Starting phenix.real_space_refine on Sat Jun 6 16:11:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wp6_66135/06_2026/9wp6_66135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wp6_66135/06_2026/9wp6_66135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wp6_66135/06_2026/9wp6_66135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wp6_66135/06_2026/9wp6_66135.map" model { file = "/net/cci-nas-00/data/ceres_data/9wp6_66135/06_2026/9wp6_66135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wp6_66135/06_2026/9wp6_66135.cif" } resolution = 1.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 18553 2.51 5 N 5041 2.21 5 O 5658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29350 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2947 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2918 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 2930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2930 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2922 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 4, 'GLU:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2928 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2955 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2984 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2887 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "I" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2943 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "J" Number of atoms: 2936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2936 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 363} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 7.36, per 1000 atoms: 0.25 Number of scatterers: 29350 At special positions: 0 Unit cell: (154.33, 156.86, 108.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 5658 8.00 N 5041 7.00 C 18553 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: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6884 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 25 sheets defined 35.1% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.992A pdb=" N LEU A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 157 through 166 removed outlier: 3.772A pdb=" N ALA A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 219 through 234 Processing helix chain 'A' and resid 258 through 280 removed outlier: 4.341A pdb=" N GLY A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 327 removed outlier: 4.410A pdb=" N GLU A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 removed outlier: 3.515A pdb=" N GLY A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 376 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 409 through 421 removed outlier: 4.233A pdb=" N LEU A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 removed outlier: 4.009A pdb=" N LEU B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 157 through 166 removed outlier: 3.647A pdb=" N ALA B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 258 through 279 removed outlier: 4.350A pdb=" N GLY B 262 " --> pdb=" O GLY B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 312 through 327 removed outlier: 4.396A pdb=" N GLU B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.545A pdb=" N LEU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 376 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 410 through 420 removed outlier: 4.167A pdb=" N LEU B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 removed outlier: 4.070A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 166 removed outlier: 3.807A pdb=" N ALA C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 219 through 234 Processing helix chain 'C' and resid 258 through 280 removed outlier: 4.249A pdb=" N GLY C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 312 through 326 removed outlier: 4.199A pdb=" N GLU C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 336 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 369 through 376 Processing helix chain 'C' and resid 390 through 403 Processing helix chain 'C' and resid 409 through 420 removed outlier: 3.655A pdb=" N LYS C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 60 removed outlier: 4.033A pdb=" N LEU D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 166 removed outlier: 3.697A pdb=" N ALA D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 219 through 234 Processing helix chain 'D' and resid 258 through 280 removed outlier: 4.298A pdb=" N GLY D 262 " --> pdb=" O GLY D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 312 through 327 removed outlier: 4.422A pdb=" N GLU D 316 " --> pdb=" O GLY D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 336 Processing helix chain 'D' and resid 338 through 342 removed outlier: 4.300A pdb=" N ARG D 341 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 376 Processing helix chain 'D' and resid 390 through 403 Processing helix chain 'D' and resid 412 through 422 removed outlier: 3.660A pdb=" N ALA D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 60 removed outlier: 4.014A pdb=" N LEU E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 157 through 166 removed outlier: 3.744A pdb=" N ALA E 161 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 219 through 234 Processing helix chain 'E' and resid 258 through 280 removed outlier: 4.300A pdb=" N GLY E 262 " --> pdb=" O GLY E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 312 through 327 removed outlier: 4.219A pdb=" N GLU E 316 " --> pdb=" O GLY E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.545A pdb=" N ARG E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 338 through 343' Processing helix chain 'E' and resid 369 through 376 Processing helix chain 'E' and resid 390 through 403 Processing helix chain 'E' and resid 409 through 421 Processing helix chain 'F' and resid 54 through 60 removed outlier: 3.988A pdb=" N LEU F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 157 through 166 removed outlier: 3.559A pdb=" N ALA F 161 " --> pdb=" O LYS F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 174 Processing helix chain 'F' and resid 219 through 234 Processing helix chain 'F' and resid 258 through 279 removed outlier: 4.335A pdb=" N GLY F 262 " --> pdb=" O GLY