Starting phenix.real_space_refine on Sat Feb 7 13:54:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7x_70210/02_2026/9o7x_70210.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7x_70210/02_2026/9o7x_70210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o7x_70210/02_2026/9o7x_70210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7x_70210/02_2026/9o7x_70210.map" model { file = "/net/cci-nas-00/data/ceres_data/9o7x_70210/02_2026/9o7x_70210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7x_70210/02_2026/9o7x_70210.cif" } resolution = 3.17 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 235 5.16 5 C 21412 2.51 5 N 5439 2.21 5 O 5645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s 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: 32731 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 8055 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1063, 8045 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 595 Unresolved non-hydrogen angles: 737 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 14, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 385 Conformer: "B" Number of residues, atoms: 1063, 8045 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 595 Unresolved non-hydrogen angles: 737 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 14, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 385 bond proxies already assigned to first conformer: 8218 Chain: "C" Number of atoms: 8029 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1063, 8019 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 13, 'TYR:plan': 4, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 387 Conformer: "B" Number of residues, atoms: 1063, 8019 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 13, 'TYR:plan': 4, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 16, 'TRP:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 387 bond proxies already assigned to first conformer: 8191 Chain: "A" Number of atoms: 7908 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1052, 7898 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 1009} Chain breaks: 8 Unresolved non-hydrogen bonds: 665 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 553 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 16, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 18, 'TRP:plan': 2, 'PHE:plan': 5, 'ASN:plan1': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 408 Conformer: "B" Number of residues, atoms: 1052, 7898 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 1009} Chain breaks: 8 Unresolved non-hydrogen bonds: 665 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 553 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLU:plan': 27, 'ARG:plan': 16, 'ASP:plan': 14, 'HIS:plan': 5, 'GLN:plan1': 18, 'TRP:plan': 2, 'PHE:plan': 5, 'ASN:plan1': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 408 bond proxies already assigned to first conformer: 8065 Chain: "B" Number of atoms: 7899 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1050, 7889 Classifications: {'peptide': 1050} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 1007} Chain breaks: 8 Unresolved non-hydrogen bonds: 662 Unresolved non-hydrogen angles: 815 Unresolved non-hydrogen dihedrals: 552 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 16, 'ASP:plan': 14, 'HIS:plan': 6, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 4, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 407 Conformer: "B" Number of residues, atoms: 1050, 7889 Classifications: {'peptide': 1050} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 1007} Chain breaks: 8 Unresolved non-hydrogen bonds: 662 Unresolved non-hydrogen angles: 815 Unresolved non-hydrogen dihedrals: 552 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLU:plan': 28, 'ARG:plan': 16, 'ASP:plan': 14, 'HIS:plan': 6, 'GLN:plan1': 17, 'TRP:plan': 2, 'ASN:plan1': 4, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 407 bond proxies already assigned to first conformer: 8056 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: "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} 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: "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} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS D 674 " occ=0.42 ... (18 atoms not shown) pdb=" NE2BHIS D 674 " occ=0.58 residue: pdb=" N AHIS C 674 " occ=0.38 ... (18 atoms not shown) pdb=" NE2BHIS C 674 " occ=0.62 residue: pdb=" N AHIS A 674 " occ=0.51 ... (18 atoms not shown) pdb=" NE2BHIS A 674 " occ=0.49 residue: pdb=" N AHIS B 674 " occ=0.40 ... (18 atoms not shown) pdb=" NE2BHIS B 674 " occ=0.60 Time building chain proxies: 13.72, per 1000 atoms: 0.42 Number of scatterers: 32731 At special positions: 0 Unit cell: (134.638, 135.464, 164.374, 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 235 16.00 O 5645 8.00 N 5439 7.00 C 21412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D1044 " - pdb=" SG CYS D1061 " distance=2.05 Simple disulfide: pdb=" SG CYS C1044 " - pdb=" SG CYS C1061 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1061 " distance=2.03 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1061 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 2.7 seconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7982 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 17 sheets defined 67.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'D' and resid 30 through 36 Processing helix chain 'D' and resid 130 through 141 removed outlier: 3.679A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 181 removed outlier: 3.537A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 209 Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.632A pdb=" N ILE D 223 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 224 " --> pdb=" O TRP D 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 220 through 224' Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.572A pdb=" N ILE D 231 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 308 through 319 removed outlier: 4.018A pdb=" N SER D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 Processing helix chain 'D' and resid 353 through 368 Processing helix chain 'D' and resid 371 through 387 Processing helix chain 'D' and resid 404 through 418 removed outlier: 3.995A pdb=" N ALA D 408 " --> pdb=" O ASP D 404 " (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 removed outlier: 3.503A pdb=" N GLY D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 564 Processing helix chain 'D' and resid 613 through 625 removed outlier: 3.865A pdb=" N GLU D 617 " --> pdb=" O PHE D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.790A pdb=" N GLN D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.667A 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: 3.703A 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: 3.534A pdb=" N ILE D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 removed outlier: 3.696A 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: 3.993A pdb=" N LEU D 765 " --> pdb=" O PRO D 762 " (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 917 Processing helix chain 'D' and resid 918 through 939 Processing helix chain 'D' and resid 943 through 968 removed outlier: 3.779A pdb=" N ASP D 947 " --> pdb=" O PRO D 943 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU D 964 " --> pdb=" O TYR D 960 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP D 965 " --> pdb=" O ILE D 961 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 1010 removed outlier: 4.600A pdb=" N ILE D 985 " --> pdb=" O GLY D 981 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1030 removed outlier: 3.713A pdb=" N PHE D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N MET D1026 " --> pdb=" O ASN D1022 " (cutoff:3.500A) Proline residue: D1027 - end of helix Processing helix chain 'D' and resid 1036 through 1040 removed outlier: 3.702A pdb=" N ILE D1040 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1094 removed