Starting phenix.real_space_refine on Fri Mar 6 13:05:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uuz_20903/03_2026/6uuz_20903_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uuz_20903/03_2026/6uuz_20903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uuz_20903/03_2026/6uuz_20903_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uuz_20903/03_2026/6uuz_20903_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uuz_20903/03_2026/6uuz_20903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uuz_20903/03_2026/6uuz_20903.map" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 180 5.16 5 C 20340 2.51 5 N 5388 2.21 5 O 5898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31818 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "B" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "C" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 11.31, per 1000 atoms: 0.36 Number of scatterers: 31818 At special positions: 0 Unit cell: (140.07, 162.69, 167.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 12 15.00 O 5898 8.00 N 5388 7.00 C 20340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.05 Conformation dependent library (CDL) restraints added in 2.2 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 32 sheets defined 44.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.597A pdb=" N LEU A 50 " --> pdb=" O HIS A 47 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 52 " --> pdb=" O TRP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.655A pdb=" N ILE A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.561A pdb=" N ALA A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 349 through 362 removed outlier: 3.918A pdb=" N THR A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.690A pdb=" N HIS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.853A pdb=" N GLY A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.564A pdb=" N ALA A 413 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE A 414 " --> pdb=" O MET A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.513A pdb=" N HIS A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.574A pdb=" N SER A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 697 through 707 removed outlier: 3.748A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 733 removed outlier: 3.543A pdb=" N ILE A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 783 removed outlier: 3.596A pdb=" N ALA A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 783 " --> pdb=" O LEU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 807 removed outlier: 3.630A pdb=" N ASN A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 831 removed outlier: 3.678A pdb=" N ALA A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 868 through 878 Processing helix chain 'A' and resid 883 through 897 removed outlier: 3.623A pdb=" N GLN A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 937 through 951 removed outlier: 3.553A pdb=" N ALA A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 963 removed outlier: 4.053A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 removed outlier: 3.593A pdb=" N LEU A 990 " --> pdb=" O ARG A 986 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 3.790A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1040 removed outlier: 4.185A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS A1040 " --> pdb=" O MET A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1055 removed outlier: 3.621A pdb=" N ILE A1052 " --> pdb=" O ALA A1048 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY A1055 " --> pdb=" O TYR A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1079 removed outlier: 3.690A pdb=" N PHE A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1091 removed outlier: 3.561A pdb=" N ILE A1091 " --> pdb=" O TRP A1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 19 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.598A pdb=" N LEU B 50 " --> pdb=" O HIS B 47 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 52 " --> pdb=" O TRP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.655A pdb=" N ILE B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.562A pdb=" N ALA B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 349 through 362 removed outlier: 3.918A pdb=" N THR B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.690A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.853A pdb=" N GLY B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.565A pdb=" N ALA B 413 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE B 414 " --> pdb=" O MET B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 505 through 519 Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.513A pdb=" N HIS B 563 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.574A pdb=" N SER B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 617 Processing helix chain 'B' and resid 642 through 649 Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 697 through 707 removed outlier: 3.748A pdb=" N ARG B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 733 removed outlier: 3.543A pdb=" N ILE B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 783 removed outlier: 3.596A pdb=" N ALA B 782 " --> pdb=" O ALA B 778 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 807 removed outlier: 3.630A pdb=" N ASN B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 831 removed outlier: 3.678A pdb=" N ALA B 828 " --> pdb=" O ASP B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 868 through 878 Processing helix chain 'B' and resid 883 through 897 removed outlier: 3.621A pdb=" N GLN B 888 " --> pdb=" O LYS B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 916 Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 937 through 951 removed outlier: 3.553A pdb=" N ALA B 943 " --> pdb=" O LEU B 939 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 963 removed outlier: 4.053A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 997 removed outlier: 3.594A pdb=" N LEU B 990 " --> pdb=" O ARG B 986 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 996 " --> pdb=" O ASP B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1018 removed outlier: 3.790A pdb=" N SER B1016 " --> pdb=" O LYS B1012 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1040 removed outlier: 4.183A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B1040 " --> pdb=" O MET B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1055 removed outlier: 3.627A pdb=" N ILE B1052 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY B1055 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1079 removed outlier: 3.690A pdb=" N PHE B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1091 removed outlier: 3.561A pdb=" N ILE B1091 " --> pdb=" O TRP B1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.598A pdb=" N LEU C 50 " --> pdb=" O HIS C 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 52 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.655A pdb=" N ILE C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 177 through 194 removed outlier: 3.561A pdb=" N ALA C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'C' and resid 349 through 362 removed outlier: 3.918A pdb=" N THR C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.691A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 399 removed outlier: 3.853A pdb=" N GLY C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.564A pdb=" N ALA C 413 " --> pdb=" O HIS C 410 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE C 414 " --> pdb=" O MET C 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 410 through 414' Processing helix chain 'C' and resid 505 through 519 Processing helix chain 'C' and resid 555 through 563 removed outlier: 3.513A pdb=" N HIS C 563 " --> pdb=" O ALA C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.574A