F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 312 through 327 removed outlier: 4.262A pdb=" N GLU F 316 " --> pdb=" O GLY F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 336 removed outlier: 3.948A pdb=" N GLY F 336 " --> pdb=" O ILE F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 369 through 376 Processing helix chain 'F' and resid 390 through 403 Processing helix chain 'F' and resid 412 through 418 Processing helix chain 'G' and resid 54 through 60 removed outlier: 3.983A pdb=" N LEU G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 157 through 167 removed outlier: 3.682A pdb=" N ALA G 161 " --> pdb=" O LYS G 157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP G 167 " --> pdb=" O GLN G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 174 Processing helix chain 'G' and resid 219 through 234 Processing helix chain 'G' and resid 258 through 280 removed outlier: 4.177A pdb=" N GLY G 262 " --> pdb=" O GLY G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 310 Processing helix chain 'G' and resid 312 through 327 removed outlier: 4.225A pdb=" N GLU G 316 " --> pdb=" O GLY G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 335 Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 369 through 376 Processing helix chain 'G' and resid 390 through 403 Processing helix chain 'G' and resid 412 through 420 Processing helix chain 'H' and resid 54 through 60 removed outlier: 3.987A pdb=" N LEU H 58 " --> pdb=" O ARG H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 157 through 166 removed outlier: 3.623A pdb=" N ALA H 161 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 174 Processing helix chain 'H' and resid 219 through 234 Processing helix chain 'H' and resid 258 through 280 removed outlier: 4.257A pdb=" N GLY H 262 " --> pdb=" O GLY H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 310 Processing helix chain 'H' and resid 312 through 327 removed outlier: 4.245A pdb=" N GLU H 316 " --> pdb=" O GLY H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 336 Processing helix chain 'H' and resid 336 through 342 removed outlier: 3.525A pdb=" N ARG H 342 " --> pdb=" O GLY H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 376 Processing helix chain 'H' and resid 390 through 403 Processing helix chain 'H' and resid 411 through 420 Processing helix chain 'I' and resid 54 through 60 removed outlier: 3.953A pdb=" N LEU I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 157 through 166 removed outlier: 3.621A pdb=" N ALA I 161 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 174 Processing helix chain 'I' and resid 219 through 234 Processing helix chain 'I' and resid 258 through 280 removed outlier: 4.305A pdb=" N GLY I 262 " --> pdb=" O GLY I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 305 through 310 Processing helix chain 'I' and resid 312 through 327 removed outlier: 4.426A pdb=" N GLU I 316 " --> pdb=" O GLY I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 336 Processing helix chain 'I' and resid 369 through 376 Processing helix chain 'I' and resid 390 through 403 Processing helix chain 'I' and resid 412 through 421 removed outlier: 3.590A pdb=" N ALA I 416 " --> pdb=" O GLU I 412 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 60 removed outlier: 3.989A pdb=" N LEU J 58 " --> pdb=" O ARG J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 101 Processing helix chain 'J' and resid 157 through 167 removed outlier: 3.622A pdb=" N ALA J 161 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 174 Processing helix chain 'J' and resid 219 through 234 Processing helix chain 'J' and resid 258 through 279 removed outlier: 4.280A pdb=" N GLY J 262 " --> pdb=" O GLY J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 305 through 310 Processing helix chain 'J' and resid 312 through 326 removed outlier: 4.206A pdb=" N GLU J 316 " --> pdb=" O GLY J 312 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 336 removed outlier: 4.229A pdb=" N GLY J 336 " --> pdb=" O ILE J 332 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 376 Processing helix chain 'J' and resid 390 through 403 Processing helix chain 'J' and resid 411 through 421 removed outlier: 4.006A pdb=" N ALA J 415 " --> pdb=" O ALA J 411 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.970A pdb=" N GLY A 38 " --> pdb=" O VAL G 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 removed outlier: 5.111A pdb=" N LEU A 123 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 146 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP A 144 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 71 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL A 141 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A 73 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS A 143 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A 75 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR A 145 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N VAL A 77 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER A 86 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY B 242 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER B 238 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN B 252 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR B 240 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU B 250 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLY B 242 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N GLN B 248 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE B 177 " --> pdb=" O PRO B 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 107 removed outlier: 5.111A pdb=" N LEU A 123 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 146 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP A 144 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 71 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL A 141 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A 73 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS A 143 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A 75 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR A 145 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N VAL A 77 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER A 86 