: 1057, 7932 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1013} Chain breaks: 7 Unresolved non-hydrogen bonds: 664 Unresolved non-hydrogen angles: 821 Unresolved non-hydrogen dihedrals: 551 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 15, 'TYR:plan': 4, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 403 bond proxies already assigned to first conformer: 8101 Chain: "B" Number of atoms: 7954 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 7944 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1013} Chain breaks: 7 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 810 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 27, 'ARG:plan': 14, 'PHE:plan': 5, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'ASN:plan1': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 409 Conformer: "B" Number of residues, atoms: 1057, 7944 Classifications: {'peptide': 1057} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1013} Chain breaks: 7 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 810 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 27, 'ARG:plan': 14, 'PHE:plan': 5, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 17, 'ASN:plan1': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 409 bond proxies already assigned to first conformer: 8111 Chain: "C" Number of atoms: 8016 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 7998 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1017} Chain breaks: 6 Unresolved non-hydrogen bonds: 627 Unresolved non-hydrogen angles: 773 Unresolved non-hydrogen dihedrals: 520 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 393 Conformer: "B" Number of residues, atoms: 1061, 7998 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1017} Chain breaks: 6 Unresolved non-hydrogen bonds: 627 Unresolved non-hydrogen angles: 773 Unresolved non-hydrogen dihedrals: 520 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 15, 'ASP:plan': 15, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 393 bond proxies already assigned to first conformer: 8162 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: "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: "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: 5 residue: pdb=" N AHIS A 674 " occ=0.32 ... (18 atoms not shown) pdb=" NE2BHIS A 674 " occ=0.68 residue: pdb=" N AHIS D 674 " occ=0.41 ... (18 atoms not shown) pdb=" NE2BHIS D 674 " occ=0.59 residue: pdb=" N AHIS B 674 " occ=0.40 ... (18 atoms not shown) pdb=" NE2BHIS B 674 " occ=0.60 residue: pdb=" N AHIS C 674 " occ=0.30 ... (18 atoms not shown) pdb=" NE2BHIS C 674 " occ=0.70 residue: pdb=" N AMET C 988 " occ=0.49 ... (14 atoms not shown) pdb=" CE BMET C 988 " occ=0.51 Time building chain proxies: 13.61, per 1000 atoms: 0.42 Number of scatterers: 32704 At special positions: 0 Unit cell: (135.464, 132.16, 161.07, 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 237 16.00 O 5648 8.00 N 5441 7.00 C 21378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1061 " distance=2.03 Simple disulfide: pdb=" SG CYS D1044 " - pdb=" SG CYS D1061 " distance=2.02 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1061 " distance=2.03 Simple disulfide: pdb=" SG CYS C1044 " - pdb=" SG CYS C1061 " distance=2.04 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: 2.69 Conformation dependent library (CDL) restraints added in 2.6 seconds 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7990 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 15 sheets defined 66.9% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 removed outlier: 3.798A pdb=" N PHE A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.801A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 181 Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.741A pdb=" N ILE A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.565A pdb=" N GLN A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.753A pdb=" N ILE A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'A' and resid 353 through 367 removed outlier: 3.958A pdb=" N ARG A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.687A pdb=" N ALA A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.801A pdb=" N ASN A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 440 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 566 Processing helix chain 'A' and resid 613 through 625 removed outlier: 3.891A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.578A pdb=" N GLN A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.599A 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: 3.523A 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 713 through 721 Processing helix chain 'A' and resid 723 through 729 removed outlier: 3.641A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 761 through 764 Processing helix chain 'A' and resid 835 through 845 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 Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.795A pdb=" N ASP A 947 " --> pdb=" O PRO A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 972 through 1010 removed outlier: 3.809A pdb=" N TYR A 976 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1030 removed outlier: 3.701A pdb=" N PHE A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET A1026 " --> pdb=" O ASN A1022 " (cutoff:3.500A) Proline residue: A1027 - end of helix Processing helix chain 'A' and resid 1036 through 1040 removed outlier: 3.716A pdb=" N ILE A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1081 removed outlier: 3.854A pdb=" N ALA A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1094 removed outlier: 3.727A pdb=" N THR A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1120 removed outlier: 3.572A pdb=" N VAL A1098 " --> pdb=" O THR A1094 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TYR A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1126 No H-bonds generated for 'chain 'A' and resid 1124 through 1126' Processing helix chain 'A' and resid 1127 through 1145 removed outlier: 4.190A pdb=" N SER A1131 " --> pdb=" O LEU A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1191 Processing helix chain 'A' and resid 1192 through 1232 Processing helix chain 'D' and resid 31 through 36 removed outlier: 3.517A pdb=" N PHE D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 141 removed outlier: 3.756A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 182 removed outlier: 3.757A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 209 Processing helix chain 'D' and resid 226 through 231 removed outlier: 4.085A pdb=" N ILE D 231 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 removed outlier: 3.612A pdb=" N GLN D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.675A 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 367 Processing helix chain 'D' and resid 372 through 387 Processing helix chain 'D' and resid 388 through 392 removed outlier: 3.680A pdb=" N LEU D 391 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.725A pdb=" N ASN D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 433 through 440 Processing helix chain 'D' and resid 451 through 463 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 564 Processing helix chain 'D' and resid 613 through 625 removed outlier: 3.916A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET D 625 " --> pdb=" O TRP D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.654A pdb=" N GLN D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 662 Processing helix chain 'D' and resid 665 through 694 removed outlier: 3.597A 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: 3.586A pdb=" N ILE D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 removed outlier: 3.620A pdb=" N GLY D 742 " --> pdb=" O ASP D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 760 Processing helix chain 'D' and resid 761 through 767 removed outlier: 4.035A pdb=" N LEU D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 766 " --> pdb=" O SER D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 846 Processing helix chain 'D' and resid 847 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: 3.535A pdb=" N VAL D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 940 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 968 removed outlier: 3.755A pdb=" N ASP D 947 " --> pdb=" O PRO D 943 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU D 964 " --> pdb=" O TYR D 