pdb=" N SER C 581 " --> pdb=" O SER C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 617 Processing helix chain 'C' and resid 642 through 649 Processing helix chain 'C' and resid 666 through 678 Processing helix chain 'C' and resid 697 through 707 removed outlier: 3.749A pdb=" N ARG C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C 707 " --> pdb=" O ARG C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 733 removed outlier: 3.543A pdb=" N ILE C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 783 removed outlier: 3.596A pdb=" N ALA C 782 " --> pdb=" O ALA C 778 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY C 783 " --> pdb=" O LEU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 807 removed outlier: 3.630A pdb=" N ASN C 807 " --> pdb=" O ASP C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 831 removed outlier: 3.678A pdb=" N ALA C 828 " --> pdb=" O ASP C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 868 through 878 Processing helix chain 'C' and resid 883 through 897 removed outlier: 3.622A pdb=" N GLN C 888 " --> pdb=" O LYS C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 916 Processing helix chain 'C' and resid 919 through 929 Processing helix chain 'C' and resid 937 through 951 removed outlier: 3.553A pdb=" N ALA C 943 " --> pdb=" O LEU C 939 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 963 removed outlier: 4.053A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 997 removed outlier: 3.594A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN C 996 " --> pdb=" O ASP C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 3.790A pdb=" N SER C1016 " --> pdb=" O LYS C1012 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1040 removed outlier: 4.184A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS C1040 " --> pdb=" O MET C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1055 removed outlier: 3.628A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C1055 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1079 removed outlier: 3.690A pdb=" N PHE C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1091 removed outlier: 3.561A pdb=" N ILE C1091 " --> pdb=" O TRP C1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 40 through 46 Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.597A pdb=" N LEU D 50 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D 52 " --> pdb=" O TRP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 161 through 169 removed outlier: 3.655A pdb=" N ILE D 165 " --> pdb=" O ASN D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 177 through 194 removed outlier: 3.561A pdb=" N ALA D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP D 194 " --> pdb=" O ASN D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 247 through 260 Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'D' and resid 349 through 362 removed outlier: 3.917A pdb=" N THR D 353 " --> pdb=" O ASN D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 removed outlier: 3.690A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 399 removed outlier: 3.854A pdb=" N GLY D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.564A pdb=" N ALA D 413 " --> pdb=" O HIS D 410 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE D 414 " --> pdb=" O MET D 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 410 through 414' Processing helix chain 'D' and resid 505 through 519 Processing helix chain 'D' and resid 555 through 563 removed outlier: 3.513A pdb=" N HIS D 563 " --> pdb=" O ALA D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.574A pdb=" N SER D 581 " --> pdb=" O SER D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 617 Processing helix chain 'D' and resid 642 through 649 Processing helix chain 'D' and resid 666 through 678 Processing helix chain 'D' and resid 697 through 707 removed outlier: 3.749A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 707 " --> pdb=" O ARG D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 733 removed outlier: 3.543A pdb=" N ILE D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 783 removed outlier: 3.595A pdb=" N ALA D 782 " --> pdb=" O ALA D 778 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY D 783 " --> pdb=" O LEU D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 807 removed outlier: 3.629A pdb=" N ASN D 807 " --> pdb=" O ASP D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 831 removed outlier: 3.678A pdb=" N ALA D 828 " --> pdb=" O ASP D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 865 Processing helix chain 'D' and resid 868 through 878 Processing helix chain 'D' and resid 883 through 897 removed outlier: 3.621A pdb=" N GLN D 888 " --> pdb=" O LYS D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 916 Processing helix chain 'D' and resid 919 through 929 Processing helix chain 'D' and resid 937 through 951 removed outlier: 3.553A pdb=" N ALA D 943 " --> pdb=" O LEU D 939 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 963 removed outlier: 4.053A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 997 removed outlier: 3.595A pdb=" N LEU D 990 " --> pdb=" O ARG D 986 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN D 996 " --> pdb=" O ASP D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1018 removed outlier: 3.790A pdb=" N SER D1016 " --> pdb=" O LYS D1012 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1040 removed outlier: 4.184A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS D1040 " --> pdb=" O MET D1036 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1055 removed outlier: 3.627A pdb=" N ILE D1052 " --> pdb=" O ALA D1048 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY D1055 " --> pdb=" O TYR D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1057 through 1079 removed outlier: 3.690A pdb=" N PHE D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1091 removed outlier: 3.561A pdb=" N ILE D1091 " --> pdb=" O TRP D1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 5.350A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR A 199 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA A 125 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU A 201 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE A 123 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN A 203 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A 121 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 5 removed outlier: 5.350A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.427A pdb=" N VAL A 57 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL A 74 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.627A pdb=" N LYS A 336 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE A 376 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU A 338 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG A 378 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE A 340 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 543 removed outlier: 7.144A pdb=" N ALA A 527 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE A 553 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N MET A 529 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA A 499 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET A 529 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 501 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS A 498 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 594 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 634 through 635 removed outlier: 6.841A pdb=" N VAL A 657 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY A 684 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 659 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA A 686 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER A 661 