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY B 242 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER B 238 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN B 252 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR B 240 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU B 250 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLY B 242 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N GLN B 248 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE B 177 " --> pdb=" O PRO B 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 282 through 284 Processing sheet with id=AA5, first strand: chain 'A' and resid 282 through 284 removed outlier: 5.982A pdb=" N PHE A 177 " --> pdb=" O PRO A 255 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN A 248 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLY A 242 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU A 250 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR A 240 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLN A 252 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER A 238 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY A 242 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N SER E 86 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL E 77 " --> pdb=" O CYS E 143 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR E 145 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 127 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP E 144 " --> pdb=" O PRO E 125 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR E 146 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU E 123 " --> pdb=" O TYR E 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 41 Processing sheet with id=AA7, first strand: chain 'B' and resid 104 through 107 removed outlier: 5.152A pdb=" N LEU B 123 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR B 146 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP B 144 " --> pdb=" O PRO B 125 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE B 71 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL B 141 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU B 73 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS B 143 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE B 75 " --> pdb=" O CYS B 143 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 145 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL B 77 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N SER B 86 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY C 242 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER C 238 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN C 252 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR C 240 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU C 250 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLY C 242 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLN C 248 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE C 177 " --> pdb=" O PRO C 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 104 through 107 removed outlier: 5.152A pdb=" N LEU B 123 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR B 146 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP B 144 " --> pdb=" O PRO B 125 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE B 71 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL B 141 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU B 73 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS B 143 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE B 75 " --> pdb=" O CYS B 143 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 145 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL B 77 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N SER B 86 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY C 242 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER C 238 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN C 252 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR C 240 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU C 250 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLY C 242 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLN C 248 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE C 177 " --> pdb=" O PRO C 255 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS C 300 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 38 through 42 Processing sheet with id=AB1, first strand: chain 'C' and resid 104 through 107 removed outlier: 5.160A pdb=" N LEU C 123 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR C 146 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP C 144 " --> pdb=" O PRO C 125 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 127 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL C 77 " --> pdb=" O CYS C 143 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR C 145 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N SER C 86 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY D 242 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER D 238 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN D 252 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR D 240 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU D 250 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY D 242 " --> pdb=" O GLN D 248 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLN D 248 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE D 177 " --> pdb=" O PRO D 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 104 through 107 removed outlier: 5.160A pdb=" N LEU C 123 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR C 146 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP C 144 " --> pdb=" O PRO C 125 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 127 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL C 77 " --> pdb=" O CYS C 143 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR C 145 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N SER C 86 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY D 242 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER D 238 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN D 252 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR D 240 