960 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASP D 965 " --> pdb=" O ILE D 961 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 1010 removed outlier: 4.684A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1030 removed outlier: 3.802A pdb=" N PHE D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 4.557A 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: 3.730A pdb=" N ILE D1040 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1093 removed outlier: 3.966A pdb=" N ALA D1070 " --> pdb=" O TRP D1066 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL D1084 " --> pdb=" O ASN D1080 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN D1085 " --> pdb=" O ILE D1081 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1120 removed outlier: 4.684A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.489A 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 1144 removed outlier: 4.393A pdb=" N SER D1131 " --> pdb=" O LEU D1127 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS D1141 " --> pdb=" O PHE D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1191 Processing helix chain 'D' and resid 1192 through 1232 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 163 through 181 removed outlier: 3.564A pdb=" N THR B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.751A pdb=" N ILE B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.797A pdb=" N GLN B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.635A pdb=" N ILE B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.835A 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 367 removed outlier: 3.590A pdb=" N ARG B 357 " --> pdb=" O ASN B 353 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 388 removed outlier: 3.837A pdb=" N LYS B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 418 removed outlier: 3.628A pdb=" N ASN B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 440 removed outlier: 3.505A 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: 3.876A pdb=" N GLU B 617 " --> pdb=" O PHE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.698A pdb=" N GLN B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 662 Processing helix chain 'B' and resid 665 through 694 removed outlier: 3.744A 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 706 through 710 removed outlier: 4.148A pdb=" N SER B 710 " --> pdb=" O LYS B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 723 through 729 Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 751 through 760 Processing helix chain 'B' and resid 761 through 767 removed outlier: 4.230A pdb=" N LEU B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 766 " --> pdb=" O SER B 763 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.723A pdb=" N ASP B 947 " --> pdb=" O PRO B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 968 Processing helix chain 'B' and resid 972 through 1010 removed outlier: 3.528A pdb=" N TYR B 976 " --> pdb=" O TYR B 972 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1030 removed outlier: 3.632A pdb=" N LYS B1021 " --> pdb=" O TRP B1017 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N MET B1026 " --> pdb=" O ASN B1022 " (cutoff:3.500A) Proline residue: B1027 - end of helix Processing helix chain 'B' and resid 1031 through 1033 No H-bonds generated for 'chain 'B' and resid 1031 through 1033' Processing helix chain 'B' and resid 1036 through 1040 removed outlier: 3.798A pdb=" N ILE B1040 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1094 removed outlier: 4.243A pdb=" N ALA B1070 " --> pdb=" O TRP B1066 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL B1084 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN B1085 " --> pdb=" O ILE B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1120 removed outlier: 4.710A pdb=" N TYR B1111 " --> pdb=" O LYS B1107 " (cutoff:3.500A) removed outlier: 4.565A 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: 4.009A pdb=" N SER B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1191 removed outlier: 3.580A pdb=" N GLU B1175 " --> pdb=" O HIS B1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1232 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.715A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 181 removed outlier: 4.306A pdb=" N THR C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 209 Processing helix chain 'C' and resid 273 through 287 Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.683A pdb=" N SER C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 344 Processing helix chain 'C' and resid 353 through 368 Processing helix chain 'C' and resid 371 through 387 Processing helix chain 'C' and resid 409 through 418 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 493 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: 3.754A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET C 625 " --> pdb=" O TRP C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.838A pdb=" N GLN C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.754A 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: 3.636A 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 713 through 721 Processing helix chain 'C' and resid 723 through 729 Processing helix chain 'C' and resid 729 through 741 Processing helix chain 'C' and resid 751 through 760 Processing helix chain 'C' and resid 761 through 767 removed outlier: 4.450A 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: 3.581A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE C 957 " --> pdb=" O CYS C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 968 removed outlier: 4.230A pdb=" N ILE C 966 " --> pdb=" O ARG C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 1010 removed outlier: 3.600A pdb=" N TYR C 976 " --> pdb=" O TYR C 972 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1030 removed outlier: 3.612A pdb=" N LYS C1021 " --> pdb=" O TRP C1017 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N MET C1026 " --> pdb=" O ASN C1022 " (cutoff:3.500A) Proline residue: C1027 - end of helix Processing helix chain 'C' and resid 1031 through 1033 No H-bonds generated for 'chain 'C' and resid 1031 through 1033' Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.630A pdb=" N ILE C1040 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1081 removed outlier: 4.045A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1094 removed outlier: 3.698A pdb=" N THR C1094 " --> pdb=" O VAL C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1094 through 1120 removed outlier: 3.628A pdb=" N VAL C1098 " --> pdb=" O THR C1094 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR C1111 " --> pdb=" O LYS C1107 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN C1112 " --> pdb=" O PHE C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1127 Processing helix chain 'C' and resid 1128 through 1145 removed outlier: 3.622A pdb=" N THR C1134 " --> pdb=" O PHE C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1191 Processing helix chain 'C' and resid 1192 through 1232 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 240 removed outlier: 5.727A pdb=" N THR A 108 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL A 236 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU A 110 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN A 112 " --> pdb=" O PRO A 238 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLN A 240 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA A 105 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N PHE A 259 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N MET A 121 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU A 261 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL A 123 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ASP A 263 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 125 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 186 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA5, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.747A pdb=" N GLN D 99 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 233 through 240 removed outlier: 7.150A pdb=" N PHE D 106 " --> pdb=" O ARG D 233 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL D 235 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 108 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N PHE D 259 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N MET D 121 