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA A 658 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU A 716 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 660 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 3 through 5 removed outlier: 5.349A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR B 199 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA B 125 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU B 201 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE B 123 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN B 203 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL B 121 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 5 removed outlier: 5.349A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.426A pdb=" N VAL B 57 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL B 74 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 92 through 95 Processing sheet with id=AB4, first strand: chain 'B' and resid 263 through 268 Processing sheet with id=AB5, first strand: chain 'B' and resid 275 through 277 removed outlier: 6.626A pdb=" N LYS B 336 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE B 376 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 338 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ARG B 378 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 340 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 537 through 543 removed outlier: 7.144A pdb=" N ALA B 527 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE B 553 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N MET B 529 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 498 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE B 594 " --> pdb=" O ILE B 621 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 634 through 635 removed outlier: 6.842A pdb=" N VAL B 657 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY B 684 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR B 659 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA B 686 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER B 661 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA B 658 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU B 716 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 660 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.350A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR C 199 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA C 125 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU C 201 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE C 123 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN C 203 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL C 121 " --> pdb=" O ASN C 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.350A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.426A pdb=" N VAL C 57 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL C 74 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 92 through 95 Processing sheet with id=AC3, first strand: chain 'C' and resid 263 through 268 Processing sheet with id=AC4, first strand: chain 'C' and resid 275 through 277 removed outlier: 6.627A pdb=" N LYS C 336 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE C 376 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU C 338 " --> pdb=" O PHE C 376 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG C 378 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE C 340 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 537 through 543 removed outlier: 7.144A pdb=" N ALA C 527 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHE C 553 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET C 529 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS C 498 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE C 594 " --> pdb=" O ILE C 621 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 634 through 635 removed outlier: 6.841A pdb=" N VAL C 657 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLY C 684 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR C 659 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALA C 686 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER C 661 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA C 658 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU C 716 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL C 660 " --> pdb=" O LEU C 716 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 5 removed outlier: 5.350A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR D 199 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA D 125 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU D 201 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE D 123 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN D 203 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL D 121 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 3 through 5 removed outlier: 5.350A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 32 through 34 removed outlier: 7.426A pdb=" N VAL D 57 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL D 74 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AD2, first strand: chain 'D' and resid 263 through 268 Processing sheet with id=AD3, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.627A pdb=" N LYS D 336 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE D 376 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU D 338 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG D 378 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE D 340 " --> pdb=" O ARG D 378 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 537 through 543 removed outlier: 7.144A pdb=" N ALA D 527 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE D 553 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET D 529 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS D 498 " --> pdb=" O VAL D 566 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE D 594 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 634 through 635 removed outlier: 6.841A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA D 658 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU D 716 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 660 " --> pdb=" O LEU D 716 " (cutoff:3.500A) 1388 hydrogen bonds defined for protein. 4020 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: 7.57 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9871 1.34 - 1.46: 6972 1.46 - 1.58: 15361 1.58 - 1.70: 20 1.70 - 1.83: 292 Bond restraints: 32516 Sorted by residual: bond pdb=" C4A COA A1201 " pdb=" C5A COA A1201 " ideal model delta sigma weight residual 1.395 1.470 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" O3B COA C1201 " pdb=" P3B COA C1201 " ideal model delta sigma weight residual 1.683 1.608 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C4A COA C1201 " pdb=" C5A COA C1201 " ideal model delta sigma weight residual 1.395 1.470 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C4A COA D1201 " pdb=" C5A COA D1201 " ideal model delta sigma weight residual 1.395 1.470 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O3B COA B1201 " pdb=" P3B COA B1201 " ideal model delta sigma weight residual 1.683 1.608 0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 32511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 43079 3.00 - 6.01: 851 6.01 - 9.01: 114 9.01 - 12.02: 12 12.02 - 15.02: 4 Bond angle restraints: 44060 Sorted by residual: angle pdb=" N LEU D 575 " pdb=" CA LEU D 575 " pdb=" C LEU D 575 " ideal model delta sigma weight residual 113.28 106.83 6.45 1.22e+00 6.72e-01 2.79e+01 angle pdb=" N CYS D 845 " pdb=" CA CYS D 845 " pdb=" C CYS D 845 " ideal model delta sigma weight residual 110.91 116.94 -6.03 1.17e+00 7.31e-01 2.66e+01 angle pdb=" N CYS A 845 " pdb=" CA CYS A 845 " pdb=" C CYS A 