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU D 250 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY D 242 " --> pdb=" O GLN D 248 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLN D 248 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE D 177 " --> pdb=" O PRO D 255 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 41 through 43 Processing sheet with id=AB4, first strand: chain 'D' and resid 104 through 107 removed outlier: 5.172A pdb=" N LEU D 123 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR D 146 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP D 144 " --> pdb=" O PRO D 125 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 127 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D 71 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL D 141 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLU D 73 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N CYS D 143 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE D 75 " --> pdb=" O CYS D 143 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR D 145 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N VAL D 77 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER D 86 " --> pdb=" O GLY E 242 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLY E 242 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER E 238 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN E 252 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR E 240 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU E 250 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLY E 242 " --> pdb=" O GLN E 248 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLN E 248 " --> pdb=" O GLY E 242 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE E 177 " --> pdb=" O PRO E 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 104 through 107 removed outlier: 5.172A pdb=" N LEU D 123 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR D 146 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP D 144 " --> pdb=" O PRO D 125 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 127 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D 71 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL D 141 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLU D 73 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N CYS D 143 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE D 75 " --> pdb=" O CYS D 143 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR D 145 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N VAL D 77 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER D 86 " --> pdb=" O GLY E 242 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLY E 242 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER E 238 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN E 252 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR E 240 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU E 250 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLY E 242 " --> pdb=" O GLN E 248 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLN E 248 " --> pdb=" O GLY E 242 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE E 177 " --> pdb=" O PRO E 255 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 39 through 42 Processing sheet with id=AB7, first strand: chain 'F' and resid 104 through 107 removed outlier: 5.199A pdb=" N LEU F 123 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR F 146 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP F 144 " --> pdb=" O PRO F 125 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F 127 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE F 71 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL F 141 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLU F 73 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS F 143 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE F 75 " --> pdb=" O CYS F 143 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR F 145 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL F 77 " --> pdb=" O THR F 145 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N SER F 86 " --> pdb=" O GLY G 242 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY G 242 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER G 238 " --> pdb=" O THR F 90 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN G 252 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR G 240 " --> pdb=" O GLU G 250 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU G 250 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLY G 242 " --> pdb=" O GLN G 248 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLN G 248 " --> pdb=" O GLY G 242 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE G 177 " --> pdb=" O PRO G 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 104 through 107 removed outlier: 5.199A pdb=" N LEU F 123 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR F 146 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP F 144 " --> pdb=" O PRO F 125 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F 127 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE F 71 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL F 141 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLU F 73 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS F 143 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE F 75 " --> pdb=" O CYS F 143 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR F 145 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL F 77 " --> pdb=" O THR F 145 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N SER F 86 " --> pdb=" O GLY G 242 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY G 242 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER G 238 " --> pdb=" O THR F 90 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN G 252 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR G 240 " --> pdb=" O GLU G 250 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU G 250 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLY G 242 " --> pdb=" O GLN G 248 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLN G 248 " --> pdb=" O GLY G 242 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE G 177 " --> pdb=" O PRO G 255 