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU D 261 " --> pdb=" O MET D 121 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL D 123 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP D 263 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 125 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 328 Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 40 Processing sheet with id=AB1, first strand: chain 'B' and resid 119 through 123 removed outlier: 7.218A pdb=" N PHE B 106 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B 108 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 237 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 110 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 186 removed outlier: 6.681A pdb=" N LEU B 150 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU B 302 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER B 152 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL B 327 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA B 301 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N CYS B 329 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 326 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE B 395 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 328 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 37 through 40 Processing sheet with id=AB4, first strand: chain 'C' and resid 217 through 220 removed outlier: 7.514A pdb=" N GLY C 217 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA C 262 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA C 219 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N PHE C 259 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N MET C 121 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU C 261 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 123 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASP C 263 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 125 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA C 105 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 217 through 220 removed outlier: 7.514A pdb=" N GLY C 217 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA C 262 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA C 219 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N PHE C 259 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N MET C 121 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU C 261 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 123 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASP C 263 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 125 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA C 105 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 237 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 110 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 186 removed outlier: 6.029A pdb=" N VAL C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE C 395 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL C 328 " --> pdb=" O PHE C 395 " (cutoff:3.500A) 2044 hydrogen bonds defined for protein. 6071 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: 5.87 Time building geometry restraints manager: 3.54 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: 6597 1.33 - 1.46: 8922 1.46 - 1.58: 17592 1.58 - 1.71: 3 1.71 - 1.84: 398 Bond restraints: 33512 Sorted by residual: bond pdb=" CA PRO D 527 " pdb=" C PRO D 527 " ideal model delta sigma weight residual 1.517 1.461 0.056 6.70e-03 2.23e+04 6.96e+01 bond pdb=" C PRO A 761 " pdb=" N PRO A 762 " ideal model delta sigma weight residual 1.334 1.386 -0.052 8.40e-03 1.42e+04 3.85e+01 bond pdb=" N VAL D 394 " pdb=" CA VAL D 394 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.17e-02 7.31e+03 1.26e+01 bond pdb=" CG1 ILE D 151 " pdb=" CD1 ILE D 151 " ideal model delta sigma weight residual 1.513 1.382 0.131 3.90e-02 6.57e+02 1.13e+01 bond pdb=" N ILE A 956 " pdb=" CA ILE A 956 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.15e+00 ... (remaining 33507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 43943 2.91 - 5.82: 1522 5.82 - 8.73: 239 8.73 - 11.64: 32 11.64 - 14.55: 14 Bond angle restraints: 45750 Sorted by residual: angle pdb=" N ASP C 406 " pdb=" CA ASP C 406 " pdb=" C ASP C 406 " ideal model delta sigma weight residual 113.28 103.30 9.98 1.22e+00 6.72e-01 6.69e+01 angle pdb=" N VAL B 297 " pdb=" CA VAL B 297 " pdb=" CB VAL B 297 " ideal model delta sigma weight residual 111.21 120.68 -9.47 1.40e+00 5.10e-01 4.58e+01 angle pdb=" N LEU C 429 " pdb=" CA LEU C 429 " pdb=" C LEU C 429 " ideal model delta sigma weight residual 110.97 103.78 7.19 1.09e+00 8.42e-01 4.35e+01 angle pdb=" O PRO D 527 " pdb=" C PRO D 527 " pdb=" N PRO D 528 " ideal model delta sigma weight residual 121.15 118.10 3.05 4.70e-01 4.53e+00 4.22e+01 angle pdb=" N PRO C1125 " pdb=" CA PRO C1125 " pdb=" C PRO C1125 " ideal model delta sigma weight residual 110.70 118.27 -7.57 1.22e+00 6.72e-01 3.85e+01 ... (remaining 45745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.57: 19528 24.57 - 49.14: 1235 49.14 - 73.72: 199 73.72 - 98.29: 10 98.29 - 122.86: 12 Dihedral angle restraints: 20984 sinusoidal: 8637 harmonic: 12347 Sorted by residual: dihedral pdb=" CB CYS C1044 " pdb=" SG CYS C1044 " pdb=" SG CYS C1061 " pdb=" CB CYS C1061 " ideal model delta sinusoidal sigma weight residual 93.00 167.54 -74.54 1 1.00e+01 1.00e-02 7.04e+01 dihedral pdb=" CA MET A 625 " pdb=" C MET A 625 " pdb=" N LYS A 626 " pdb=" CA LYS A 626 " ideal model delta harmonic sigma weight residual 180.00 150.14 29.86 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ASN A 353 " pdb=" C ASN A 353 " pdb=" N GLU A 354 " pdb=" CA GLU A 354 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 20981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4766 0.106 - 0.212: 507 0.212 - 0.318: 49 0.318 - 0.423: 12 0.423 - 0.529: 5 Chirality restraints: 5339 Sorted by residual: chirality pdb=" CG LEU B 414 " pdb=" CB LEU B 414 " pdb=" CD1 LEU B 414 " pdb=" CD2 LEU B 414 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" CB ILE B 218 " pdb=" CA ILE B 218 " pdb=" CG1 ILE B 218 " pdb=" CG2 ILE B 218 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CG LEU D 150 " pdb=" CB LEU D 150 " pdb=" CD1 LEU D 150 " pdb=" CD2 LEU D 150 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.52e+00 ... (remaining 5336 not shown) Planarity restraints: 5642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 854 " 0.048 2.00e-02 2.50e+03 4.40e-02 3.39e+01 pdb=" CG PHE D 854 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 PHE D 854 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE D 854 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 854 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 854 " 0.029 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 TRP D 142 " 0.032 2.00e-02 2.50e+03 3.45e-02 2.97e+01 pdb=" CG TRP D 142 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP D 142 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP D 142 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 142 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 142 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 142 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 142 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 142 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP D 142 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 866 " -0.027 2.00e-02 2.50e+03 3.99e-02 2.79e+01 pdb=" CG PHE D 866 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 PHE D 866 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE D 866 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE D 866 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 866 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 866 " -0.000 2.00e-02 2.50e+03 ... (remaining 5639 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 3 2.44 - 3.05: 19792 3.05 - 3.67: 51521 3.67 - 4.28: 72680 4.28 - 4.90: 118186 Nonbonded interactions: 262182 Sorted by model distance: nonbonded pdb=" CB LYS D1062 " pdb=" NZ LYS D1062 " model vdw 1.823 3.520 nonbonded pdb=" CA LYS D1062 " pdb=" NZ LYS D1062 " model vdw 2.317 3.550 nonbonded pdb=" O LEU C 463 " pdb=" NH1 ARG C 465 " model vdw 2.333 3.120 nonbonded pdb=" N TRP B 221 " pdb=" O ALA B 262 " model vdw 2.453 3.120 nonbonded pdb=" N VAL A 328 " pdb=" O VAL A 328 " model vdw 2.469 2.496 ... (remaining 