845 " ideal model delta sigma weight residual 110.91 116.94 -6.03 1.17e+00 7.31e-01 2.65e+01 angle pdb=" N CYS B 845 " pdb=" CA CYS B 845 " pdb=" C CYS B 845 " ideal model delta sigma weight residual 110.91 116.94 -6.03 1.17e+00 7.31e-01 2.65e+01 angle pdb=" N CYS C 845 " pdb=" CA CYS C 845 " pdb=" C CYS C 845 " ideal model delta sigma weight residual 110.91 116.90 -5.99 1.17e+00 7.31e-01 2.62e+01 ... (remaining 44055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 17780 17.68 - 35.36: 1446 35.36 - 53.03: 254 53.03 - 70.71: 67 70.71 - 88.39: 13 Dihedral angle restraints: 19560 sinusoidal: 7920 harmonic: 11640 Sorted by residual: dihedral pdb=" CA ILE A 980 " pdb=" C ILE A 980 " pdb=" N ASN A 981 " pdb=" CA ASN A 981 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ILE C 980 " pdb=" C ILE C 980 " pdb=" N ASN C 981 " pdb=" CA ASN C 981 " ideal model delta harmonic sigma weight residual -180.00 -154.22 -25.78 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA ILE D 980 " pdb=" C ILE D 980 " pdb=" N ASN D 981 " pdb=" CA ASN D 981 " ideal model delta harmonic sigma weight residual -180.00 -154.22 -25.78 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 19557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3825 0.072 - 0.145: 943 0.145 - 0.217: 104 0.217 - 0.290: 20 0.290 - 0.362: 20 Chirality restraints: 4912 Sorted by residual: chirality pdb=" CB VAL B 904 " pdb=" CA VAL B 904 " pdb=" CG1 VAL B 904 " pdb=" CG2 VAL B 904 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CB VAL A 904 " pdb=" CA VAL A 904 " pdb=" CG1 VAL A 904 " pdb=" CG2 VAL A 904 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CB VAL D 904 " pdb=" CA VAL D 904 " pdb=" CG1 VAL D 904 " pdb=" CG2 VAL D 904 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 4909 not shown) Planarity restraints: 5624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P COA C1201 " 0.334 2.00e-02 2.50e+03 2.82e-01 9.97e+02 pdb=" C5P COA C1201 " -0.089 2.00e-02 2.50e+03 pdb=" C6P COA C1201 " 0.184 2.00e-02 2.50e+03 pdb=" N4P COA C1201 " -0.491 2.00e-02 2.50e+03 pdb=" O5P COA C1201 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P COA A1201 " 0.296 2.00e-02 2.50e+03 2.47e-01 7.65e+02 pdb=" C5P COA A1201 " -0.080 2.00e-02 2.50e+03 pdb=" C6P COA A1201 " 0.188 2.00e-02 2.50e+03 pdb=" N4P COA A1201 " -0.420 2.00e-02 2.50e+03 pdb=" O5P COA A1201 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P COA B1201 " -0.279 2.00e-02 2.50e+03 2.39e-01 7.13e+02 pdb=" C5P COA B1201 " 0.062 2.00e-02 2.50e+03 pdb=" C6P COA B1201 " 0.021 2.00e-02 2.50e+03 pdb=" N4P COA B1201 " 0.401 2.00e-02 2.50e+03 pdb=" O5P COA B1201 " -0.205 2.00e-02 2.50e+03 ... (remaining 5621 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6969 2.78 - 3.31: 28497 3.31 - 3.84: 53054 3.84 - 4.37: 64137 4.37 - 4.90: 108847 Nonbonded interactions: 261504 Sorted by model distance: nonbonded pdb=" NZ LYS D 964 " pdb=" O8A COA B1201 " model vdw 2.253 3.120 nonbonded pdb=" O ASN A1020 " pdb=" ND2 ASN A1020 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR D 199 " pdb=" OE2 GLU D 201 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR C 199 " pdb=" OE2 GLU C 201 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR A 199 " pdb=" OE2 GLU A 201 " model vdw 2.276 3.040 ... (remaining 261499 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.40 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: 0.680 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: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 35.640 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 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 : 0.007 0.104 32516 Z= 0.307 Angle : 1.055 15.025 44060 Z= 0.568 Chirality : 0.065 0.362 4912 Planarity : 0.011 0.282 5624 Dihedral : 13.593 88.391 12168 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.62 % Favored : 94.19 % Rotamer: Outliers : 1.45 % Allowed : 3.36 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -4.07 (0.10), residues: 4068 helix: -2.84 (0.09), residues: 1716 sheet: -1.85 (0.20), residues: 524 loop : -2.71 (0.12), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1085 TYR 0.020 0.003 TYR C 288 PHE 0.029 0.003 PHE C 376 TRP 0.009 0.002 TRP B 877 HIS 0.014 0.002 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00695 (32516) covalent geometry : angle 1.05534 (44060) hydrogen bonds : bond 0.15328 ( 1364) hydrogen bonds : angle 7.53201 ( 4020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 584 time to evaluate : 1.036 Fit side-chains REVERT: A 259 LYS cc_start: 0.6356 (pttp) cc_final: 0.5553 (mppt) REVERT: A 504 MET cc_start: 0.8634 (tpt) cc_final: 0.8422 (tpt) REVERT: A 586 MET cc_start: 0.7924 (mtm) cc_final: 0.7690 (mtt) REVERT: A 895 MET cc_start: 0.8391 (mtm) cc_final: 0.7951 (mtp) REVERT: A 995 ARG cc_start: 0.6763 (mtt-85) cc_final: 0.6328 (mtt90) REVERT: A 996 GLN cc_start: 0.7335 (mt0) cc_final: 0.6927 (tm-30) REVERT: B 259 LYS cc_start: 0.6337 (pttp) cc_final: 0.5531 (mppt) REVERT: B 504 MET cc_start: 0.8659 (tpt) cc_final: 0.8438 (tpt) REVERT: B 586 MET cc_start: 0.7899 (mtm) cc_final: 0.7670 (mtt) REVERT: B 835 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8514 (ptt180) REVERT: B 895 MET cc_start: 0.8383 (mtm) cc_final: 0.7914 (mtp) REVERT: B 996 GLN cc_start: 0.7363 (mt0) cc_final: 0.6968 (tm-30) REVERT: C 259 LYS cc_start: 0.6357 (pttp) cc_final: 0.5556 (mppt) REVERT: C 504 MET cc_start: 0.8657 (tpt) cc_final: 0.8435 (tpt) REVERT: C 586 MET cc_start: 0.7901 (mtm) cc_final: 0.7677 (mtt) REVERT: C 835 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8537 (ptt180) REVERT: C 895 MET cc_start: 0.8388 (mtm) cc_final: 0.7935 (mtp) REVERT: C 995 ARG cc_start: 0.6761 (mtt-85) cc_final: 0.6350 (mtt90) REVERT: C 996 GLN cc_start: 0.7362 (mt0) cc_final: 0.6972 (tm-30) REVERT: D 259 LYS cc_start: 0.6311 (pttp) cc_final: 0.5525 (mppt) REVERT: D 504 MET cc_start: 0.8641 (tpt) cc_final: 0.8423 (tpt) REVERT: D 586 MET cc_start: 0.7917 (mtm) cc_final: 0.7690 (mtt) REVERT: D 835 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8540 (ptt180) REVERT: D 895 MET cc_start: 0.8387 (mtm) cc_final: 0.7970 (mtp) REVERT: D 995 ARG cc_start: 0.6763 (mtt-85) cc_final: 0.6323 (mtt90) REVERT: D 996 GLN cc_start: 0.7348 (mt0) cc_final: 0.6919 (tm-30) outliers start: 45 outliers final: 14 residues processed: 623 average time/residue: 0.6384 time to fit residues: 471.2014 Evaluate side-chains 407 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 390 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 976 ARG Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 913 CYS Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 913 CYS Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 913 CYS Chi-restraints excluded: chain D residue 1021 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN A 332 HIS A 371 HIS A 638 ASN A 850 GLN A 888 GLN A 900 HIS A 908 HIS A 961 ASN B 61 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS B 371 HIS B 638 ASN B 850 GLN B 900 HIS B 908 HIS B 961 ASN C 61 GLN ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS C 371 HIS C 638 ASN C 850 GLN C 900 HIS C 908 HIS C 961 ASN C1098 HIS D 61 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 HIS D 371 HIS D 638 ASN D 850 GLN D 900 HIS D 908 HIS D 961 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.233017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.199282 restraints weight = 64378.355| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 4.34 r_work: 0.3861 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32516 Z= 0.166 Angle : 0.656 7.902 44060 Z= 0.343 Chirality : 0.047 0.200 4912 Planarity : 0.005 0.060 5624 Dihedral : 8.371 58.776 4707 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.90 % Allowed : 11.64 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.79 (0.12), residues: 