outlier: 3.952A pdb=" N ALA D1070 " --> pdb=" O TRP D1066 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL D1084 " --> pdb=" O ASN D1080 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN D1085 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D1094 " --> pdb=" O VAL D1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1120 removed outlier: 4.702A pdb=" N TYR D1111 " --> pdb=" O LYS D1107 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1124 through 1126 No H-bonds generated for 'chain 'D' and resid 1124 through 1126' Processing helix chain 'D' and resid 1127 through 1145 removed outlier: 4.315A pdb=" N SER D1131 " --> pdb=" O LEU D1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1191 Processing helix chain 'D' 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: 3.813A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 181 removed outlier: 3.588A 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 220 through 224 removed outlier: 3.636A pdb=" N ILE C 223 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 224 " --> pdb=" O TRP C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 224' Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.626A pdb=" N ILE C 231 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.727A pdb=" N GLN C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.936A pdb=" N SER C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 353 through 368 removed outlier: 3.570A pdb=" N ARG C 357 " --> pdb=" O ASN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 Processing helix chain 'C' and resid 404 through 418 removed outlier: 4.185A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.592A pdb=" N ALA C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 465 through 475 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 removed outlier: 3.592A pdb=" N LEU C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) 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: 3.951A pdb=" N GLU C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.562A pdb=" N GLN C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.699A 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: 3.645A pdb=" N SER C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 704 Processing helix chain 'C' and resid 706 through 710 removed outlier: 4.042A pdb=" N SER C 710 " --> pdb=" O LYS C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 721 Processing helix chain 'C' and resid 723 through 728 removed outlier: 3.532A pdb=" N ILE C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 742 removed outlier: 3.674A pdb=" N GLY C 742 " --> pdb=" O ASP C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 760 Processing helix chain 'C' and resid 761 through 767 removed outlier: 4.029A 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 917 Processing helix chain 'C' and resid 918 through 939 Processing helix chain 'C' and resid 943 through 968 removed outlier: 3.711A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 964 " --> pdb=" O TYR C 960 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASP C 965 " --> pdb=" O ILE C 961 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE C 966 " --> pdb=" O ARG C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 1010 removed outlier: 3.521A pdb=" N TYR C 976 " --> pdb=" O TYR C 972 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1030 removed outlier: 3.608A pdb=" N PHE C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 4.868A 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: 3.714A pdb=" N ILE C1040 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1082 removed outlier: 3.917A pdb=" N ALA C1070 " --> pdb=" O TRP C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1094 Processing helix chain 'C' and resid 1094 through 1120 removed outlier: 3.676A pdb=" N VAL C1098 " --> pdb=" O THR C1094 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR C1111 " --> pdb=" O LYS C1107 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN C1112 " --> pdb=" O PHE C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1144 removed outlier: 4.335A pdb=" N ILE C1129 " --> pdb=" O PRO C1125 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE C1130 " --> pdb=" O PRO C1126 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER C1131 " --> pdb=" O LEU C1127 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1191 Processing helix chain 'C' and resid 1192 through 1232 removed outlier: 3.765A pdb=" N ARG C1196 " --> pdb=" O SER C1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 59 through 63 removed outlier: 4.305A pdb=" N HIS A 63 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.637A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 181 removed outlier: 3.835A pdb=" N LYS A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 removed outlier: 3.528A pdb=" N HIS A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.692A pdb=" N ILE A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.555A pdb=" N LEU A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 removed outlier: 4.174A pdb=" N ASN A 290 " --> pdb=" O GLN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 4.083A pdb=" N SER A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 353 through 368 removed outlier: 3.659A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.564A pdb=" N GLU A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.784A pdb=" N THR A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 431 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 475 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: 4.001A pdb=" N GLU A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 625 " --> pdb=" O TRP A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.550A pdb=" N GLN A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 662 Processing helix chain 'A' and resid 665 through 694 removed outlier: 3.553A 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 728 removed outlier: 3.699A pdb=" N ILE A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.581A pdb=" N GLY A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 761 through 764 Processing helix chain 'A' and resid 835 through 846 Processing helix chain 'A' and resid 847 through 872 removed outlier: 3.925A pdb=" N VAL A 870 " --> pdb=" O PHE A 866 " (cutoff:3.500A) 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 967 removed outlier: 3.581A pdb=" N TYR A 958 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 960 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 964 " --> pdb=" O TYR A 960 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 1010 removed outlier: 4.377A pdb=" N ILE A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1030 removed outlier: 3.838A pdb=" N PHE A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET A1026 " --> pdb=" O ASN A1022 " (cutoff:3.500A) Proline residue: A1027 - end of helix Processing helix chain 'A' and resid 1031 through 1033 No H-bonds generated for 'chain 'A' and resid 1031 through 1033' Processing helix chain 'A' and resid 1036 through 1040 removed outlier: 3.701A pdb=" N ILE A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1081 removed outlier: 3.763A pdb=" N ALA A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1094 Processing helix chain 'A' and resid 1094 through 1109 Processing helix chain 'A' and resid 1109 through 1120 Processing helix chain 'A' and resid 1127 through 1143 Processing helix chain 'A' and resid 1163 through 1191 Processing helix chain 'A' and resid 1192 through 1232 removed outlier: 3.851A pdb=" N ARG A1203 " --> pdb=" O VAL A1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.880A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 181 removed outlier: 3.648A pdb=" N ALA B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.705A pdb=" N ILE B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.742A pdb=" N GLN B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 4.085A pdb=" N SER B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 