262177 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 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 35 or (resid 36 through 37 and (name N or nam \ e CA or name C or name O or name CB )) or resid 38 or (resid 39 through 40 and ( \ name N or name CA or name C or name O or name CB )) or resid 41 or (resid 42 and \ (name N or name CA or name C or name O or name CB )) or resid 43 through 99 or \ (resid 100 and (name N or name CA or name C or name O or name CB )) or resid 101 \ through 133 or (resid 134 and (name N or name CA or name C or name O or name CB \ )) or resid 135 through 137 or (resid 138 and (name N or name CA or name C or n \ ame O or name CB )) or resid 139 through 148 or (resid 149 and (name N or name C \ A or name C or name O or name CB )) or resid 150 through 222 or (resid 223 and ( \ name N or name CA or name C or name O or name CB )) or resid 224 through 229 or \ (resid 230 and (name N or name CA or name C or name O or name CB )) or resid 231 \ through 248 or (resid 249 and (name N or name CA or name C or name O or name CB \ )) or resid 250 through 356 or (resid 357 and (name N or name CA or name C or n \ ame O or name CB )) or resid 358 through 396 or (resid 397 and (name N or name C \ A or name C or name O or name CB )) or resid 398 through 405 or (resid 406 throu \ gh 408 and (name N or name CA or name C or name O or name CB )) or resid 409 thr \ ough 413 or (resid 414 through 415 and (name N or name CA or name C or name O or \ name CB )) or resid 416 through 426 or (resid 427 through 428 and (name N or na \ me CA or name C or name O or name CB )) or resid 429 through 504 or (resid 505 a \ nd (name N or name CA or name C or name O or name CB )) or resid 506 through 673 \ or resid 675 through 987 or resid 989 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 or (resid 39 through 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 or (resid 42 and (name N or n \ ame CA or name C or name O or name CB )) or resid 43 through 99 or (resid 100 an \ d (name N or name CA or name C or name O or name CB )) or resid 101 through 133 \ or (resid 134 and (name N or name CA or name C or name O or name CB )) or resid \ 135 through 148 or (resid 149 and (name N or name CA or name C or name O or name \ CB )) or resid 150 through 222 or (resid 223 and (name N or name CA or name C o \ r name O or name CB )) or resid 224 through 229 or (resid 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 through 251 or (resid 252 an \ d (name N or name CA or name C or name O or name CB )) or resid 253 through 254 \ or (resid 255 and (name N or name CA or name C or name O or name CB )) or resid \ 256 through 259 or (resid 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 285 or (resid 286 and (name N or name CA or name C o \ r name O or name CB )) or resid 287 through 356 or (resid 357 and (name N or nam \ e CA or name C or name O or name CB )) or resid 358 through 396 or (resid 397 an \ d (name N or name CA or name C or name O or name CB )) or resid 398 through 405 \ or (resid 406 through 408 and (name N or name CA or name C or name O or name CB \ )) or resid 409 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or resid 416 through 426 or (resid 427 through 42 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 429 through \ 478 or (resid 479 and (name N or name CA or name C or name O or name CB )) or re \ sid 480 through 504 or (resid 505 and (name N or name CA or name C or name O or \ name CB )) or resid 506 through 673 or resid 675 through 987 or resid 989 throug \ h 1055 or resid 1057 through 1208 or (resid 1209 and (name N or name CA or name \ C or name O or name CB )) or resid 1210 through 1406)) selection = (chain 'C' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 35 or (resid 36 through 37 and (name N or nam \ e CA or name C or name O or name CB )) or resid 38 through 41 or (resid 42 and ( \ name N or name CA or name C or name O or name CB )) or resid 43 through 99 or (r \ esid 100 and (name N or name CA or name C or name O or name CB )) or resid 101 t \ hrough 133 or (resid 134 and (name N or name CA or name C or name O or name CB ) \ ) or resid 135 through 137 or (resid 138 and (name N or name CA or name C or nam \ e O or name CB )) or resid 139 through 148 or (resid 149 and (name N or name CA \ or name C or name O or name CB )) or resid 150 through 222 or (resid 223 and (na \ me N or name CA or name C or name O or name CB )) or resid 224 through 248 or (r \ esid 249 and (name N or name CA or name C or name O or name CB )) or resid 250 t \ hrough 251 or (resid 252 and (name N or name CA or name C or name O or name CB ) \ ) or resid 253 through 254 or (resid 255 and (name N or name CA or name C or nam \ e O or name CB )) or resid 256 through 259 or (resid 260 and (name N or name CA \ or name C or name O or name CB )) or resid 261 through 278 or (resid 279 and (na \ me N or name CA or name C or name O or name CB )) or resid 280 through 285 or (r \ esid 286 and (name N or name CA or name C or name O or name CB )) or resid 287 t \ hrough 356 or (resid 357 and (name N or name CA or name C or name O or name CB ) \ ) or resid 358 through 394 or (resid 395 and (name N or name CA or name C or nam \ e O or name CB )) or resid 396 or (resid 397 and (name N or name CA or name C or \ name O or name CB )) or resid 398 or resid 404 through 406 or (resid 407 throug \ h 408 and (name N or name CA or name C or name O or name CB )) or resid 409 thro \ ugh 412 or (resid 413 through 415 and (name N or name CA or name C or name O or \ name CB )) or resid 416 through 478 or (resid 479 and (name N or name CA or name \ C or name O or name CB )) or resid 480 through 528 or (resid 529 and (name N or \ name CA or name C or name O or name CB )) or resid 530 through 649 or (resid 65 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 651 through \ 673 or resid 675 through 986 or (resid 987 and (name N or name CA or name C or n \ ame O or name CB )) or resid 989 through 1161 or (resid 1162 and (name N or name \ CA or name C or name O or name CB )) or resid 1163 through 1208 or (resid 1209 \ and (name N or name CA or name C or name O or name CB )) or resid 1210 through 1 \ 406)) selection = (chain 'D' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 35 or (resid 36 through 37 and (name N or nam \ e CA or name C or name O or name CB )) or resid 38 or (resid 39 through 40 and ( \ name N or name CA or name C or name O or name CB )) or resid 41 through 137 or ( \ resid 138 and (name N or name CA or name C or name O or name CB )) or resid 139 \ through 229 or (resid 230 and (name N or name CA or name C or name O or name CB \ )) or resid 231 through 248 or (resid 249 and (name N or name CA or name C or na \ me O or name CB )) or resid 250 through 254 or (resid 255 and (name N or name CA \ or name C or name O or name CB )) or resid 256 through 259 or (resid 260 and (n \ ame N or name CA or name C or name O or name CB )) or resid 261 through 405 or ( \ resid 406 through 408 and (name N or name CA or name C or name O or name CB )) o \ r resid 409 through 413 or (resid 414 through 415 and (name N or name CA or name \ C or name O or name CB )) or resid 416 through 426 or (resid 427 through 428 an \ d (name N or name CA or name C or name O or name CB )) or resid 429 through 478 \ or (resid 479 and (name N or name CA or name C or name O or name CB )) or resid \ 480 through 504 or (resid 505 and (name N or name CA or name C or name O or name \ CB )) or resid 506 through 528 or (resid 529 and (name N or name CA or name C o \ r name O or name CB )) or resid 530 through 673 or resid 675 through 987 or resi \ d 989 through 1048 or resid 1056 through 1208 or (resid 1209 and (name N or name \ CA or name C or name O or name CB )) or resid 1210 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 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: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 37.310 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.008 0.131 33516 Z= 0.418 Angle : 1.274 18.061 45758 Z= 0.711 Chirality : 0.070 0.529 5339 Planarity : 0.010 0.118 5642 Dihedral : 15.765 122.859 12982 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 1.31 % Allowed : 12.73 % Favored : 85.96 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.65 % 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: -1.88 (0.11), residues: 4184 helix: -0.76 (0.09), residues: 2605 sheet: -1.51 (0.31), residues: 256 loop : -1.92 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A1188 TYR 0.068 0.004 TYR B 37 PHE 0.098 0.004 PHE D 854 TRP 0.089 0.005 TRP D 142 HIS 0.016 0.003 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00843 (33512) covalent geometry : angle 1.27055 (45750) SS BOND : bond 0.00686 ( 4) SS BOND : angle 7.62920 ( 8) hydrogen bonds : bond 0.13632 ( 2039) hydrogen bonds : angle 6.67831 ( 6071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 309 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.6856 (m-80) cc_final: 0.6564 (m-80) REVERT: A 242 MET cc_start: 0.1408 (tpt) cc_final: 0.1168 (tpt) REVERT: A 397 MET cc_start: 0.8414 (tmm) cc_final: 0.7956 (ttt) REVERT: A 505 LEU cc_start: 0.9242 (mt) cc_final: 0.8819 (mt) REVERT: A 999 MET cc_start: 0.8562 (mtm) cc_final: 0.8194 (mtm) REVERT: A 1133 MET cc_start: 0.8690 (ttp) cc_final: 0.8413 (ttm) REVERT: D 36 PHE cc_start: 0.5237 (m-80) cc_final: 0.4824 (m-80) REVERT: D 138 MET cc_start: 0.8310 (ptt) cc_final: 0.7355 (tmm) REVERT: D 242 MET cc_start: 0.2356 (tpt) cc_final: 0.1989 (tpt) REVERT: D 655 MET cc_start: 0.9182 (mtm) cc_final: 0.8905 (mtp) REVERT: D 734 MET cc_start: 0.7982 (mtm) cc_final: 0.7556 (mpp) REVERT: D 746 MET cc_start: 0.7707 (ttp) cc_final: 0.7480 (ttt) REVERT: D 902 MET cc_start: 0.7893 (mmt) cc_final: 0.7521 (mtt) REVERT: D 1203 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8671 (mtt-85) REVERT: B 121 MET cc_start: 0.6810 (mtt) cc_final: 0.6525 (ptp) REVERT: B 127 PHE cc_start: 0.6894 (p90) cc_final: 0.6370 (p90) REVERT: B 242 MET cc_start: 0.3614 (tpt) cc_final: 0.3411 (tpt) REVERT: B 255 MET cc_start: 0.7894 (mmm) cc_final: 0.7008 (mtm) REVERT: B 544 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8415 (mm) REVERT: B 932 SER cc_start: 0.9198 (m) cc_final: 0.8800 (p) REVERT: B 1047 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.6718 (m-40) REVERT: B 1062 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8448 (mptt) REVERT: C 174 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8730 (mm) REVERT: C 313 ILE cc_start: 0.8288 (mm) cc_final: 0.7818 (tp) REVERT: C 338 ILE cc_start: 0.7720 (pp) cc_final: 0.7298 (pt) REVERT: C 457 MET cc_start: 0.7758 (mmm) cc_final: 0.6947 (tpp) REVERT: C 478 SER cc_start: 0.6203 (OUTLIER) cc_final: 0.5820 (m) outliers start: 40 outliers final: 12 residues processed: 345 average time/residue: 0.1953 time to fit residues: 112.6819 Evaluate side-chains 258 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 1062 LYS Chi-restraints excluded: chain D residue 1203 ARG Chi-restraints excluded: chain D residue 1204 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1062 LYS Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 1062 LYS Chi-restraints excluded: chain C residue 1204 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 GLN D 955 ASN ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 HIS C 295 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.074177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.052479 restraints weight = 242520.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.054827 restraints weight = 101004.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.055715 restraints weight = 55580.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.056427 restraints weight = 37362.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.056562 restraints weight = 32472.720| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33516 Z= 0.169 Angle : 0.651 9.739 45758 Z= 0.336 Chirality : 0.042 0.248 5339 Planarity : 0.005 0.076 5642 Dihedral : 9.264 75.011 6265 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.89 % Allowed : 13.21 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.06 (0.13), residues: 4184 helix: 0.87 (0.10), residues: 2646 sheet: -1.35 (0.31), residues: 274 loop : -1.62 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 747 TYR 0.023 0.002 TYR B 958 PHE 0.031 0.002 PHE D 854 TRP 0.039 0.002 TRP B 621 HIS 0.009 0.001 HIS B1171 Details of bonding type rmsd covalent geometry : bond 0.00374 (33512) covalent geometry : angle 0.65127 (45750) SS BOND : bond 0.00237 ( 4) SS BOND : angle 1.16389 ( 8) hydrogen bonds : bond 0.05034 ( 2039) hydrogen bonds : angle 4.59081 ( 6071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 249 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 MET cc_start: 0.8203 (tmm) cc_final: 0.7838 (ttm) REVERT: A 902 MET cc_start: 0.7190 (mtt) cc_final: 0.6824 (mtt) REVERT: A 1133 MET cc_start: 0.8784 (ttp) cc_final: 0.8463 (ttm) REVERT: A 1187 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8567 (t0) REVERT: D 138 MET cc_start: 0.7925 (ptt) cc_final: 0.6939 (tmm) REVERT: D 242 MET cc_start: 0.2963 (tpt) cc_final: 0.2493 (tpt) REVERT: D 505 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9007 (mm) REVERT: D 734 MET cc_start: 0.7864 (mtm) cc_final: 0.7557 (mtm) REVERT: D 902 MET cc_start: 0.7909 (mmt) cc_final: 0.7690 (mtt) REVERT: B 202 LEU cc_start: 0.8820 (tt) cc_final: 0.8224 (tp) REVERT: B 370 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: B 655 MET cc_start: 0.8818 (ttp) cc_final: 0.8592 (ttm) REVERT: B 932 SER cc_start: 0.9225 (m) cc_final: 0.8853 (p) REVERT: B 1047 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.6915 (m-40) REVERT: C 338 ILE cc_start: 0.7509 (pp) cc_final: 0.7190 (pt) REVERT: C 457 MET cc_start: 0.8131 (mmm) cc_final: 0.7304 (tpp) REVERT: C 479 MET cc_start: 0.7366 (mmm) cc_final: 0.7112 (mmm) REVERT: C 741 MET cc_start: 0.9036 (mmm) cc_final: 0.8716 (mmt) outliers start: 57 outliers final: 22 residues processed: 299 average time/residue: 0.1779 time to fit residues: 91.5949 Evaluate side-chains 257 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 370 TYR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 409 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 417 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 400 optimal weight: 7.9990 chunk 366 optimal weight: 0.9980 chunk 398 optimal weight: 1.9990 chunk 375 optimal weight: 9.9990 chunk 304 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 HIS ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.073196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051061 restraints weight = 289694.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.053701 restraints weight = 110875.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.054672 restraints weight = 53614.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.055086 restraints weight = 36203.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.055206 restraints weight = 35479.350| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33516 Z= 0.189 Angle : 0.638 9.120 45758 Z= 0.325 Chirality : 0.042 0.323 5339 Planarity : 0.005 0.065 5642 Dihedral : 8.173 59.619 6237 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.86 % Allowed : 13.08 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.13), residues: 4184 helix: 1.52 (0.10), residues: 2655 sheet: -1.24 (0.32), residues: 278 loop : -1.52 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 357 TYR 0.021 0.002 TYR B1028 PHE 0.031 0.002 PHE B 866 TRP 0.028 0.002 TRP B 621 HIS 0.005 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00424 (33512) covalent geometry : angle 0.63756 (45750) SS BOND : bond 0.00071 ( 4) SS BOND : angle 1.01329 ( 8) hydrogen bonds : bond 0.04865 ( 2039) hydrogen bonds : angle 4.31497 ( 6071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 31 TRP cc_start: 0.6559 (t60) cc_final: 0.6137 (t60) REVERT: A 397 MET cc_start: 0.8239 (tmm) cc_final: 0.7983 (ttm) REVERT: A 625 MET cc_start: 0.9085 (ptp) cc_final: 0.8682 (ptp) REVERT: A 902 MET cc_start: 0.7486 (mtt) cc_final: 0.7227 (mtt) REVERT: A 1133 MET cc_start: 0.8751 (ttp) cc_final: 0.8439 (ttm) REVERT: D 138 MET cc_start: 0.7991 (ptt) cc_final: 0.6961 (tmm) REVERT: D 242 MET cc_start: 0.2819 (tpt) cc_final: 0.2222 (tpt) REVERT: D 259 PHE cc_start: 0.5412 (m-80) cc_final: 0.4599 (m-80) REVERT: D 505 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9028 (mm) REVERT: B 255 MET cc_start: 0.8349 (tpp) cc_final: 0.8045 (tpp) REVERT: B 370 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6965 (m-80) REVERT: B 1047 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7083 (m-40) REVERT: C 255 MET cc_start: 0.8287 (mtm) cc_final: 0.7852 (tpp) REVERT: C 356 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6840 (mm) REVERT: C 397 MET cc_start: 0.6764 (tpt) cc_final: 0.6153 (tpt) REVERT: C 457 MET cc_start: 0.8040 (mmm) cc_final: 0.7158 (tpp) REVERT: C 479 MET cc_start: 0.7316 (mmm) cc_final: 0.7109 (mmm) REVERT: C 699 MET cc_start: 0.9106 (mmm) cc_final: 0.8736 (mmt) REVERT: C 739 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8180 (mtt) outliers start: 56 outliers final: 27 residues processed: 281 average time/residue: 0.1777 time to fit residues: 86.5236 Evaluate side-chains 257 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 370 TYR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 20 optimal weight: 10.0000 chunk 326 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 352 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 370 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 291 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 ASN C1093 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.071675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.049631 restraints weight = 280411.