4068 helix: -1.37 (0.11), residues: 1748 sheet: -1.58 (0.20), residues: 584 loop : -2.37 (0.13), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 995 TYR 0.016 0.002 TYR D 196 PHE 0.018 0.002 PHE B 405 TRP 0.008 0.001 TRP D 84 HIS 0.006 0.001 HIS D1086 Details of bonding type rmsd covalent geometry : bond 0.00394 (32516) covalent geometry : angle 0.65612 (44060) hydrogen bonds : bond 0.04301 ( 1364) hydrogen bonds : angle 5.26171 ( 4020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 412 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.5962 (pttp) cc_final: 0.5412 (mtmt) REVERT: A 586 MET cc_start: 0.8003 (mtm) cc_final: 0.7795 (mtm) REVERT: A 895 MET cc_start: 0.8564 (mtm) cc_final: 0.8282 (mtp) REVERT: B 259 LYS cc_start: 0.5870 (pttp) cc_final: 0.5318 (mtmt) REVERT: B 586 MET cc_start: 0.8006 (mtm) cc_final: 0.7800 (mtm) REVERT: B 895 MET cc_start: 0.8550 (mtm) cc_final: 0.8255 (mtp) REVERT: C 259 LYS cc_start: 0.5882 (pttp) cc_final: 0.5322 (mtmt) REVERT: C 586 MET cc_start: 0.8028 (mtm) cc_final: 0.7817 (mtm) REVERT: C 895 MET cc_start: 0.8561 (mtm) cc_final: 0.8269 (mtp) REVERT: D 259 LYS cc_start: 0.5895 (pttp) cc_final: 0.5335 (mtmt) REVERT: D 586 MET cc_start: 0.7969 (mtm) cc_final: 0.7757 (mtm) REVERT: D 777 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.7029 (tp40) REVERT: D 895 MET cc_start: 0.8576 (mtm) cc_final: 0.8259 (mtp) outliers start: 60 outliers final: 26 residues processed: 449 average time/residue: 0.5676 time to fit residues: 311.2855 Evaluate side-chains 395 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 368 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 1081 GLN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 913 CYS Chi-restraints excluded: chain B residue 1081 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 913 CYS Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 777 GLN Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 913 CYS Chi-restraints excluded: chain D residue 1081 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 18 optimal weight: 5.9990 chunk 132 optimal weight: 40.0000 chunk 282 optimal weight: 0.8980 chunk 227 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 157 optimal weight: 0.0470 chunk 126 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 329 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A1098 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B1098 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.233565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.193653 restraints weight = 69604.038| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 5.79 r_work: 0.3801 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32516 Z= 0.142 Angle : 0.600 6.985 44060 Z= 0.312 Chirality : 0.046 0.190 4912 Planarity : 0.005 0.058 5624 Dihedral : 7.429 57.803 4696 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.40 % Allowed : 14.22 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.12), residues: 4068 helix: -0.63 (0.12), residues: 1764 sheet: -1.16 (0.20), residues: 600 loop : -2.28 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 995 TYR 0.014 0.001 TYR C 993 PHE 0.026 0.001 PHE C 405 TRP 0.009 0.001 TRP A 84 HIS 0.005 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00337 (32516) covalent geometry : angle 0.60036 (44060) hydrogen bonds : bond 0.03626 ( 1364) hydrogen bonds : angle 4.79082 ( 4020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 389 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.5724 (pttp) cc_final: 0.5109 (mtmt) REVERT: A 278 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.5875 (tmm) REVERT: A 307 TYR cc_start: 0.7193 (p90) cc_final: 0.6985 (p90) REVERT: A 586 MET cc_start: 0.7999 (mtm) cc_final: 0.7733 (mtm) REVERT: A 678 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7811 (m) REVERT: A 691 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.7485 (ttp-170) REVERT: A 777 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7206 (tp40) REVERT: A 835 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8028 (ttm170) REVERT: A 895 MET cc_start: 0.8551 (mtm) cc_final: 0.8245 (mtp) REVERT: B 259 LYS cc_start: 0.5687 (pttp) cc_final: 0.5086 (mtmt) REVERT: B 278 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.5818 (tmm) REVERT: B 586 MET cc_start: 0.8010 (mtm) cc_final: 0.7750 (mtm) REVERT: B 678 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7771 (m) REVERT: B 691 ARG cc_start: 0.7807 (ttp-170) cc_final: 0.7492 (ttp-170) REVERT: B 835 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7921 (ttm170) REVERT: B 895 MET cc_start: 0.8561 (mtm) cc_final: 0.8237 (mtp) REVERT: C 259 LYS cc_start: 0.5718 (pttp) cc_final: 0.5101 (mtmt) REVERT: C 278 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.5769 (tmm) REVERT: C 307 TYR cc_start: 0.7243 (p90) cc_final: 0.7030 (p90) REVERT: C 586 MET cc_start: 0.8022 (mtm) cc_final: 0.7751 (mtm) REVERT: C 678 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7739 (m) REVERT: C 691 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7463 (ttp-170) REVERT: C 835 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7844 (ttm170) REVERT: C 895 MET cc_start: 0.8553 (mtm) cc_final: 0.8247 (mtp) REVERT: D 259 LYS cc_start: 0.5730 (pttp) cc_final: 0.5109 (mtmt) REVERT: D 278 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.5809 (tmm) REVERT: D 307 TYR cc_start: 0.7201 (p90) cc_final: 0.6992 (p90) REVERT: D 586 MET cc_start: 0.7994 (mtm) cc_final: 0.7742 (mtm) REVERT: D 678 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7817 (m) REVERT: D 691 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7515 (ttp-170) REVERT: D 835 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7897 (ttm170) REVERT: D 895 MET cc_start: 0.8588 (mtm) cc_final: 0.8295 (mtp) outliers start: 77 outliers final: 22 residues processed: 430 average time/residue: 0.5792 time to fit residues: 303.0515 Evaluate side-chains 390 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 355 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 913 CYS Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 913 CYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 1022 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 61 optimal weight: 7.9990 chunk 320 optimal weight: 7.9990 chunk 217 optimal weight: 30.0000 chunk 260 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 205 optimal weight: 7.9990 chunk 29 optimal weight: 40.0000 chunk 313 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 252 optimal weight: 0.0570 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D1098 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.234424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.215212 restraints weight = 59197.738| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 1.76 r_work: 0.4092 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4061 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32516 Z= 0.157 Angle : 0.607 8.240 44060 Z= 0.312 Chirality : 0.046 0.195 4912 Planarity : 0.004 0.058 5624 Dihedral : 7.292 59.278 4695 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.58 % Allowed : 15.29 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.79 (0.12), residues: 4068 helix: -0.31 (0.12), residues: 1768 sheet: -0.93 (0.21), residues: 592 loop : -2.20 (0.13), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 995 TYR 0.015 0.001 TYR D 993 PHE 0.021 0.002 PHE D 405 TRP 0.009 0.001 TRP D 84 HIS 0.005 0.001 HIS D1086 Details of bonding type rmsd covalent geometry : bond 0.00378 (32516) covalent geometry : angle 0.60656 (44060) hydrogen bonds : bond 0.03610 ( 1364) hydrogen bonds : angle 4.68570 ( 4020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 361 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.6128 (tmm) REVERT: A 586 MET cc_start: 0.7883 (mtm) cc_final: 0.7626 (mtm) REVERT: A 678 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7609 (m) REVERT: A 691 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7441 (ttp-170) REVERT: A 835 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7788 (ttm170) REVERT: A 895 MET cc_start: 0.8513 (mtm) cc_final: 0.8244 (mtp) REVERT: B 278 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.6134 (tmm) REVERT: B 307 TYR cc_start: 0.7033 (p90) cc_final: 0.6829 (p90) REVERT: B 575 LEU cc_start: 0.8934 (pp) cc_final: 0.8723 (pp) REVERT: B 586 MET cc_start: 0.7884 (mtm) cc_final: 0.7631 (mtm) REVERT: B 678 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7572 (m) REVERT: B 691 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.7379 (ttp-170) REVERT: B 835 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7747 (ttm170) REVERT: B 895 MET cc_start: 0.8524 (mtm) cc_final: 0.8233 (mtp) REVERT: B 976 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7582 (ptp90) REVERT: C 278 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6117 (tmm) REVERT: C 586 MET cc_start: 0.7881 (mtm) cc_final: 0.7625 (mtm) REVERT: C 678 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7616 (m) REVERT: C 691 ARG cc_start: 0.7670 (ttp-170) cc_final: 0.7384 (ttp-170) REVERT: C 835 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7616 (ttm170) REVERT: C 895 MET cc_start: 0.8505 (mtm) cc_final: 0.8231 (mtp) REVERT: D 278 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6097 (tmm) REVERT: D 586 MET cc_start: 0.7902 (mtm) cc_final: 0.7667 (mtm) REVERT: D 599 GLU cc_start: 0.7535 (tp30) cc_final: 0.7294 (tt0) REVERT: D 678 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7686 (m) REVERT: D 691 ARG cc_start: 0.7711 (ttp80) cc_final: 0.7489 (ttp-170) REVERT: D 835 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7710 (ttm170) REVERT: D 895 MET cc_start: 0.8533 (mtm) cc_final: 0.8274 (mtp) outliers start: 83 outliers final: 26 residues processed: 412 average time/residue: 0.5537 time to fit residues: 278.1294 Evaluate side-chains 381 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 342 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 1081 GLN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 913 CYS Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 1081 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 1081 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 163 optimal weight: 0.0030 chunk 145 optimal weight: 8.9990 chunk 306 optimal weight: 40.0000 chunk 270 optimal weight: 8.9990 chunk 193 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 324 optimal weight: 10.0000 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.234763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.214705 restraints weight = 67113.624| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 1.70 r_work: 0.4068 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4029 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32516 Z= 0.143 Angle : 0.590 7.912 44060 Z= 0.303 Chirality : 0.045 0.188 4912 Planarity : 0.004 0.057 5624 Dihedral : 7.035 59.496 4694 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.02 % Allowed : 15.97 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.50 (0.13), residues: 4068 helix: 0.04 (0.12), residues: 1748 sheet: -0.78 (0.21), residues: 592 loop : -2.14 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 995 TYR 0.014 0.001 TYR D 993 PHE 0.020 0.001 PHE C 405 TRP 0.009 0.001 TRP B 84 HIS 0.005 0.001 HIS D1086 Details of bonding type rmsd covalent geometry : bond 0.00343 (32516) covalent geometry : angle 0.58990 (44060) hydrogen bonds : bond 0.03475 ( 1364) hydrogen bonds : angle 4.59771 ( 4020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 374 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.6083 (tmm) REVERT: A 307 TYR cc_start: 0.7088 (p90) cc_final: 0.6874 (p90) REVERT: A 586 MET cc_start: 0.7979 (mtm) cc_final: 0.7722 (mtm) REVERT: A 678 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7700 (m) REVERT: A 691 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7428 (ttp-170) REVERT: A 835 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7669 (ttm170) REVERT: A 895 MET cc_start: 0.8551 (mtm) cc_final: 0.8273 (mtp) REVERT: B 278 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.6071 (tmm) REVERT: B 307 TYR cc_start: 0.7093 (p90) cc_final: 0.6879 (p90) REVERT: B 586 MET cc_start: 0.7997 (mtm) cc_final: 0.7714 (mtm) REVERT: B 678 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7661 (m) REVERT: B 835 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7672 (ttm170) REVERT: B 895 MET cc_start: 0.8548 (mtm) cc_final: 0.8231 (mtp) REVERT: C 278 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.6045 (tmm) REVERT: C 307 TYR cc_start: 0.7118 (p90) cc_final: 0.6883 (p90) REVERT: C 586 MET cc_start: 0.7969 (mtm) cc_final: 0.7708 (mtm) REVERT: C 678 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7666 (m) REVERT: C 691 ARG cc_start: 0.7709 (ttp-170) cc_final: 0.7423 (ttp-170) REVERT: C 895 MET cc_start: 0.8544 (mtm) cc_final: 0.8246 (mtp) REVERT: D 278 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.6056 (tmm) REVERT: D 307 TYR cc_start: 0.7087 (p90) cc_final: 0.6854 (p90) REVERT: D 586 MET cc_start: 0.7970 (mtm) cc_final: 0.7721 (mtm) REVERT: D 678 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7671 (m) REVERT: D 835 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7676 (ttm170) REVERT: D 895 MET cc_start: 0.8540 (mtm) cc_final: 0.8283 (mtp) REVERT: D 976 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7558 (ptp90) outliers start: 64 outliers final: 26 residues processed: 413 average time/residue: 0.5578 time to fit residues: 282.0323 Evaluate side-chains 386 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 348 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 913 CYS Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 976 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 112 optimal weight: 2.9990 chunk 357 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 282 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 276 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.232487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.212320 restraints weight = 71646.677| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 1.70 r_work: 0.4010 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3983 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3976 r_free = 0.3976 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3976 r_free = 0.3976 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 32516 Z= 0.194 Angle : 0.637 10.919 44060 Z= 0.326 Chirality : 0.048 0.206 4912 Planarity : 0.005 0.062 5624 Dihedral : 7.097 59.483 4689 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.61 % Allowed : 15.83 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.44 (0.13), residues: 4068 helix: 0.04 (0.12), residues: 1752 sheet: -0.80 (0.21), residues: 640 loop : -2.06 (0.13), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 995 TYR 0.016 0.002 TYR B 993 PHE 0.025 0.002 PHE A 998 TRP 0.009 0.001 TRP C 84 HIS 0.006 0.001 HIS D1086 Details of bonding type rmsd covalent geometry : bond 0.00474 (32516) covalent geometry : angle 0.63708 (44060) hydrogen bonds : bond 0.03797 ( 1364) hydrogen bonds : angle 4.69032 ( 4020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 354 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.6169 (tmm) REVERT: A 307 TYR cc_start: 0.7063 (p90) cc_final: 0.6853 (p90) REVERT: A 586 MET cc_start: 0.8015 (mtm) cc_final: 0.7751 (mtm) REVERT: A 895 MET cc_start: 0.8559 (mtm) cc_final: 0.8316 (mtp) REVERT: B 278 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.6183 (tmm) REVERT: B 307 TYR cc_start: 0.7073 (p90) cc_final: 0.6866 (p90) REVERT: B 