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS G 300 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY G 358 " --> pdb=" O VAL G 368 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 282 through 284 removed outlier: 3.864A pdb=" N HIS F 300 " --> pdb=" O GLU F 180 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY F 358 " --> pdb=" O VAL F 368 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 282 through 284 removed outlier: 5.936A pdb=" N PHE F 177 " --> pdb=" O PRO F 255 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN F 248 " --> pdb=" O GLY F 242 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLY F 242 " --> pdb=" O GLN F 248 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU F 250 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR F 240 " --> pdb=" O GLU F 250 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLN F 252 " --> pdb=" O SER F 238 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER F 238 " --> pdb=" O THR J 90 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY F 242 " --> pdb=" O SER J 86 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER J 86 " --> pdb=" O GLY F 242 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE J 71 " --> pdb=" O VAL J 139 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL J 141 " --> pdb=" O ILE J 71 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLU J 73 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS J 143 " --> pdb=" O GLU J 73 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE J 75 " --> pdb=" O CYS J 143 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR J 145 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N VAL J 77 " --> pdb=" O THR J 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA J 127 " --> pdb=" O ILE J 142 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP J 144 " --> pdb=" O PRO J 125 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR J 146 " --> pdb=" O LEU J 123 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU J 123 " --> pdb=" O TYR J 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 104 through 107 removed outlier: 5.238A pdb=" N LEU G 123 " --> pdb=" O TYR G 146 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR G 146 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP G 144 " --> pdb=" O PRO G 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA G 127 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE G 71 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL G 141 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU G 73 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N CYS G 143 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE G 75 " --> pdb=" O CYS G 143 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR G 145 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N VAL G 77 " --> pdb=" O THR G 145 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER G 86 " --> pdb=" O GLY H 242 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY H 242 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER H 238 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN H 252 " --> pdb=" O SER H 238 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR H 240 " --> pdb=" O GLU H 250 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU H 250 " --> pdb=" O THR H 240 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY H 242 " --> pdb=" O GLN H 248 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLN H 248 " --> pdb=" O GLY H 242 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE H 177 " --> pdb=" O PRO H 255 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 104 through 107 removed outlier: 5.238A pdb=" N LEU G 123 " --> pdb=" O TYR G 146 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR G 146 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP G 144 " --> pdb=" O PRO G 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA G 127 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE G 71 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL G 141 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU G 73 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N CYS G 143 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE G 75 " --> pdb=" O CYS G 143 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR G 145 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N VAL G 77 " --> pdb=" O THR G 145 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER G 86 " --> pdb=" O GLY H 242 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY H 242 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER H 238 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN H 252 " --> pdb=" O SER H 238 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR H 240 " --> pdb=" O GLU H 250 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU H 250 " --> pdb=" O THR H 240 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY H 242 " --> pdb=" O GLN H 248 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLN H 248 " --> pdb=" O GLY H 242 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE H 177 " --> pdb=" O PRO H 255 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY H 358 " --> pdb=" O VAL H 368 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 104 through 107 removed outlier: 5.205A pdb=" N LEU H 123 " --> pdb=" O TYR H 146 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N TYR H 146 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP H 144 " --> pdb=" O PRO H 125 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA H 127 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE H 71 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL H 141 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLU H 73 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS H 143 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE H 75 " --> pdb=" O CYS H 143 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N THR H 145 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N VAL H 77 " --> pdb=" O THR H 145 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N SER H 86 " --> pdb=" O GLY I 242 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY I 242 " --> pdb=" O SER H 86 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER I 238 