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.052257 restraints weight = 112640.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.053224 restraints weight = 52538.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.053555 restraints weight = 35689.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.053702 restraints weight = 35725.458| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 33516 Z= 0.255 Angle : 0.694 11.673 45758 Z= 0.353 Chirality : 0.043 0.232 5339 Planarity : 0.005 0.064 5642 Dihedral : 8.146 59.679 6236 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.11 % Allowed : 13.44 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.75 (0.13), residues: 4184 helix: 1.61 (0.10), residues: 2647 sheet: -1.41 (0.31), residues: 279 loop : -1.46 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 357 TYR 0.026 0.002 TYR C 345 PHE 0.039 0.002 PHE B 866 TRP 0.027 0.002 TRP B 621 HIS 0.007 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00571 (33512) covalent geometry : angle 0.69353 (45750) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.95396 ( 8) hydrogen bonds : bond 0.05104 ( 2039) hydrogen bonds : angle 4.41766 ( 6071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 233 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 653 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9086 (ttmm) REVERT: A 902 MET cc_start: 0.7558 (mtt) cc_final: 0.7264 (mtt) REVERT: A 1133 MET cc_start: 0.8774 (ttp) cc_final: 0.8488 (ttm) REVERT: A 1135 MET cc_start: 0.5323 (tmm) cc_final: 0.5009 (tmm) REVERT: D 242 MET cc_start: 0.3162 (tpt) cc_final: 0.2502 (tpt) REVERT: D 259 PHE cc_start: 0.5574 (m-80) cc_final: 0.4682 (m-80) REVERT: D 505 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9045 (mm) REVERT: D 545 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7886 (mpm) REVERT: B 242 MET cc_start: 0.3114 (tpt) cc_final: 0.2844 (tpt) REVERT: B 255 MET cc_start: 0.8667 (tpp) cc_final: 0.8070 (tpp) REVERT: B 370 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: B 461 LEU cc_start: 0.9341 (mt) cc_final: 0.9132 (mp) REVERT: B 1047 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7262 (m-40) REVERT: C 255 MET cc_start: 0.8264 (mtm) cc_final: 0.7917 (tpp) REVERT: C 397 MET cc_start: 0.6682 (tpt) cc_final: 0.6108 (tpt) REVERT: C 407 LEU cc_start: 0.8540 (mp) cc_final: 0.7889 (tt) REVERT: C 457 MET cc_start: 0.8192 (mmm) cc_final: 0.7213 (tpp) REVERT: C 503 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: C 625 MET cc_start: 0.8990 (ptp) cc_final: 0.8639 (ptp) REVERT: C 739 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8194 (mtt) outliers start: 64 outliers final: 34 residues processed: 285 average time/residue: 0.1835 time to fit residues: 90.0507 Evaluate side-chains 263 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1183 ARG Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 370 TYR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain B residue 1208 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 91 optimal weight: 0.8980 chunk 413 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 400 optimal weight: 4.9990 chunk 326 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 347 optimal weight: 20.0000 chunk 366 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 343 HIS ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 HIS ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.072482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050269 restraints weight = 326841.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.052839 restraints weight = 121403.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054030 restraints weight = 57694.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.054725 restraints weight = 37014.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.054736 restraints weight = 34772.647| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33516 Z= 0.169 Angle : 0.593 11.155 45758 Z= 0.301 Chirality : 0.040 0.249 5339 Planarity : 0.004 0.057 5642 Dihedral : 7.788 59.399 6236 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.38 % Allowed : 13.88 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 1.15 (0.13), residues: 4184 helix: 1.94 (0.10), residues: 2656 sheet: -1.23 (0.31), residues: 281 loop : -1.39 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 747 TYR 0.019 0.001 TYR A 958 PHE 0.028 0.002 PHE B 866 TRP 0.030 0.002 TRP B 621 HIS 0.004 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00378 (33512) covalent geometry : angle 0.59312 (45750) SS BOND : bond 0.00062 ( 4) SS BOND : angle 0.66587 ( 8) hydrogen bonds : bond 0.04590 ( 2039) hydrogen bonds : angle 4.14879 ( 6071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: A 741 MET cc_start: 0.9025 (mmm) cc_final: 0.8787 (mmt) REVERT: A 890 PHE cc_start: 0.7655 (m-10) cc_final: 0.7325 (m-10) REVERT: A 902 MET cc_start: 0.7561 (mtt) cc_final: 0.7258 (mtt) REVERT: A 1133 MET cc_start: 0.8775 (ttp) cc_final: 0.8494 (ttm) REVERT: A 1135 MET cc_start: 0.5288 (tmm) cc_final: 0.4929 (tmm) REVERT: D 242 MET cc_start: 0.3134 (tpt) cc_final: 0.2430 (tpt) REVERT: D 259 PHE cc_start: 0.5583 (m-80) cc_final: 0.4681 (m-80) REVERT: D 505 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9040 (mm) REVERT: D 999 MET cc_start: 0.8740 (mtp) cc_final: 0.8462 (ttm) REVERT: B 255 MET cc_start: 0.8608 (tpp) cc_final: 0.8315 (tpp) REVERT: B 370 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6907 (m-80) REVERT: B 397 MET cc_start: 0.7607 (tmm) cc_final: 0.7120 (tmm) REVERT: B 1047 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7291 (m-40) REVERT: C 255 MET cc_start: 0.8322 (mtm) cc_final: 0.7984 (tpp) REVERT: C 407 LEU cc_start: 0.8412 (mp) cc_final: 0.7761 (tt) REVERT: C 503 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: C 699 MET cc_start: 0.9026 (mmm) cc_final: 0.8666 (mmt) REVERT: C 739 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8157 (mtt) REVERT: C 741 MET cc_start: 0.9138 (mmm) cc_final: 0.8606 (mmt) REVERT: C 978 MET cc_start: 0.7867 (mtt) cc_final: 0.7611 (mtm) outliers start: 41 outliers final: 26 residues processed: 261 average time/residue: 0.1743 time to fit residues: 79.9368 Evaluate side-chains 247 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 370 TYR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 184 optimal weight: 0.9980 chunk 114 optimal weight: 0.0370 chunk 255 optimal weight: 8.9990 chunk 325 optimal weight: 8.9990 chunk 296 optimal weight: 0.7980 chunk 338 optimal weight: 0.0000 chunk 176 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 0.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 GLN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN B 867 ASN ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.074150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.052122 restraints weight = 350008.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.055060 restraints weight = 128543.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.056176 restraints weight = 53841.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.056307 restraints weight = 36775.