586 MET cc_start: 0.8028 (mtm) cc_final: 0.7774 (mtm) REVERT: B 599 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7189 (tp30) REVERT: B 895 MET cc_start: 0.8541 (mtm) cc_final: 0.8293 (mtp) REVERT: B 976 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7562 (ptp90) REVERT: C 278 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.6172 (tmm) REVERT: C 307 TYR cc_start: 0.7086 (p90) cc_final: 0.6875 (p90) REVERT: C 586 MET cc_start: 0.8003 (mtm) cc_final: 0.7744 (mtm) REVERT: C 835 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7706 (ttm170) REVERT: C 895 MET cc_start: 0.8535 (mtm) cc_final: 0.8295 (mtp) REVERT: C 976 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7654 (ptp90) REVERT: D 278 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.6205 (tmm) REVERT: D 307 TYR cc_start: 0.7073 (p90) cc_final: 0.6873 (p90) REVERT: D 586 MET cc_start: 0.8012 (mtm) cc_final: 0.7774 (mtm) REVERT: D 678 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7732 (m) REVERT: D 895 MET cc_start: 0.8545 (mtm) cc_final: 0.8305 (mtp) REVERT: D 976 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7581 (ptp90) outliers start: 84 outliers final: 37 residues processed: 404 average time/residue: 0.6193 time to fit residues: 302.7682 Evaluate side-chains 382 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 336 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 976 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 42 optimal weight: 9.9990 chunk 336 optimal weight: 40.0000 chunk 193 optimal weight: 4.9990 chunk 373 optimal weight: 10.0000 chunk 393 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 358 optimal weight: 10.0000 chunk 274 optimal weight: 0.0980 chunk 175 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.230629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.196142 restraints weight = 50816.832| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 4.03 r_work: 0.3833 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 32516 Z= 0.223 Angle : 0.662 9.857 44060 Z= 0.341 Chirality : 0.049 0.231 4912 Planarity : 0.005 0.065 5624 Dihedral : 7.158 59.898 4688 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.93 % Favored : 94.98 % Rotamer: Outliers : 2.35 % Allowed : 16.81 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.46 (0.13), residues: 4068 helix: -0.05 (0.12), residues: 1712 sheet: -0.79 (0.21), residues: 640 loop : -1.94 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 653 TYR 0.017 0.002 TYR D 993 PHE 0.029 0.002 PHE D 998 TRP 0.014 0.001 TRP B 84 HIS 0.006 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.00548 (32516) covalent geometry : angle 0.66204 (44060) hydrogen bonds : bond 0.04004 ( 1364) hydrogen bonds : angle 4.73280 ( 4020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 347 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.6065 (tmm) REVERT: A 307 TYR cc_start: 0.7160 (p90) cc_final: 0.6897 (p90) REVERT: A 586 MET cc_start: 0.8064 (mtm) cc_final: 0.7797 (mtm) REVERT: A 895 MET cc_start: 0.8600 (mtm) cc_final: 0.8359 (mtp) REVERT: A 1081 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7710 (mt0) REVERT: B 278 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.6085 (tmm) REVERT: B 307 TYR cc_start: 0.7189 (p90) cc_final: 0.6986 (p90) REVERT: B 586 MET cc_start: 0.8055 (mtm) cc_final: 0.7794 (mtm) REVERT: B 599 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7665 (tp30) REVERT: B 895 MET cc_start: 0.8609 (mtm) cc_final: 0.8362 (mtp) REVERT: B 976 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7456 (ptp90) REVERT: C 278 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6063 (tmm) REVERT: C 307 TYR cc_start: 0.7187 (p90) cc_final: 0.6928 (p90) REVERT: C 586 MET cc_start: 0.8051 (mtm) cc_final: 0.7782 (mtm) REVERT: C 599 GLU cc_start: 0.8122 (tp30) cc_final: 0.7562 (tt0) REVERT: C 835 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.7788 (ttm170) REVERT: C 895 MET cc_start: 0.8596 (mtm) cc_final: 0.8356 (mtp) REVERT: C 976 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7616 (ptp90) REVERT: D 278 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.6056 (tmm) REVERT: D 307 TYR cc_start: 0.7147 (p90) cc_final: 0.6877 (p90) REVERT: D 586 MET cc_start: 0.8060 (mtm) cc_final: 0.7818 (mtm) REVERT: D 895 MET cc_start: 0.8596 (mtm) cc_final: 0.8371 (mtp) REVERT: D 976 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7471 (ptp90) outliers start: 75 outliers final: 33 residues processed: 393 average time/residue: 0.6336 time to fit residues: 300.5009 Evaluate side-chains 370 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 328 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1081 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 945 MET Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 27 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 110 optimal weight: 0.0010 chunk 114 optimal weight: 20.0000 chunk 219 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 259 optimal weight: 0.9980 chunk 314 optimal weight: 0.0010 chunk 271 optimal weight: 6.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.235947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.196826 restraints weight = 71135.995| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 5.37 r_work: 0.3803 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32516 Z= 0.119 Angle : 0.589 11.262 44060 Z= 0.301 Chirality : 0.045 0.244 4912 Planarity : 0.004 0.057 5624 Dihedral : 6.751 59.362 4688 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.78 % Allowed : 17.52 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.19 (0.13), residues: 4068 helix: 0.23 (0.12), residues: 1744 sheet: -0.64 (0.22), residues: 592 loop : -1.90 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 127 TYR 0.013 0.001 TYR B 993 PHE 0.019 0.001 PHE A 405 TRP 0.017 0.001 TRP B 276 HIS 0.005 0.000 HIS D1086 Details of bonding type rmsd covalent geometry : bond 0.00281 (32516) covalent geometry : angle 0.58859 (44060) hydrogen bonds : bond 0.03371 ( 1364) hydrogen bonds : angle 4.49964 ( 4020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 362 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.5566 (tmm) REVERT: A 307 TYR cc_start: 0.7237 (p90) cc_final: 0.7016 (p90) REVERT: A 337 ILE cc_start: 0.6755 (mp) cc_final: 0.6484 (mm) REVERT: A 586 MET cc_start: 0.8069 (mtm) cc_final: 0.7841 (mtm) REVERT: A 895 MET cc_start: 0.8548 (mtm) cc_final: 0.8239 (mtp) REVERT: B 278 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.5558 (tmm) REVERT: B 337 ILE cc_start: 0.6813 (mp) cc_final: 0.6560 (mm) REVERT: B 586 MET cc_start: 0.8045 (mtm) cc_final: 0.7824 (mtm) REVERT: B 599 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7555 (tp30) REVERT: B 833 LEU cc_start: 0.7911 (pt) cc_final: 0.7613 (pp) REVERT: B 895 MET cc_start: 0.8558 (mtm) cc_final: 0.8238 (mtp) REVERT: B 976 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7448 (ptp90) REVERT: C 278 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.5556 (tmm) REVERT: C 307 TYR cc_start: 0.7275 (p90) cc_final: 0.7043 (p90) REVERT: C 575 LEU cc_start: 0.8978 (pp) cc_final: 0.8762 (pp) REVERT: C 586 MET cc_start: 0.8025 (mtm) cc_final: 0.7797 (mtm) REVERT: C 599 GLU cc_start: 0.8068 (tp30) cc_final: 0.7313 (tt0) REVERT: C 895 MET cc_start: 0.8543 (mtm) cc_final: 0.8236 (mtp) REVERT: D 278 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.5556 (tmm) REVERT: D 307 TYR cc_start: 0.7233 (p90) cc_final: 0.6992 (p90) REVERT: D 895 MET cc_start: 0.8535 (mtm) cc_final: 0.8261 (mtp) REVERT: D 976 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7445 (ptp90) outliers start: 56 outliers final: 28 residues processed: 402 average time/residue: 0.5818 time to fit residues: 285.1888 Evaluate side-chains 376 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 