removed outlier: 3.618A pdb=" N LYS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 368 Processing helix chain 'B' and resid 371 through 388 removed outlier: 3.603A pdb=" N HIS B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 418 removed outlier: 3.550A pdb=" N ALA B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 465 through 474 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 564 Processing helix chain 'B' and resid 613 through 625 removed outlier: 3.938A pdb=" N GLU B 617 " --> pdb=" O PHE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.520A pdb=" N GLN B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 662 Processing helix chain 'B' and resid 665 through 694 removed outlier: 3.625A pdb=" N SER B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 704 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 723 through 728 removed outlier: 3.719A pdb=" N ILE B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.664A pdb=" N GLY B 742 " --> pdb=" O ASP B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 removed outlier: 3.553A pdb=" N ILE B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 764 Processing helix chain 'B' and resid 835 through 846 Processing helix chain 'B' and resid 847 through 872 removed outlier: 3.662A pdb=" N ALA B 858 " --> pdb=" O PHE B 854 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 870 " --> pdb=" O PHE B 866 " (cutoff:3.500A) 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 940 removed outlier: 3.531A pdb=" N VAL B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 940 " --> pdb=" O ILE B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 962 removed outlier: 3.741A pdb=" N TYR B 958 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 960 " --> pdb=" O ILE B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 967 removed outlier: 4.051A pdb=" N ILE B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 1010 removed outlier: 4.393A pdb=" N ILE B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASP B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B1004 " --> pdb=" O SER B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1030 removed outlier: 3.913A pdb=" N PHE B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET B1026 " --> pdb=" O ASN B1022 " (cutoff:3.500A) Proline residue: B1027 - end of helix removed outlier: 3.696A pdb=" N MET B1030 " --> pdb=" O MET B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1040 removed outlier: 3.713A pdb=" N ILE B1040 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1081 removed outlier: 3.835A pdb=" N ALA B1070 " --> pdb=" O TRP B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1093 Processing helix chain 'B' and resid 1094 through 1109 Processing helix chain 'B' and resid 1109 through 1120 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: 4.278A pdb=" N SER B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B1133 " --> pdb=" O ILE B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1191 removed outlier: 3.977A pdb=" N GLU B1175 " --> pdb=" O HIS B1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1232 removed outlier: 3.501A pdb=" N ARG B1198 " --> pdb=" O ASP B1194 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B1206 " --> pdb=" O GLU B1202 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B1209 " --> pdb=" O GLU B1205 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS B1219 " --> pdb=" O ASN B1215 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B1220 " --> pdb=" O GLU B1216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.665A pdb=" N GLN D 99 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 232 through 240 removed outlier: 6.668A pdb=" N PHE D 106 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG D 237 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR D 108 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N TYR D 239 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU D 110 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA D 105 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 184 through 186 removed outlier: 6.464A pdb=" N VAL D 326 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE D 395 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 328 " --> pdb=" O PHE D 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 1047 through 1048 Processing sheet with id=AA5, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.592A pdb=" N GLN C 99 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 232 through 240 removed outlier: 6.713A pdb=" N PHE C 106 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR C 108 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N TYR C 239 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLU C 110 " --> pdb=" O TYR C 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 126 removed outlier: 6.363A pdb=" N VAL C 125 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 186 removed outlier: 6.216A pdb=" N VAL C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE C 395 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL C 328 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1047 through 1048 Processing sheet with id=AB1, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.694A pdb=" N GLN A 99 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 232 through 240 removed outlier: 6.917A pdb=" N PHE A 106 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR A 108 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA A 105 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N PHE A 259 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N MET A 121 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU A 261 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL A 123 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASP A 263 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 125 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 184 through 186 removed outlier: 7.917A pdb=" N VAL A 327 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ALA A 301 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1047 through 1048 Processing sheet with id=AB5, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.662A pdb=" N GLN B 99 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 232 through 240 removed outlier: 6.765A pdb=" N PHE B 106 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR B 108 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TYR B 239 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU B 110 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ALA B 105 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N PHE B 259 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N MET B 121 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU B 261 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 123 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASP B 263 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 125 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 184 through 186 removed outlier: 7.082A pdb=" N ILE B 151 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU B 150 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU B 302 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N SER B 152 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL B 304 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N HIS B 154 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL B 327 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA B 301 " --> pdb=" O VAL B 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 1047 through 1048 2038 hydrogen bonds defined for protein. 