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN I 252 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR I 240 " --> pdb=" O GLU I 250 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU I 250 " --> pdb=" O THR I 240 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLY I 242 " --> pdb=" O GLN I 248 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLN I 248 " --> pdb=" O GLY I 242 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE I 177 " --> pdb=" O PRO I 255 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 104 through 107 removed outlier: 5.205A pdb=" N LEU H 123 " --> pdb=" O TYR H 146 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N TYR H 146 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP H 144 " --> pdb=" O PRO H 125 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA H 127 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE H 71 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL H 141 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLU H 73 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS H 143 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE H 75 " --> pdb=" O CYS H 143 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N THR H 145 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N VAL H 77 " --> pdb=" O THR H 145 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N SER H 86 " --> pdb=" O GLY I 242 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY I 242 " --> pdb=" O SER H 86 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER I 238 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN I 252 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR I 240 " --> pdb=" O GLU I 250 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU I 250 " --> pdb=" O THR I 240 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLY I 242 " --> pdb=" O GLN I 248 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLN I 248 " --> pdb=" O GLY I 242 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE I 177 " --> pdb=" O PRO I 255 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS I 300 " --> pdb=" O GLU I 180 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY I 358 " --> pdb=" O VAL I 368 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 104 through 107 removed outlier: 5.205A pdb=" N LEU I 123 " --> pdb=" O TYR I 146 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR I 146 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP I 144 " --> pdb=" O PRO I 125 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA I 127 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE I 71 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL I 141 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU I 73 " --> pdb=" O VAL I 141 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS I 143 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE I 75 " --> pdb=" O CYS I 143 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR I 145 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N VAL I 77 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER I 86 " --> pdb=" O GLY J 242 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY J 242 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER J 238 " --> pdb=" O THR I 90 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN J 252 " --> pdb=" O SER J 238 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR J 240 " --> pdb=" O GLU J 250 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU J 250 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLY J 242 " --> pdb=" O GLN J 248 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLN J 248 " --> pdb=" O GLY J 242 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE J 177 " --> pdb=" O PRO J 255 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 104 through 107 removed outlier: 5.205A pdb=" N LEU I 123 " --> pdb=" O TYR I 146 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR I 146 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP I 144 " --> pdb=" O PRO I 125 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA I 127 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE I 71 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL I 141 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU I 73 " --> pdb=" O VAL I 141 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS I 143 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE I 75 " --> pdb=" O CYS I 143 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR I 145 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N VAL I 77 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER I 86 " --> pdb=" O GLY J 242 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY J 242 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER J 238 " --> pdb=" O THR I 90 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN J 252 " --> pdb=" O SER J 238 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR J 240 " --> pdb=" O GLU J 250 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU J 250 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLY J 242 " --> pdb=" O GLN J 248 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLN J 248 " --> pdb=" O GLY J 242 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE J 177 " --> pdb=" O PRO J 255 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY J 358 " --> pdb=" O VAL J 368 " (cutoff:3.500A) 1466 hydrogen bonds defined for protein. 