342 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 263 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 382 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 213 optimal weight: 0.0970 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.245045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.226863 restraints weight = 66847.275| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 1.68 r_work: 0.4276 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4233 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4237 r_free = 0.4237 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4237 r_free = 0.4237 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32516 Z= 0.124 Angle : 0.594 10.667 44060 Z= 0.303 Chirality : 0.045 0.267 4912 Planarity : 0.004 0.056 5624 Dihedral : 6.486 59.799 4676 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.34 % Allowed : 18.65 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.03 (0.13), residues: 4068 helix: 0.33 (0.12), residues: 1748 sheet: -0.52 (0.22), residues: 592 loop : -1.79 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 676 TYR 0.014 0.001 TYR D 993 PHE 0.018 0.001 PHE C 405 TRP 0.012 0.001 TRP D 84 HIS 0.005 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.00294 (32516) covalent geometry : angle 0.59414 (44060) hydrogen bonds : bond 0.03468 ( 1364) hydrogen bonds : angle 4.44248 ( 4020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 355 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ILE cc_start: 0.6909 (mp) cc_final: 0.6669 (mm) REVERT: A 895 MET cc_start: 0.8455 (mtm) cc_final: 0.8177 (mtp) REVERT: A 1081 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: B 278 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.5871 (tmm) REVERT: B 337 ILE cc_start: 0.6957 (mp) cc_final: 0.6711 (mm) REVERT: B 895 MET cc_start: 0.8482 (mtm) cc_final: 0.8182 (mtp) REVERT: B 976 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7466 (ptp90) REVERT: C 278 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.5838 (tmm) REVERT: C 337 ILE cc_start: 0.6958 (mp) cc_final: 0.6718 (mm) REVERT: C 575 LEU cc_start: 0.8900 (pp) cc_final: 0.8679 (pp) REVERT: C 698 MET cc_start: 0.6934 (tpp) cc_final: 0.6729 (tpp) REVERT: C 895 MET cc_start: 0.8454 (mtm) cc_final: 0.8170 (mtp) REVERT: C 976 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7546 (ptp90) REVERT: D 278 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.5846 (tmm) REVERT: D 337 ILE cc_start: 0.6947 (mp) cc_final: 0.6708 (mm) REVERT: D 895 MET cc_start: 0.8467 (mtm) cc_final: 0.8184 (mtp) REVERT: D 976 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7469 (ptp90) outliers start: 41 outliers final: 25 residues processed: 388 average time/residue: 0.6008 time to fit residues: 283.7454 Evaluate side-chains 373 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 341 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1081 GLN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 236 optimal weight: 7.9990 chunk 352 optimal weight: 0.6980 chunk 402 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 319 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 405 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.242813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.224506 restraints weight = 66671.289| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 1.67 r_work: 0.4251 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4203 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4208 r_free = 0.4208 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4208 r_free = 0.4208 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32516 Z= 0.163 Angle : 0.629 13.276 44060 Z= 0.319 Chirality : 0.046 0.201 4912 Planarity : 0.005 0.058 5624 Dihedral : 6.501 59.560 4676 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.28 % Allowed : 18.94 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.06 (0.13), residues: 4068 helix: 0.28 (0.12), residues: 1752 sheet: -0.52 (0.23), residues: 592 loop : -1.78 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 676 TYR 0.015 0.001 TYR B 993 PHE 0.032 0.002 PHE D 959 TRP 0.012 0.001 TRP B 84 HIS 0.005 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.00398 (32516) covalent geometry : angle 0.62857 (44060) hydrogen bonds : bond 0.03654 ( 1364) hydrogen bonds : angle 4.52593 ( 4020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 337 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ILE cc_start: 0.6907 (mp) cc_final: 0.6658 (mm) REVERT: A 895 MET cc_start: 0.8509 (mtm) cc_final: 0.8241 (mtp) REVERT: A 963 MET cc_start: 0.7732 (ptp) cc_final: 0.7424 (ptp) REVERT: A 1081 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: B 278 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6052 (tmm) REVERT: B 337 ILE cc_start: 0.6958 (mp) cc_final: 0.6721 (mm) REVERT: B 833 LEU cc_start: 0.7837 (pt) cc_final: 0.7633 (pt) REVERT: B 895 MET cc_start: 0.8538 (mtm) cc_final: 0.8246 (mtp) REVERT: B 976 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7419 (ptp90) REVERT: C 278 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6020 (tmm) REVERT: C 337 ILE cc_start: 0.6944 (mp) cc_final: 0.6699 (mm) REVERT: C 575 LEU cc_start: 0.8940 (pp) cc_final: 0.8705 (pp) REVERT: C 835 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7731 (ttm170) REVERT: C 895 MET cc_start: 0.8501 (mtm) cc_final: 0.8228 (mtp) REVERT: C 976 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7507 (ptp90) REVERT: D 278 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6016 (tmm) REVERT: D 337 ILE cc_start: 0.6944 (mp) cc_final: 0.6706 (mm) REVERT: D 895 MET cc_start: 0.8517 (mtm) cc_final: 0.8250 (mtp) REVERT: D 976 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7479 (ptp90) outliers start: 39 outliers final: 27 residues processed: 369 average time/residue: 0.6242 time to fit residues: 277.7549 Evaluate side-chains 361 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 326 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1081 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1022 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 976 ARG Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 38 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 156 optimal weight: 8.9990 chunk 380 optimal weight: 0.0670 chunk 387 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 341 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS A 545 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 545 HIS ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 545 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 545 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.244802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.213138 restraints weight = 52375.758| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 4.40 r_work: 0.3970 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32516 Z= 0.123 Angle : 0.594 10.424 44060 Z= 0.302 Chirality : 0.045 0.202 4912 Planarity : 0.004 0.055 5624 Dihedral : 6.264 59.628 4676 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.37 % Allowed : 18.91 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.90 (0.13), residues: 4068 helix: 0.43 (0.12), residues: 1768 sheet: -0.36 (0.23), residues: 572 loop : -1.76 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 703 TYR 0.019 0.001 TYR D 579 PHE 0.020 0.001 PHE C 347 TRP 0.012 0.001 TRP B 84 HIS 0.004 0.000 HIS C1086 Details of bonding type rmsd covalent geometry : bond 0.00294 (32516) covalent geometry : angle 0.59412 (44060) hydrogen bonds : bond 0.03355 ( 1364) hydrogen bonds : angle 4.41549 ( 4020) =============================================================================== Job complete usr+sys time: 11174.60 seconds wall clock time: 191 minutes 13.21 seconds (11473.21 seconds total)