6043 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 3.09 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: 6298 1.33 - 1.46: 8921 1.46 - 1.58: 17925 1.58 - 1.71: 0 1.71 - 1.84: 394 Bond restraints: 33538 Sorted by residual: bond pdb=" C LEU A1127 " pdb=" O LEU A1127 " ideal model delta sigma weight residual 1.236 1.284 -0.049 1.29e-02 6.01e+03 1.43e+01 bond pdb=" C LEU C1123 " pdb=" N PRO C1124 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.18e-02 7.18e+03 1.13e+01 bond pdb=" N ILE B 352 " pdb=" CA ILE B 352 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.20e-02 6.94e+03 9.32e+00 bond pdb=" N ILE D 213 " pdb=" CA ILE D 213 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.17e-02 7.31e+03 9.17e+00 bond pdb=" N ASN B 353 " pdb=" CA ASN B 353 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 8.91e+00 ... (remaining 33533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 44266 2.52 - 5.05: 1272 5.05 - 7.57: 190 7.57 - 10.09: 42 10.09 - 12.61: 12 Bond angle restraints: 45782 Sorted by residual: angle pdb=" CA PHE B 726 " pdb=" CB PHE B 726 " pdb=" CG PHE B 726 " ideal model delta sigma weight residual 113.80 119.73 -5.93 1.00e+00 1.00e+00 3.52e+01 angle pdb=" N LEU A 410 " pdb=" CA LEU A 410 " pdb=" CB LEU A 410 " ideal model delta sigma weight residual 109.94 101.27 8.67 1.49e+00 4.50e-01 3.38e+01 angle pdb=" C LYS D 203 " pdb=" CA LYS D 203 " pdb=" CB LYS D 203 " ideal model delta sigma weight residual 110.96 102.07 8.89 1.54e+00 4.22e-01 3.33e+01 angle pdb=" N LYS D 203 " pdb=" CA LYS D 203 " pdb=" C LYS D 203 " ideal model delta sigma weight residual 110.97 104.81 6.16 1.09e+00 8.42e-01 3.19e+01 angle pdb=" N ARG A1196 " pdb=" CA ARG A1196 " pdb=" C ARG A1196 " ideal model delta sigma weight residual 112.54 105.78 6.76 1.22e+00 6.72e-01 3.07e+01 ... (remaining 45777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 19540 24.55 - 49.09: 1227 49.09 - 73.64: 198 73.64 - 98.19: 12 98.19 - 122.73: 12 Dihedral angle restraints: 20989 sinusoidal: 8656 harmonic: 12333 Sorted by residual: dihedral pdb=" CD ARG D 210 " pdb=" NE ARG D 210 " pdb=" CZ ARG D 210 " pdb=" NH1 ARG D 210 " ideal model delta sinusoidal sigma weight residual 0.00 72.71 -72.71 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS D1044 " pdb=" SG CYS D1044 " pdb=" SG CYS D1061 " pdb=" CB CYS D1061 " ideal model delta sinusoidal sigma weight residual -86.00 -157.62 71.62 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CD ARG C 210 " pdb=" NE ARG C 210 " pdb=" CZ ARG C 210 " pdb=" NH1 ARG C 210 " ideal model delta sinusoidal sigma weight residual 0.00 64.89 -64.89 1 1.00e+01 1.00e-02 5.53e+01 ... (remaining 20986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4516 0.076 - 0.153: 733 0.153 - 0.229: 86 0.229 - 0.305: 8 0.305 - 0.382: 4 Chirality restraints: 5347 Sorted by residual: chirality pdb=" CG LEU B 356 " pdb=" CB LEU B 356 " pdb=" CD1 LEU B 356 " pdb=" CD2 LEU B 356 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA PRO C1125 " pdb=" N PRO C1125 " pdb=" C PRO C1125 " pdb=" CB PRO C1125 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA LYS D 203 " pdb=" N LYS D 203 " pdb=" C LYS D 203 " pdb=" CB LYS D 203 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 5344 not shown) Planarity restraints: 5639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 210 " 1.063 9.50e-02 1.11e+02 4.76e-01 1.37e+02 pdb=" NE ARG D 210 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG D 210 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG D 210 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG D 210 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 210 " -1.004 9.50e-02 1.11e+02 4.50e-01 1.22e+02 pdb=" NE ARG C 210 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG C 210 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 210 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 210 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1183 " 0.523 9.50e-02 1.11e+02 2.35e-01 3.37e+01 pdb=" NE ARG A1183 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A1183 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A1183 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1183 " 0.018 2.00e-02 2.50e+03 ... (remaining 5636 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7280 2.79 - 3.32: 31259 3.32 - 3.84: 54453 3.84 - 4.37: 62984 4.37 - 4.90: 107161 Nonbonded interactions: 263137 Sorted by model distance: nonbonded pdb=" ND2 ASN C1092 " pdb=" ND2 ASN B1092 " model vdw 2.259 3.200 nonbonded pdb=" CG GLU D1205 " pdb=" NH1 ARG A1203 " model vdw 2.335 3.520 nonbonded pdb=" O ILE B 352 " pdb=" NE ARG B 357 " model vdw 2.409 3.120 nonbonded pdb=" N THR A1134 " pdb=" OG1 THR A1134 " model vdw 2.433 2.496 nonbonded pdb=" OE2 GLU B 489 " pdb=" OH TYR B 562 " model vdw 2.443 3.040 ... (remaining 263132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 132 or (resid 133 and (name N or n \ ame CA or name C or name O or name CB )) or resid 134 through 137 or (resid 138 \ and (name N or name CA or name C or name O or name CB )) or resid 139 through 15 \ 6 or (resid 157 through 158 and (name N or name CA or name C or name O or name C \ B )) or resid 159 through 207 or (resid 208 and (name N or name CA or name C or \ name O or name CB )) or resid 209 through 342 or (resid 343 through 344 and (nam \ e N or name CA or name C or name O or name CB )) or resid 345 through 385 or (re \ sid 386 through 390 and (name N or name CA or name C or name O or name CB )) or \ resid 391 through 395 or (resid 396 and (name N or name CA or name C or name O o \ r name CB )) or resid 404 through 414 or (resid 415 and (name N or name CA or na \ me C or name O or name CB )) or resid 416 through 673 or resid 675 through 1049 \ or resid 1055 through 1144 or resid 1155 through 1194 or (resid 1195 and (name N \ or name CA or name C or name O or name CB )) or resid 1196 through 1406)) selection = (chain 'B' and (resid 30 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 105 or (resid 106 and (name N or n \ ame CA or name C or name O or name CB )) or resid 107 through 275 or (resid 276 \ through 277 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 8 through 280 or (resid 281 and (name N or name CA or name C or name O or name C \ B )) or resid 282 through 288 or (resid 289 through 292 and (name N or name CA o \ r name C or name O or name CB )) or resid 293 through 294 or (resid 295 and (nam \ e N or name CA or name C or name O or name CB )) or resid 296 through 381 or (re \ sid 382 through 384 and (name N or name CA or name C or name O or name CB )) or \ resid 385 through 387 or (resid 388 through 390 and (name N or name CA or name C \ or name O or name CB )) or resid 391 through 414 or (resid 415 and (name N or n \ ame CA or name C or name O or name CB )) or resid 416 through 673 or resid 675 t \ hrough 1049 or resid 1055 through 1144 or resid 1155 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 through 105 or (resid 106 and (name N or name CA or nam \ e C or name O or name CB )) or resid 107 through 132 or (resid 133 and (name N o \ r name CA or name C or name O or name CB )) or resid 134 through 137 or (resid 1 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 139 through \ 156 or (resid 157 through 158 and (name N or name CA or name C or name O or nam \ e CB )) or resid 159 through 207 or (resid 208 and (name N or name CA or name C \ or name O or name CB )) or resid 209 through 241 or resid 249 through 275 or (re \ sid 276 through 277 and (name N or name CA or name C or name O or name CB )) or \ resid 278 or (resid 279 and (name N or name CA or name C or name O or name CB )) \ or resid 280 or (resid 281 and (name N or name CA or name C or name O or name C \ B )) or resid 282 through 288 or (resid 289 through 292 and (name N or name CA o \ r name C or name O or name CB )) or resid 293 through 294 or (resid 295 and (nam \ e N or name CA or name C or name O or name CB )) or resid 296 through 342 or (re \ sid 343 through 344 and (name N or name CA or name C or name O or name CB )) or \ resid 345 through 381 or (resid 382 through 384 and (name N or name CA or name C \ or name O or name CB )) or resid 385 or (resid 386 through 390 and (name N or n \ ame CA or name C or name O or name CB )) or resid 391 through 394 or (resid 395 \ through 396 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 4 through 406 or (resid 407 through 