4104 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: 6.11 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5043 1.31 - 1.44: 8010 1.44 - 1.56: 16903 1.56 - 1.68: 0 1.68 - 1.81: 146 Bond restraints: 30102 Sorted by residual: bond pdb=" C LEU J 398 " pdb=" O LEU J 398 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.17e-02 7.31e+03 1.83e+01 bond pdb=" C LEU G 398 " pdb=" O LEU G 398 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.17e-02 7.31e+03 1.29e+01 bond pdb=" CA ASP G 390 " pdb=" C ASP G 390 " ideal model delta sigma weight residual 1.519 1.481 0.037 1.15e-02 7.56e+03 1.05e+01 bond pdb=" C GLY G 178 " pdb=" O GLY G 178 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.35e-02 5.49e+03 9.64e+00 bond pdb=" CA LEU J 398 " pdb=" C LEU J 398 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.30e-02 5.92e+03 9.51e+00 ... (remaining 30097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 40287 1.63 - 3.27: 574 3.27 - 4.90: 122 4.90 - 6.54: 18 6.54 - 8.17: 5 Bond angle restraints: 41006 Sorted by residual: angle pdb=" N VAL G 257 " pdb=" CA VAL G 257 " pdb=" C VAL G 257 " ideal model delta sigma weight residual 108.23 116.40 -8.17 1.53e+00 4.27e-01 2.85e+01 angle pdb=" N ILE F 82 " pdb=" CA ILE F 82 " pdb=" C ILE F 82 " ideal model delta sigma weight residual 113.71 108.96 4.75 9.50e-01 1.11e+00 2.50e+01 angle pdb=" N VAL A 139 " pdb=" CA VAL A 139 " pdb=" C VAL A 139 " ideal model delta sigma weight residual 108.80 115.58 -6.78 1.46e+00 4.69e-01 2.16e+01 angle pdb=" N VAL B 139 " pdb=" CA VAL B 139 " pdb=" C VAL B 139 " ideal model delta sigma weight residual 108.80 115.52 -6.72 1.46e+00 4.69e-01 2.12e+01 angle pdb=" N VAL A 190 " pdb=" CA VAL A 190 " pdb=" C VAL A 190 " ideal model delta sigma weight residual 113.53 109.35 4.18 9.80e-01 1.04e+00 1.82e+01 ... (remaining 41001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 17130 16.45 - 32.91: 478 32.91 - 49.36: 86 49.36 - 65.81: 6 65.81 - 82.26: 6 Dihedral angle restraints: 17706 sinusoidal: 6782 harmonic: 10924 Sorted by residual: dihedral pdb=" CA GLY G 254 " pdb=" C GLY G 254 " pdb=" N PRO G 255 " pdb=" CA PRO G 255 " ideal model delta harmonic sigma weight residual 0.00 -19.66 19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP I 189 " pdb=" CB ASP I 189 " pdb=" CG ASP I 189 " pdb=" OD1 ASP I 189 " ideal model delta sinusoidal sigma weight residual -30.00 -85.64 55.64 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU G 277 " pdb=" CG GLU G 277 " pdb=" CD GLU G 277 " pdb=" OE1 GLU G 277 " ideal model delta sinusoidal sigma weight residual 0.00 -82.26 82.26 1 3.00e+01 1.11e-03 9.23e+00 ... (remaining 17703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3915 0.070 - 0.139: 447 0.139 - 0.209: 15 0.209 - 0.279: 4 0.279 - 0.348: 5 Chirality restraints: 4386 Sorted by residual: chirality pdb=" CA PHE G 165 " pdb=" N PHE G 165 " pdb=" C PHE G 165 " pdb=" CB PHE G 165 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA PHE J 165 " pdb=" N PHE J 165 " pdb=" C PHE J 165 " pdb=" CB PHE J 165 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ASN B 191 " pdb=" N ASN B 191 " pdb=" C ASN B 191 " pdb=" CB ASN B 191 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 4383 not shown) Planarity restraints: 5410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO J 175 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C PRO J 175 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO J 175 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP J 176 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO G 175 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.19e+00 pdb=" C PRO G 175 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO G 175 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP G 176 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 209 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C TYR A 209 " 0.025 2.00e-02 2.50e+03 pdb=" O TYR A 209 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS A 210 " -0.008 2.00e-02 2.50e+03 ... (remaining 5407 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3085 2.75 - 3.28: 28345 3.28 - 3.82: 52019 3.82 - 4.36: 60636 4.36 - 4.90: 104744 Nonbonded interactions: 248829 Sorted by model distance: nonbonded pdb=" OE1 GLU G 73 " pdb=" OG SER G 88 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR A 90 " pdb=" OH TYR B 227 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR C 90 " pdb=" OH TYR D 227 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR D 90 " pdb=" OH TYR E 227 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR F 227 " pdb=" OG1 THR J 90 " model vdw 2.225 3.040 ... (remaining 248824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 through 81 or (res \ id 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throu \ gh 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) or \ resid 118 through 191 or (resid 192 and (name N or name CA or name C or name O \ or name CB )) or resid 193 through 200 or (resid 201 and (name N or name CA or n \ ame C or name O or name CB )) or resid 202 through 256 or (resid 257 and (name N \ or name CA or name C or name O or name CB )) or resid 258 through 287 or (resid \ 288 and (name N or name CA or name C or name O or name CB )) or resid 289 throu \ gh 290 or (resid 291 and (name N or name CA or name C or name O or name CB )) or \ resid 292 through 293 or (resid 294 through 295 and (name N or name CA or name \ C or name O or name CB )) or resid 296 through 317 or (resid 318 through 320 and \ (name N or name CA or name C or name O or name CB )) or resid 321 through 336 o \ r (resid 337 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 38 through 342 or resid 352 through 388 or (resid 389 and (name N or name CA or \ name C or name O or name CB )) or resid 390 through 408 or (resid 409 through 41 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 414 through \ 421 or (resid 422 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 33 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 through 81 or (res \ id 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throu \ gh 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) or \ resid 118 through 204 or (resid 205 and (name N or name CA or name C or name O \ or name CB )) or resid 206 through 256 or (resid 257 and (name N or name CA or n \ ame C or name O or name CB )) or resid 258 through 287 or (resid 288 and (name N \ or name CA or name C or name O or name CB )) or resid 289 through 293 or (resid \ 294 through 295 and (name N or name CA or name C or name O or name CB )) or res \ id 296 through 317 or (resid 318 through 320 and (name N or name CA or name C or \ name O or name CB )) or resid 321 through 342 or resid 352 through 388 or (resi \ d 389 and (name N or name CA or name C or name O or name CB )) or resid 390 thro \ ugh 408 or (resid 409 through 413 and (name N or name CA or name C or name O or \ name CB )) or resid 414 through 421 or (resid 422 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'C' and (resid 33 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 