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.056496 restraints weight = 37253.854| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 33516 Z= 0.109 Angle : 0.547 9.978 45758 Z= 0.275 Chirality : 0.039 0.197 5339 Planarity : 0.004 0.053 5642 Dihedral : 7.261 59.993 6236 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.09 % Allowed : 14.14 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 1.55 (0.13), residues: 4184 helix: 2.25 (0.10), residues: 2661 sheet: -1.13 (0.32), residues: 281 loop : -1.20 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 747 TYR 0.022 0.001 TYR A 958 PHE 0.018 0.001 PHE B 866 TRP 0.038 0.001 TRP B 621 HIS 0.005 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00224 (33512) covalent geometry : angle 0.54696 (45750) SS BOND : bond 0.00056 ( 4) SS BOND : angle 0.40251 ( 8) hydrogen bonds : bond 0.03998 ( 2039) hydrogen bonds : angle 3.84447 ( 6071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 121 MET cc_start: 0.7161 (mmm) cc_final: 0.6761 (mmm) REVERT: A 741 MET cc_start: 0.8977 (mmm) cc_final: 0.8757 (mmt) REVERT: A 902 MET cc_start: 0.7507 (mtt) cc_final: 0.7216 (mtt) REVERT: A 1135 MET cc_start: 0.5345 (tmm) cc_final: 0.5004 (tmm) REVERT: D 242 MET cc_start: 0.2829 (tpt) cc_final: 0.2020 (tpt) REVERT: D 259 PHE cc_start: 0.5841 (m-80) cc_final: 0.4801 (m-80) REVERT: D 505 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8983 (mm) REVERT: B 397 MET cc_start: 0.7537 (tmm) cc_final: 0.7019 (tmm) REVERT: B 655 MET cc_start: 0.8698 (ttm) cc_final: 0.8496 (ttm) REVERT: B 1047 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7092 (m-40) REVERT: C 255 MET cc_start: 0.8314 (mtm) cc_final: 0.7990 (tpp) REVERT: C 345 TYR cc_start: 0.8225 (t80) cc_final: 0.8023 (t80) REVERT: C 358 ASP cc_start: 0.7564 (m-30) cc_final: 0.7341 (t70) REVERT: C 397 MET cc_start: 0.6364 (tpt) cc_final: 0.5951 (tpt) REVERT: C 407 LEU cc_start: 0.8380 (mp) cc_final: 0.7621 (tt) REVERT: C 457 MET cc_start: 0.6966 (tpp) cc_final: 0.6297 (tpp) REVERT: C 483 LEU cc_start: 0.8907 (tp) cc_final: 0.8625 (mp) REVERT: C 625 MET cc_start: 0.8822 (ptp) cc_final: 0.8525 (ptp) REVERT: C 699 MET cc_start: 0.8987 (mmm) cc_final: 0.8708 (mmt) outliers start: 32 outliers final: 19 residues processed: 260 average time/residue: 0.1858 time to fit residues: 83.1865 Evaluate side-chains 240 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 864 MET Chi-restraints excluded: chain D residue 1211 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 1113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 308 optimal weight: 2.9990 chunk 336 optimal weight: 30.0000 chunk 168 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 418 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1012 ASN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 GLN ** B1092 ASN ** 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 = 0.3675 r_free = 0.3675 target = 0.073562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051782 restraints weight = 281989.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.054426 restraints weight = 111157.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.055342 restraints weight = 53328.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.056102 restraints weight = 35993.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.056079 restraints weight = 34643.542| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 33516 Z= 0.123 Angle : 0.547 10.323 45758 Z= 0.275 Chirality : 0.039 0.183 5339 Planarity : 0.004 0.054 5642 Dihedral : 7.172 59.869 6233 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.07 % Favored : 96.91 % Rotamer: Outliers : 1.25 % Allowed : 14.43 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 4184 helix: 2.30 (0.10), residues: 2669 sheet: -1.07 (0.32), residues: 277 loop : -1.14 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1183 TYR 0.018 0.001 TYR A 958 PHE 0.018 0.001 PHE B 866 TRP 0.045 0.001 TRP B 431 HIS 0.004 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00274 (33512) covalent geometry : angle 0.54711 (45750) SS BOND : bond 0.00050 ( 4) SS BOND : angle 0.43639 ( 8) hydrogen bonds : bond 0.04022 ( 2039) hydrogen bonds : angle 3.83883 ( 6071) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 121 MET cc_start: 0.7273 (mmm) cc_final: 0.6958 (mmm) REVERT: A 902 MET cc_start: 0.7581 (mtt) cc_final: 0.7295 (mtt) REVERT: A 1135 MET cc_start: 0.5329 (tmm) cc_final: 0.4990 (tmm) REVERT: D 242 MET cc_start: 0.2829 (tpt) cc_final: 0.2011 (tpt) REVERT: D 259 PHE cc_start: 0.5622 (m-80) cc_final: 0.4718 (m-80) REVERT: D 505 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9026 (mm) REVERT: B 397 MET cc_start: 0.7599 (tmm) cc_final: 0.7071 (tmm) REVERT: B 442 PHE cc_start: 0.7909 (m-80) cc_final: 0.7611 (m-80) REVERT: B 457 MET cc_start: 0.8464 (tpp) cc_final: 0.8082 (tpp) REVERT: B 1047 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7126 (m-40) REVERT: C 210 ARG cc_start: 0.6766 (mmt180) cc_final: 0.6541 (mmt-90) REVERT: C 255 MET cc_start: 0.8311 (mtm) cc_final: 0.7997 (tpp) REVERT: C 358 ASP cc_start: 0.7512 (m-30) cc_final: 0.7294 (t70) REVERT: C 397 MET cc_start: 0.6205 (tpt) cc_final: 0.5821 (tpt) REVERT: C 407 LEU cc_start: 0.8372 (mp) cc_final: 0.7622 (tt) REVERT: C 457 MET cc_start: 0.6932 (tpp) cc_final: 0.6608 (tpp) REVERT: C 483 LEU cc_start: 0.8938 (tp) cc_final: 0.8612 (mp) REVERT: C 699 MET cc_start: 0.9020 (mmm) cc_final: 0.8660 (mmt) REVERT: C 984 MET cc_start: 0.9065 (mmm) cc_final: 0.8853 (mmm) outliers start: 37 outliers final: 26 residues processed: 253 average time/residue: 0.1743 time to fit residues: 77.2947 Evaluate side-chains 250 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 1211 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1115 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 127 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 411 optimal weight: 0.3980 chunk 201 optimal weight: 0.8980 chunk 311 optimal weight: 10.0000 chunk 312 optimal weight: 4.9990 chunk 420 optimal weight: 30.0000 chunk 109 optimal weight: 6.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.073342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.051153 restraints weight = 348685.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.053769 restraints weight = 124469.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.055085 restraints weight = 58834.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.055758 restraints weight = 36470.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.055806 restraints weight = 33846.924| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33516 Z= 0.132 Angle : 0.553 9.568 45758 Z= 0.278 Chirality : 0.039 0.301 5339 Planarity : 0.004 0.051 5642 Dihedral : 7.111 59.532 6233 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.19 % Favored : 96.79 % Rotamer: Outliers : 1.02 % Allowed : 14.78 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 1.75 (0.13), residues: 4184 helix: 2.37 (0.10), residues: 2664 sheet: -0.97 (0.33), residues: 272 loop : -1.08 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1183 TYR 0.018 0.001 TYR C 345 PHE 0.022 0.001 PHE B 866 TRP 0.032 0.001 TRP B 431 HIS 0.004 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00294 (33512) covalent geometry : angle 0.55325 (45750) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.42250 ( 8) hydrogen bonds : bond 0.04059 ( 2039) hydrogen bonds : angle 3.83946 ( 6071) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 121 MET cc_start: 0.7371 (mmm) cc_final: 0.7042 (mmm) REVERT: A 902 MET cc_start: 0.7519 (mtt) cc_final: 0.7291 (mtt) REVERT: D 242 MET cc_start: 0.2863 (tpt) cc_final: 0.1997 (tpt) REVERT: D 259 PHE cc_start: 0.5540 (m-80) cc_final: 0.4683 (m-80) REVERT: D 505 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9031 (mm) REVERT: B 397 MET cc_start: 0.7615 (tmm) cc_final: 0.7094 (tmm) REVERT: B 442 PHE cc_start: 0.7873 (m-80) cc_final: 0.7177 (m-80) REVERT: B 457 MET cc_start: 0.8490 (tpp) cc_final: 0.8189 (tpp) REVERT: B 1047 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7147 (m-40) REVERT: C 255 MET cc_start: 0.8290 (mtm) cc_final: 0.8037 (tpp) REVERT: C 358 ASP cc_start: 0.7506 (m-30) cc_final: 0.7290 (t70) REVERT: C 397 MET cc_start: 0.6222 (tpt) cc_final: 0.5880 (tpt) REVERT: C 407 LEU cc_start: 0.8415 (mp) cc_final: 0.7644 (tt) REVERT: C 457 MET cc_start: 0.6904 (tpp) cc_final: 0.6594 (tpp) REVERT: C 699 MET cc_start: 0.9019 (mmm) cc_final: 0.8660 (mmt) REVERT: C 984 MET cc_start: 0.9055 (mmm) cc_final: 0.8844 (mmm) outliers start: 30 outliers final: 23 residues processed: 246 average time/residue: 0.1828 time to fit residues: 78.1451 Evaluate side-chains 246 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1115 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 90 optimal weight: 0.8980 chunk 340 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 367 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.073963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.052200 restraints weight = 290810.