408 and (name N or name CA or name C or name \ O or name CB )) or resid 409 through 412 or (resid 413 and (name N or name CA o \ r name C or name O or name CB )) or resid 414 through 649 or (resid 650 and (nam \ e N or name CA or name C or name O or name CB )) or resid 651 through 673 or res \ id 675 through 986 or (resid 987 and (name N or name CA or name C or name O or n \ ame CB )) or resid 988 through 1049 or resid 1055 through 1161 or (resid 1162 an \ d (name N or name CA or name C or name O or name CB )) or resid 1163 through 120 \ 8 or (resid 1209 and (name N or name CA or name C or name O or name CB )) or res \ id 1210 through 1406)) selection = (chain 'D' and (resid 30 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 105 or (resid 106 and (name N or n \ ame CA or name C or name O or name CB )) or resid 107 through 118 or (resid 119 \ through 120 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 1 through 129 or (resid 130 and (name N or name CA or name C or name O or name C \ B )) or resid 131 through 132 or (resid 133 and (name N or name CA or name C or \ name O or name CB )) or resid 134 through 137 or (resid 138 and (name N or name \ CA or name C or name O or name CB )) or resid 139 through 156 or (resid 157 thro \ ugh 158 and (name N or name CA or name C or name O or name CB )) or resid 159 th \ rough 202 or (resid 203 through 204 and (name N or name CA or name C or name O o \ r name CB )) or resid 205 through 207 or (resid 208 and (name N or name CA or na \ me C or name O or name CB )) or resid 209 through 241 or resid 249 through 275 o \ r (resid 276 through 277 and (name N or name CA or name C or name O or name CB ) \ ) or resid 278 or (resid 279 and (name N or name CA or name C or name O or name \ CB )) or resid 280 or (resid 281 and (name N or name CA or name C or name O or n \ ame CB )) or resid 282 through 288 or (resid 289 through 292 and (name N or name \ CA or name C or name O or name CB )) or resid 293 through 294 or (resid 295 and \ (name N or name CA or name C or name O or name CB )) or resid 296 through 342 o \ r (resid 343 through 344 and (name N or name CA or name C or name O or name CB ) \ ) or resid 345 through 381 or (resid 382 through 384 and (name N or name CA or n \ ame C or name O or name CB )) or resid 385 or (resid 386 through 390 and (name N \ or name CA or name C or name O or name CB )) or resid 391 through 394 or (resid \ 395 through 396 and (name N or name CA or name C or name O or name CB )) or res \ id 404 through 406 or (resid 407 through 408 and (name N or name CA or name C or \ name O or name CB )) or resid 409 through 412 or (resid 413 and (name N or name \ CA or name C or name O or name CB )) or resid 414 or (resid 415 and (name N or \ name CA or name C or name O or name CB )) or resid 416 through 649 or (resid 650 \ and (name N or name CA or name C or name O or name CB )) or resid 651 through 6 \ 73 or resid 675 through 986 or (resid 987 and (name N or name CA or name C or na \ me O or name CB )) or resid 988 through 1144 or resid 1155 through 1161 or (resi \ d 1162 and (name N or name CA or name C or name O or name CB )) or resid 1163 th \ rough 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.400 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 38.050 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.006 0.084 33542 Z= 0.340 Angle : 1.000 12.613 45790 Z= 0.576 Chirality : 0.057 0.382 5347 Planarity : 0.012 0.476 5639 Dihedral : 15.708 122.734 12995 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.34 % Allowed : 14.22 % Favored : 84.44 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.11), residues: 4176 helix: -1.48 (0.08), residues: 2611 sheet: -0.99 (0.36), residues: 231 loop : -1.68 (0.15), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 876 TYR 0.030 0.002 TYR D 345 PHE 0.064 0.003 PHE B 854 TRP 0.046 0.003 TRP A 221 HIS 0.010 0.002 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00634 (33538) covalent geometry : angle 0.99955 (45782) SS BOND : bond 0.00991 ( 4) SS BOND : angle 2.87168 ( 8) hydrogen bonds : bond 0.19851 ( 2038) hydrogen bonds : angle 7.26744 ( 6043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 MET cc_start: 0.8986 (mmm) cc_final: 0.8360 (mpp) REVERT: D 356 LEU cc_start: 0.8237 (mm) cc_final: 0.7631 (pt) REVERT: C 529 ASP cc_start: 0.8953 (p0) cc_final: 0.8312 (t0) REVERT: C 625 MET cc_start: 0.9361 (mmm) cc_final: 0.9156 (mmt) REVERT: C 1188 ARG cc_start: 0.8633 (ttm110) cc_final: 0.8266 (ttp80) REVERT: A 127 PHE cc_start: 0.8075 (p90) cc_final: 0.7791 (p90) REVERT: A 221 TRP cc_start: 0.6446 (t60) cc_final: 0.5897 (t-100) REVERT: A 255 MET cc_start: 0.7869 (mtp) cc_final: 0.7249 (mmm) REVERT: A 1192 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8733 (p) REVERT: B 127 PHE cc_start: 0.8814 (p90) cc_final: 0.8516 (p90) REVERT: B 298 PRO cc_start: 0.7365 (Cg_endo) cc_final: 0.6922 (Cg_exo) REVERT: B 368 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6826 (m-10) REVERT: B 752 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8151 (mt) REVERT: B 778 MET cc_start: 0.7871 (ttp) cc_final: 0.7628 (ptm) outliers start: 42 outliers final: 18 residues processed: 295 average time/residue: 0.1860 time to fit residues: 91.2582 Evaluate side-chains 249 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1044 CYS Chi-restraints excluded: chain C residue 1062 LYS Chi-restraints excluded: chain C residue 1125 PRO Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1134 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 1133 MET Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain A residue 1141 CYS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 935 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 HIS ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 GLN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 343 HIS A1046 GLN B 136 HIS ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.080098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.053532 restraints weight = 214337.940| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.41 r_work: 0.2824 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 33542 Z= 0.256 Angle : 0.672 16.038 45790 Z= 0.346 Chirality : 0.042 0.234 5347 Planarity : 0.005 0.061 5639 Dihedral : 8.964 82.475 6265 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.72 % Allowed : 14.13 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 4176 helix: 0.94 (0.09), residues: 2640 sheet: -0.96 (0.32), residues: 295 loop : -1.28 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 557 TYR 0.019 0.001 TYR C1028 PHE 0.028 0.002 PHE A 866 TRP 0.020 0.002 TRP B 740 HIS 0.008 0.001 HIS B 723 Details of bonding type rmsd covalent geometry : bond 0.00580 (33538) covalent geometry : angle 0.67231 (45782) SS BOND : bond 0.00093 ( 4) SS BOND : angle 1.13656 ( 8) hydrogen bonds : bond 0.05375 ( 2038) hydrogen bonds : angle 4.56093 ( 6043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: D 121 MET cc_start: 0.9003 (mmm) cc_final: 0.8686 (mpp) REVERT: C 529 ASP cc_start: 0.8963 (p0) cc_final: 0.8349 (t70) REVERT: A 127 PHE cc_start: 0.8010 (p90) cc_final: 0.7705 (p90) REVERT: A 138 MET cc_start: 0.8727 (ptp) cc_final: 0.8292 (ppp) REVERT: A 221 TRP cc_start: 0.6205 (t60) cc_final: 0.5779 (t-100) REVERT: A 255 MET cc_start: 0.8277 (mtp) cc_final: 0.7623 (mmm) REVERT: A 747 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7656 (mpp80) REVERT: B 127 PHE cc_start: 0.8709 (p90) cc_final: 0.8420 (p90) REVERT: B 149 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6840 (tt) REVERT: B 368 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6721 (m-10) REVERT: B 440 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: B 778 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7495 (ptm) REVERT: B 902 MET cc_start: 0.8053 (mmm) cc_final: 0.7703 (mmt) REVERT: B 1026 MET cc_start: 0.9598 (OUTLIER) cc_final: 0.9370 (mtm) outliers start: 54 outliers final: 26 residues processed: 283 average time/residue: 0.1766 time to fit residues: 84.7916 Evaluate side-chains 256 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1178 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 746 MET Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 1062 LYS Chi-restraints excluded: chain C residue 1134 THR Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1133 MET Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain A residue 1141 CYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 1026 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 38 optimal weight: 9.9990 chunk 409 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 303 optimal weight: 0.8980 chunk 399 optimal weight: 0.7980 chunk 355 optimal weight: 0.9990 chunk 363 optimal weight: 0.0770 chunk 313 optimal weight: 0.7980 chunk 196 optimal weight: 0.0020 chunk 140 optimal weight: 20.0000 chunk 274 optimal weight: 6.9990 overall best weight: 0.5146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1176 GLN ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.081920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.055692 restraints weight = 207693.544| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.38 r_work: 0.2888 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33542 Z= 0.109 Angle : 0.528 15.942 45790 Z= 0.269 Chirality : 0.038 0.194 5347 Planarity : 0.004 0.055 5639 Dihedral : 7.748 59.413 6240 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.18 % Allowed : 14.48 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.13), residues: 4176 helix: 1.75 (0.10), residues: 2649 sheet: -0.79 (0.32), residues: 292 loop : -1.08 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1188 TYR 0.017 0.001 TYR D 958 PHE 0.024 0.001 PHE B 854 TRP 0.017 0.001 TRP D 621 HIS 0.008 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00221 (33538) covalent geometry : angle 0.52740 (45782) SS BOND : bond 0.00303 ( 4) SS BOND : angle 0.97087 ( 8) hydrogen bonds : bond 0.04428 ( 2038) hydrogen bonds : angle 4.15531 ( 6043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.916 Fit side-chains REVERT: D 121 MET cc_start: 0.9060 (mmm) cc_final: 0.8705 (mpp) REVERT: D 255 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8312 (mtp) REVERT: D 978 MET cc_start: 0.9255 (mtp) cc_final: 0.9030 (mtp) REVERT: C 242 MET cc_start: 0.7376 (mmt) cc_final: 0.7053 (mmt) REVERT: C 529 ASP cc_start: 0.8895 (p0) cc_final: 0.8256 (t0) REVERT: A 127 PHE cc_start: 0.7940 (p90) cc_final: 0.7670 (p90) REVERT: A 221 TRP cc_start: 0.6141 (t60) cc_final: 0.5783 (t-100) REVERT: A 255 MET cc_start: 0.8238 (mtp) cc_final: 0.7604 (mmm) REVERT: A 747 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7778 (mpp80) REVERT: B 127 PHE cc_start: 0.8729 (p90) cc_final: 0.8440 (p90) REVERT: B 149 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6674 (tt) REVERT: B 368 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6554 (m-10) REVERT: B 440 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: B 778 MET cc_start: 0.7682 (ttp) cc_final: 0.7413 (ptm) REVERT: B 902 MET cc_start: 0.8049 (mmm) cc_final: 0.7592 (mmt) outliers start: 37 outliers final: 18 residues processed: 262 average time/residue: 0.1506 time to fit residues: 67.3329 Evaluate side-chains 250 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 1062 LYS Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 625 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 103 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 319 optimal weight: 30.0000 chunk 316 optimal weight: 30.0000 chunk 373 optimal weight: 8.9990 chunk 260 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 210 optimal weight: 0.9980 chunk 400 optimal weight: 4.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.080882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053552 restraints weight = 200653.439| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 4.07 r_work: 0.2857 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33542 Z= 0.161 Angle : 0.545 14.986 45790 Z= 0.277 Chirality : 0.039 0.182 5347 Planarity : 0.004 0.051 5639 Dihedral : 7.478 59.604 6231 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.21 % Allowed : 14.57 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.13), residues: 4176 helix: 2.15 (0.10), residues: 2657 sheet: -0.62 (0.33), residues: 292 loop : -0.97 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 876 TYR 0.015 0.001 TYR C1028 PHE 0.024 0.001 PHE A 866 TRP 0.020 0.001 TRP A 621 HIS 0.012 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00371 (33538) covalent geometry : angle 0.54496 (45782) SS BOND : bond 0.00117 ( 4) SS BOND : angle 0.81279 ( 8) hydrogen bonds : bond 0.04391 ( 2038) hydrogen bonds : angle 4.04017 ( 6043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: D 121 MET cc_start: 0.9057 (mmm) cc_final: 0.8715 (mpp) REVERT: D 255 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8340 (mtp) REVERT: D 440 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8064 (mm110) REVERT: C 529 ASP cc_start: 0.8908 (p0) cc_final: 0.8310 (t0) REVERT: C 1062 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8573 (mmmt) REVERT: A 127 PHE cc_start: 0.7912 (p90) cc_final: 0.7642 (p90) REVERT: A 221 TRP cc_start: 0.6102 (t60) cc_final: 0.5744 (t-100) REVERT: A 255 MET cc_start: 0.8238 (mtp) cc_final: 0.7547 (mmm) REVERT: A 397 MET cc_start: 0.3881 (mmt) cc_final: 0.3412 (mmm) REVERT: A 747 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7749 (mpp80) REVERT: B 127 PHE cc_start: 0.8685 (p90) cc_final: 0.8399 (p90) REVERT: B 149 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7039 (tt) REVERT: B 368 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6412 (m-10) REVERT: B 431 TRP cc_start: 0.8442 (m-10) cc_final: 0.8129 (m-10) REVERT: B 440 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: B 902 MET cc_start: 0.7965 (mmm) cc_final: 0.7444 (mmt) outliers start: 38 outliers final: 17 residues processed: 254 average time/residue: 0.1605 time to fit residues: 70.4556 Evaluate side-chains 251 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 1062 LYS Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 625 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 148 optimal weight: 20.0000 chunk 414 optimal weight: 20.0000 chunk 145 optimal weight: 0.2980 chunk 207 optimal weight: 10.0000 chunk 288 optimal weight: 5.9990 chunk 411 optimal weight: 0.9990 chunk 296 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 chunk 102 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 867 ASN ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1093 ASN C 43 HIS C 283 HIS ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.080557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.053462 restraints weight = 252790.136| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.96 r_work: 0.2807 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33542 Z= 0.152 Angle : 0.534 14.421 45790 Z= 0.271 Chirality : 0.039 0.172 5347 Planarity : 0.004 0.050 5639 Dihedral : 7.304 59.595 6231 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.02 % Allowed : 14.92 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.13), residues: 4176 helix: 2.35 (0.10), residues: 2662 sheet: -0.50 (0.32), residues: 301 loop : -0.91 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 210 TYR 0.015 0.001 TYR D 958 PHE 0.023 0.001 PHE A 866 TRP 0.020 0.001 TRP A 740 HIS 0.005 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00346 (33538) covalent geometry : angle 0.53364 (45782) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.78134 ( 8) hydrogen bonds : bond 0.04274 ( 2038) hydrogen bonds : angle 3.95697 ( 6043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: D 121 MET cc_start: 0.9078 (mmm) cc_final: 0.8762 (mpp) REVERT: C 529 ASP cc_start: 0.8843 (p0) cc_final: 0.8250 (t0) REVERT: A 138 MET cc_start: 0.8894 (pmm) cc_final: 0.8583 (pmm) REVERT: A 221 TRP cc_start: 0.6077 (t60) cc_final: 0.5757 (t-100) REVERT: A 255 MET cc_start: 0.8324 (mtp) cc_final: 0.7618 (mmm) REVERT: A 397 MET cc_start: 0.4123 (mmt) cc_final: 0.3629 (mmm) REVERT: A 747 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7719 (mpp80) REVERT: B 127 PHE cc_start: 0.8694 (p90) cc_final: 0.8384 (p90) REVERT: B 368 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6540 (m-10) REVERT: B 431 TRP cc_start: 0.8478 (m-10) cc_final: 0.8125 (m-10) REVERT: B 440 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8187 (mp10) outliers start: 32 outliers final: 20 residues processed: 253 average time/residue: 0.1649 time to fit residues: 71.6726 Evaluate side-chains 245 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 746 MET Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 778 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 59 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 255 optimal weight: 0.0040 chunk 85 optimal weight: 0.0970 chunk 379 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 401 optimal weight: 0.9980 chunk 233 optimal weight: 20.0000 overall best weight: 1.