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054902 restraints weight = 112742.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.055917 restraints weight = 53684.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.056545 restraints weight = 35308.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.056618 restraints weight = 34316.371| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33516 Z= 0.108 Angle : 0.529 9.591 45758 Z= 0.265 Chirality : 0.038 0.281 5339 Planarity : 0.004 0.053 5642 Dihedral : 6.896 59.798 6233 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 0.99 % Allowed : 14.72 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 1.85 (0.14), residues: 4184 helix: 2.45 (0.10), residues: 2670 sheet: -0.91 (0.33), residues: 274 loop : -1.04 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1183 TYR 0.018 0.001 TYR A 958 PHE 0.018 0.001 PHE B 866 TRP 0.036 0.001 TRP B 621 HIS 0.004 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00234 (33512) covalent geometry : angle 0.52908 (45750) SS BOND : bond 0.00050 ( 4) SS BOND : angle 0.37234 ( 8) hydrogen bonds : bond 0.03846 ( 2039) hydrogen bonds : angle 3.73204 ( 6071) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 1.279 Fit side-chains REVERT: A 31 TRP cc_start: 0.6504 (t60) cc_final: 0.6081 (t60) REVERT: A 121 MET cc_start: 0.7313 (mmm) cc_final: 0.7002 (mmm) REVERT: A 902 MET cc_start: 0.7533 (mtt) cc_final: 0.7285 (mtt) REVERT: D 242 MET cc_start: 0.2721 (tpt) cc_final: 0.1795 (tpt) REVERT: D 259 PHE cc_start: 0.5501 (m-80) cc_final: 0.4650 (m-80) REVERT: D 505 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9047 (mm) REVERT: B 397 MET cc_start: 0.7595 (tmm) cc_final: 0.7051 (tmm) REVERT: B 442 PHE cc_start: 0.7692 (m-80) cc_final: 0.7030 (m-80) REVERT: B 457 MET cc_start: 0.8469 (tpp) cc_final: 0.8162 (tpp) REVERT: B 1207 MET cc_start: 0.9068 (mmm) cc_final: 0.8626 (ttm) REVERT: C 255 MET cc_start: 0.8292 (mtm) cc_final: 0.8054 (tpp) REVERT: C 358 ASP cc_start: 0.7482 (m-30) cc_final: 0.7242 (t70) REVERT: C 397 MET cc_start: 0.6100 (tpt) cc_final: 0.5786 (tpt) REVERT: C 407 LEU cc_start: 0.8425 (mp) cc_final: 0.7658 (tt) REVERT: C 457 MET cc_start: 0.6910 (tpp) cc_final: 0.6312 (tpp) REVERT: C 699 MET cc_start: 0.8984 (mmm) cc_final: 0.8670 (mmt) REVERT: C 741 MET cc_start: 0.9008 (mmm) cc_final: 0.8705 (mmt) REVERT: C 984 MET cc_start: 0.9083 (mmm) cc_final: 0.8880 (mmm) outliers start: 29 outliers final: 23 residues processed: 252 average time/residue: 0.1737 time to fit residues: 75.8962 Evaluate side-chains 246 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1115 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 65 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 239 optimal weight: 50.0000 chunk 408 optimal weight: 7.9990 chunk 391 optimal weight: 5.9990 chunk 371 optimal weight: 20.0000 chunk 182 optimal weight: 0.9990 chunk 215 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 405 optimal weight: 0.0770 chunk 228 optimal weight: 0.6980 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.073653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.051873 restraints weight = 296801.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.054546 restraints weight = 113617.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.055559 restraints weight = 53900.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.056189 restraints weight = 35350.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.056242 restraints weight = 34775.019| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33516 Z= 0.120 Angle : 0.542 10.024 45758 Z= 0.271 Chirality : 0.039 0.250 5339 Planarity : 0.004 0.052 5642 Dihedral : 6.860 58.909 6231 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.07 % Favored : 96.91 % Rotamer: Outliers : 0.93 % Allowed : 14.97 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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 (0.14), residues: 4184 helix: 2.48 (0.10), residues: 2663 sheet: -0.87 (0.33), residues: 272 loop : -0.97 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1183 TYR 0.016 0.001 TYR A 958 PHE 0.022 0.001 PHE A 379 TRP 0.035 0.001 TRP B 621 HIS 0.006 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00266 (33512) covalent geometry : angle 0.54210 (45750) SS BOND : bond 0.00053 ( 4) SS BOND : angle 0.39998 ( 8) hydrogen bonds : bond 0.03912 ( 2039) hydrogen bonds : angle 3.74570 ( 6071) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8368 Ramachandran restraints generated. 4184 Oldfield, 0 Emsley, 4184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 31 TRP cc_start: 0.6505 (t60) cc_final: 0.6104 (t60) REVERT: A 121 MET cc_start: 0.7230 (mmm) cc_final: 0.6861 (mmm) REVERT: A 242 MET cc_start: 0.1244 (tpt) cc_final: 0.0553 (tpt) REVERT: A 902 MET cc_start: 0.7548 (mtt) cc_final: 0.7303 (mtt) REVERT: D 242 MET cc_start: 0.2922 (tpt) cc_final: 0.1979 (tpt) REVERT: D 259 PHE cc_start: 0.5452 (m-80) cc_final: 0.4650 (m-80) REVERT: D 505 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9049 (mm) REVERT: B 179 MET cc_start: 0.8121 (mmm) cc_final: 0.7912 (mmm) REVERT: B 205 HIS cc_start: 0.7910 (t70) cc_final: 0.7630 (t-90) REVERT: B 397 MET cc_start: 0.7597 (tmm) cc_final: 0.7071 (tmm) REVERT: B 457 MET cc_start: 0.8472 (tpp) cc_final: 0.7995 (mmt) REVERT: C 255 MET cc_start: 0.8285 (mtm) cc_final: 0.8068 (tpp) REVERT: C 358 ASP cc_start: 0.7461 (m-30) cc_final: 0.7224 (t70) REVERT: C 397 MET cc_start: 0.6153 (tpt) cc_final: 0.5860 (tpt) REVERT: C 407 LEU cc_start: 0.8449 (mp) cc_final: 0.7723 (tt) REVERT: C 457 MET cc_start: 0.6971 (tpp) cc_final: 0.6659 (tpp) REVERT: C 699 MET cc_start: 0.8993 (mmm) cc_final: 0.8624 (mmt) REVERT: C 741 MET cc_start: 0.9018 (mmm) cc_final: 0.8676 (mmt) REVERT: C 984 MET cc_start: 0.9081 (mmm) cc_final: 0.8875 (mmm) outliers start: 27 outliers final: 24 residues processed: 246 average time/residue: 0.1702 time to fit residues: 72.4637 Evaluate side-chains 246 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1115 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 83 optimal weight: 1.9990 chunk 104 optimal weight: 30.0000 chunk 43 optimal weight: 0.0870 chunk 405 optimal weight: 0.4980 chunk 363 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 109 optimal weight: 40.0000 chunk 278 optimal weight: 4.9990 chunk 381 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 overall best weight: 2.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN C 955 ASN ** C1092 ASN ** 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 = 0.3659 r_free = 0.3659 target = 0.072884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.050556 restraints weight = 376470.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.053575 restraints weight = 133055.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.054512 restraints weight = 55675.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.054542 restraints weight = 39309.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054768 restraints weight = 41280.309| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33516 Z= 0.153 Angle : 0.575 10.608 45758 Z= 0.288 Chirality : 0.040 0.233 5339 Planarity : 0.004 0.050 5642 Dihedral : 6.953 59.464 6231 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 0.93 % Allowed : 15.13 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 1.88 (0.14), residues: 4184 helix: 2.46 (0.10), residues: 2661 sheet: -0.92 (0.33), residues: 271 loop : -0.99 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1183 TYR 0.016 0.001 TYR B 958 PHE 0.024 0.001 PHE B 866 TRP 0.036 0.001 TRP B 621 HIS 0.006 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00345 (33512) covalent geometry : angle 0.57488 (45750) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.47593 ( 8) hydrogen bonds : bond 0.04167 ( 2039) hydrogen bonds : angle 3.85631 ( 6071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5751.13 seconds wall clock time: 100 minutes 12.48 seconds (6012.48 seconds total)