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.081113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.054551 restraints weight = 239100.551| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 4.70 r_work: 0.2841 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33542 Z= 0.114 Angle : 0.515 16.299 45790 Z= 0.258 Chirality : 0.038 0.234 5347 Planarity : 0.004 0.049 5639 Dihedral : 7.160 59.463 6225 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.89 % Allowed : 15.24 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.13), residues: 4176 helix: 2.45 (0.10), residues: 2672 sheet: -0.48 (0.32), residues: 302 loop : -0.85 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 876 TYR 0.017 0.001 TYR D 958 PHE 0.021 0.001 PHE C 611 TRP 0.022 0.001 TRP D 621 HIS 0.010 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00252 (33538) covalent geometry : angle 0.51521 (45782) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.60038 ( 8) hydrogen bonds : bond 0.04007 ( 2038) hydrogen bonds : angle 3.86972 ( 6043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 121 MET cc_start: 0.9040 (mmm) cc_final: 0.8721 (mpp) REVERT: D 440 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8100 (mm110) REVERT: C 529 ASP cc_start: 0.8799 (p0) cc_final: 0.8205 (t70) REVERT: C 1133 MET cc_start: 0.8896 (mmt) cc_final: 0.8582 (mmp) REVERT: A 138 MET cc_start: 0.8932 (pmm) cc_final: 0.8571 (pmm) REVERT: A 221 TRP cc_start: 0.6156 (t60) cc_final: 0.5868 (t-100) REVERT: A 397 MET cc_start: 0.4289 (mmt) cc_final: 0.3839 (mmm) REVERT: A 747 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7788 (mpp80) REVERT: B 127 PHE cc_start: 0.8677 (p90) cc_final: 0.8375 (p90) REVERT: B 184 TRP cc_start: 0.8718 (m-10) cc_final: 0.8507 (m-10) REVERT: B 255 MET cc_start: 0.7791 (ptp) cc_final: 0.7567 (pmm) REVERT: B 368 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6354 (m-10) REVERT: B 429 LEU cc_start: 0.9400 (tp) cc_final: 0.9141 (mt) REVERT: B 431 TRP cc_start: 0.8432 (m-10) cc_final: 0.8040 (m-10) REVERT: B 440 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8282 (mp10) outliers start: 28 outliers final: 18 residues processed: 254 average time/residue: 0.1709 time to fit residues: 74.5990 Evaluate side-chains 249 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 778 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 206 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 295 optimal weight: 5.9990 chunk 26 optimal weight: 30.0000 chunk 114 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 289 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 723 HIS ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 GLN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3690 r_free = 0.3690 target = 0.078275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.051331 restraints weight = 269830.023| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.99 r_work: 0.2747 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 33542 Z= 0.251 Angle : 0.632 15.256 45790 Z= 0.317 Chirality : 0.042 0.191 5347 Planarity : 0.005 0.109 5639 Dihedral : 7.261 59.950 6225 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.15 % Allowed : 15.21 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.13), residues: 4176 helix: 2.35 (0.10), residues: 2650 sheet: -0.48 (0.32), residues: 305 loop : -0.86 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1183 TYR 0.016 0.001 TYR C1028 PHE 0.025 0.002 PHE A 866 TRP 0.023 0.002 TRP D 621 HIS 0.010 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00573 (33538) covalent geometry : angle 0.63231 (45782) SS BOND : bond 0.00212 ( 4) SS BOND : angle 0.86929 ( 8) hydrogen bonds : bond 0.04851 ( 2038) hydrogen bonds : angle 4.12747 ( 6043) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 121 MET cc_start: 0.9035 (mmm) cc_final: 0.8727 (mpp) REVERT: D 440 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8072 (mm110) REVERT: D 619 MET cc_start: 0.9242 (tpp) cc_final: 0.9023 (tpp) REVERT: D 630 MET cc_start: 0.9163 (tpp) cc_final: 0.8951 (tpp) REVERT: C 255 MET cc_start: 0.8283 (ttm) cc_final: 0.7987 (ttm) REVERT: C 529 ASP cc_start: 0.8850 (p0) cc_final: 0.8149 (t0) REVERT: A 121 MET cc_start: 0.7457 (mtm) cc_final: 0.7153 (ttp) REVERT: A 138 MET cc_start: 0.8936 (pmm) cc_final: 0.8577 (pmm) REVERT: A 747 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7747 (mpp80) REVERT: B 127 PHE cc_start: 0.8672 (p90) cc_final: 0.8404 (p90) REVERT: B 255 MET cc_start: 0.8031 (ptp) cc_final: 0.7797 (pmm) REVERT: B 368 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6545 (m-10) REVERT: B 429 LEU cc_start: 0.9409 (tp) cc_final: 0.9134 (mt) REVERT: B 440 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8355 (mp10) REVERT: B 778 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7241 (ttm) REVERT: B 1205 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8979 (tp30) outliers start: 36 outliers final: 21 residues processed: 252 average time/residue: 0.1879 time to fit residues: 80.7946 Evaluate side-chains 249 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain D residue 1178 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 979 MET Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 778 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 8 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 87 optimal weight: 0.2980 chunk 117 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 314 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 chunk 363 optimal weight: 0.9990 chunk 326 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.080754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053586 restraints weight = 300726.143| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.97 r_work: 0.2824 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33542 Z= 0.108 Angle : 0.527 16.849 45790 Z= 0.263 Chirality : 0.038 0.214 5347 Planarity : 0.004 0.049 5639 Dihedral : 7.009 59.902 6225 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.70 % Allowed : 15.66 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.14), residues: 4176 helix: 2.54 (0.10), residues: 2660 sheet: -0.39 (0.32), residues: 299 loop : -0.80 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 876 TYR 0.018 0.001 TYR D 958 PHE 0.019 0.001 PHE A 170 TRP 0.024 0.001 TRP D 621 HIS 0.004 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00230 (33538) covalent geometry : angle 0.52653 (45782) SS BOND : bond 0.00081 ( 4) SS BOND : angle 0.55591 ( 8) hydrogen bonds : bond 0.04047 ( 2038) hydrogen bonds : angle 3.87472 ( 6043) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: D 121 MET cc_start: 0.9026 (mmm) cc_final: 0.8696 (mpp) REVERT: D 619 MET cc_start: 0.9161 (tpp) cc_final: 0.8834 (tpt) REVERT: C 255 MET cc_start: 0.8231 (ttm) cc_final: 0.8031 (ttm) REVERT: C 529 ASP cc_start: 0.8853 (p0) cc_final: 0.8165 (t70) REVERT: A 121 MET cc_start: 0.7463 (mtm) cc_final: 0.7169 (ttp) REVERT: A 138 MET cc_start: 0.8938 (pmm) cc_final: 0.8554 (pmm) REVERT: A 397 MET cc_start: 0.4856 (mmt) cc_final: 0.4582 (mmt) REVERT: A 747 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7747 (mpp80) REVERT: B 127 PHE cc_start: 0.8652 (p90) cc_final: 0.8371 (p90) REVERT: B 255 MET cc_start: 0.8014 (ptp) cc_final: 0.7793 (pmm) REVERT: B 368 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6307 (m-10) REVERT: B 429 LEU cc_start: 0.9383 (tp) cc_final: 0.9125 (mt) REVERT: B 440 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8393 (mp10) REVERT: B 1205 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8834 (tp30) outliers start: 22 outliers final: 14 residues processed: 244 average time/residue: 0.1749 time to fit residues: 73.9890 Evaluate side-chains 241 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 625 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 112 optimal weight: 9.9990 chunk 319 optimal weight: 40.0000 chunk 25 optimal weight: 4.9990 chunk 132 optimal weight: 0.0030 chunk 67 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 88 optimal weight: 0.0670 chunk 2 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 overall best weight: 4.0134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 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 = 0.3696 r_free = 0.3696 target = 0.078594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.051956 restraints weight = 261338.171| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.88 r_work: 0.2764 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33542 Z= 0.214 Angle : 0.597 15.737 45790 Z= 0.298 Chirality : 0.040 0.195 5347 Planarity : 0.004 0.050 5639 Dihedral : 7.087 58.977 6225 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.77 % Allowed : 15.85 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.13), residues: 4176 helix: 2.48 (0.10), residues: 2650 sheet: -0.42 (0.32), residues: 301 loop : -0.80 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 210 TYR 0.015 0.001 TYR C1028 PHE 0.024 0.002 PHE A 866 TRP 0.032 0.002 TRP A 221 HIS 0.007 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00492 (33538) covalent geometry : angle 0.59648 (45782) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.78203 ( 8) hydrogen bonds : bond 0.04560 ( 2038) hydrogen bonds : angle 4.01021 ( 6043) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 1.159 Fit side-chains REVERT: D 121 MET cc_start: 0.9021 (mmm) cc_final: 0.8710 (mpp) REVERT: D 138 MET cc_start: 0.9412 (mtp) cc_final: 0.9069 (mtm) REVERT: D 619 MET cc_start: 0.9202 (tpp) cc_final: 0.8852 (tpp) REVERT: C 255 MET cc_start: 0.8301 (ttm) cc_final: 0.8046 (ttm) REVERT: C 529 ASP cc_start: 0.8871 (p0) cc_final: 0.8168 (t0) REVERT: A 36 PHE cc_start: 0.5874 (m-80) cc_final: 0.5557 (m-80) REVERT: A 121 MET cc_start: 0.7488 (mtm) cc_final: 0.7131 (ttp) REVERT: A 138 MET cc_start: 0.8951 (pmm) cc_final: 0.8606 (pmm) REVERT: A 179 MET cc_start: 0.9141 (tmm) cc_final: 0.8769 (tpt) REVERT: A 397 MET cc_start: 0.5251 (mmt) cc_final: 0.4936 (mmt) REVERT: A 747 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7717 (mpp80) REVERT: B 255 MET cc_start: 0.8005 (ptp) cc_final: 0.7787 (pmm) REVERT: B 368 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6368 (m-10) REVERT: B 429 LEU cc_start: 0.9399 (tp) cc_final: 0.9130 (mt) REVERT: B 440 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8337 (mp10) REVERT: B 778 MET cc_start: 0.7482 (ttm) cc_final: 0.7266 (ttm) REVERT: B 1205 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8943 (tp30) outliers start: 24 outliers final: 17 residues processed: 239 average time/residue: 0.1684 time to fit residues: 70.1500 Evaluate side-chains 239 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 625 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 268 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 195 optimal weight: 30.0000 chunk 223 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 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 = 0.3712 r_free = 0.3712 target = 0.079420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.052979 restraints weight = 240014.512| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.67 r_work: 0.2793 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33542 Z= 0.192 Angle : 0.577 15.852 45790 Z= 0.288 Chirality : 0.040 0.255 5347 Planarity : 0.004 0.048 5639 Dihedral : 7.033 59.764 6225 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.67 % Allowed : 15.91 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.13), residues: 4176 helix: 2.47 (0.10), residues: 2653 sheet: -0.41 (0.32), residues: 301 loop : -0.77 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG D1183 TYR 0.015 0.001 TYR D 958 PHE 0.023 0.001 PHE A 866 TRP 0.031 0.001 TRP A 221 HIS 0.005 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00441 (33538) covalent geometry : angle 0.57674 (45782) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.73847 ( 8) hydrogen bonds : bond 0.04443 ( 2038) hydrogen bonds : angle 3.98785 ( 6043) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: D 121 MET cc_start: 0.9013 (mmm) cc_final: 0.8694 (mpp) REVERT: D 619 MET cc_start: 0.9172 (tpp) cc_final: 0.8829 (tpp) REVERT: D 630 MET cc_start: 0.9135 (tpp) cc_final: 0.8888 (tpp) REVERT: C 255 MET cc_start: 0.8287 (ttm) cc_final: 0.8043 (ttm) REVERT: C 529 ASP cc_start: 0.8889 (p0) cc_final: 0.8191 (t0) REVERT: A 36 PHE cc_start: 0.5869 (m-80) cc_final: 0.5493 (m-80) REVERT: A 121 MET cc_start: 0.7532 (mtm) cc_final: 0.7147 (ttp) REVERT: A 138 MET cc_start: 0.8956 (pmm) cc_final: 0.8623 (pmm) REVERT: A 179 MET cc_start: 0.9111 (tmm) cc_final: 0.8805 (tpt) REVERT: A 397 MET cc_start: 0.5381 (mmt) cc_final: 0.4887 (mmt) REVERT: A 747 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7737 (mpp80) REVERT: B 255 MET cc_start: 0.7975 (ptp) cc_final: 0.7747 (pmm) REVERT: B 368 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6379 (m-10) REVERT: B 429 LEU cc_start: 0.9375 (tp) cc_final: 0.9111 (mt) REVERT: B 778 MET cc_start: 0.7475 (ttm) cc_final: 0.7254 (ttm) REVERT: B 1205 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8982 (tp30) outliers start: 21 outliers final: 16 residues processed: 244 average time/residue: 0.1711 time to fit residues: 72.4871 Evaluate side-chains 243 residues out of total 3759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 854 PHE Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 1178 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 625 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 74 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 384 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 275 optimal weight: 0.4980 chunk 244 optimal weight: 7.9990 chunk 387 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 110 optimal weight: 30.0000 chunk 247 optimal weight: 0.0000 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.080405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053565 restraints weight = 205810.394| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.09 r_work: 0.2846 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33542 Z= 0.121 Angle : 0.531 16.323 45790 Z= 0.264 Chirality : 0.038 0.271 5347 Planarity : 0.004 0.053 5639 Dihedral : 6.882 59.167 6225 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.57 % Allowed : 16.10 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.14), residues: 4176 helix: 2.59 (0.10), residues: 2656 sheet: -0.38 (0.32), residues: 300 loop : -0.74 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 210 TYR 0.016 0.001 TYR C 958 PHE 0.019 0.001 PHE A 170 TRP 0.033 0.001 TRP A 221 HIS 0.006 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00269 (33538) covalent geometry : angle 0.53105 (45782) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.60657 ( 8) hydrogen bonds : bond 0.04029 ( 2038) hydrogen bonds : angle 3.84701 ( 6043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9467.47 seconds wall clock time: 162 minutes 25.43 seconds (9745.43 seconds total)