through 116 or (re \ sid 117 and (name N or name CA or name C or name O or name CB )) or resid 118 th \ rough 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) \ or resid 193 through 200 or (resid 201 and (name N or name CA or name C or name \ O or name CB )) or resid 202 through 204 or (resid 205 and (name N or name CA o \ r name C or name O or name CB )) or resid 206 through 256 or (resid 257 and (nam \ e N or name CA or name C or name O or name CB )) or resid 258 through 290 or (re \ sid 291 and (name N or name CA or name C or name O or name CB )) or resid 292 th \ rough 293 or (resid 294 through 295 and (name N or name CA or name C or name O o \ r name CB )) or resid 296 through 342 or resid 352 through 388 or (resid 389 and \ (name N or name CA or name C or name O or name CB )) or resid 390 through 408 o \ r (resid 409 through 413 and (name N or name CA or name C or name O or name CB ) \ ) or resid 414 through 421 or (resid 422 and (name N or name CA or name C or nam \ e O or name CB )))) selection = (chain 'D' and (resid 33 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 81 or (resid 82 and (name N or nam \ e CA or name C or name O or name CB )) or resid 83 through 116 or (resid 117 and \ (name N or name CA or name C or name O or name CB )) or resid 118 through 191 o \ r (resid 192 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 93 through 200 or (resid 201 and (name N or name CA or name C or name O or name \ CB )) or resid 202 through 204 or (resid 205 and (name N or name CA or name C or \ name O or name CB )) or resid 206 through 211 or (resid 212 and (name N or name \ CA or name C or name O or name CB )) or resid 213 through 256 or (resid 257 and \ (name N or name CA or name C or name O or name CB )) or resid 258 through 287 o \ r (resid 288 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 89 through 290 or (resid 291 and (name N or name CA or name C or name O or name \ CB )) or resid 292 through 293 or (resid 294 through 295 and (name N or name CA \ or name C or name O or name CB )) or resid 296 through 317 or (resid 318 through \ 320 and (name N or name CA or name C or name O or name CB )) or resid 321 throu \ gh 342 or resid 352 through 388 or (resid 389 and (name N or name CA or name C o \ r name O or name CB )) or resid 390 through 421 or (resid 422 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 33 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 81 or (resid 82 and (name N or nam \ e CA or name C or name O or name CB )) or resid 83 through 116 or (resid 117 and \ (name N or name CA or name C or name O or name CB )) or resid 118 through 191 o \ r (resid 192 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 93 through 200 or (resid 201 and (name N or name CA or name C or name O or name \ CB )) or resid 202 through 204 or (resid 205 and (name N or name CA or name C or \ name O or name CB )) or resid 206 through 211 or (resid 212 and (name N or name \ CA or name C or name O or name CB )) or resid 213 through 256 or (resid 257 and \ (name N or name CA or name C or name O or name CB )) or resid 258 through 287 o \ r (resid 288 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 89 through 290 or (resid 291 and (name N or name CA or name C or name O or name \ CB )) or resid 292 through 293 or (resid 294 through 295 and (name N or name CA \ or name C or name O or name CB )) or resid 296 through 317 or (resid 318 through \ 320 and (name N or name CA or name C or name O or name CB )) or resid 321 throu \ gh 342 or resid 352 through 388 or (resid 389 and (name N or name CA or name C o \ r name O or name CB )) or resid 390 through 409 or (resid 410 through 413 and (n \ ame N or name CA or name C or name O or name CB )) or resid 414 through 422)) selection = (chain 'F' and (resid 33 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 through 81 or (res \ id 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throu \ gh 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) or \ resid 118 through 191 or (resid 192 and (name N or name CA or name C or name O \ or name CB )) or resid 193 through 200 or (resid 201 and (name N or name CA or n \ ame C or name O or name CB )) or resid 202 through 204 or (resid 205 and (name N \ or name CA or name C or name O or name CB )) or resid 206 through 211 or (resid \ 212 and (name N or name CA or name C or name O or name CB )) or resid 213 throu \ gh 256 or (resid 257 and (name N or name CA or name C or name O or name CB )) or \ resid 258 through 287 or (resid 288 and (name N or name CA or name C or name O \ or name CB )) or resid 289 through 290 or (resid 291 and (name N or name CA or n \ ame C or name O or name CB )) or resid 292 through 293 or (resid 294 through 295 \ and (name N or name CA or name C or name O or name CB )) or resid 296 through 3 \ 17 or (resid 318 through 320 and (name N or name CA or name C or name O or name \ CB )) or resid 321 through 342 or resid 352 through 361 or (resid 362 and (name \ N or name CA or name C or name O or name CB )) or resid 363 through 388 or (resi \ d 389 and (name N or name CA or name C or name O or name CB )) or resid 390 thro \ ugh 408 or (resid 409 through 413 and (name N or name CA or name C or name O or \ name CB )) or resid 414 through 421 or (resid 422 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'G' and (resid 33 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 through 81 or (res \ id 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throu \ gh 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 200 or (resid 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 204 or (resid 205 and (name N or name CA or n \ ame C or name O or name CB )) or resid 206 through 211 or (resid 212 and (name N \ or name CA or name C or name O or name CB )) or resid 213 through 287 or (resid \ 288 and (name N or name CA or name C or name O or name CB )) or resid 289 throu \ gh 290 or (resid 291 and (name N or name CA or name C or name O or name CB )) or \ resid 292 through 293 or (resid 294 through 295 and (name N or name CA or name \ C or name O or name CB )) or resid 296 through 317 or (resid 318 through 320 and \ (name N or name CA or name C or name O or name CB )) or resid 321 through 336 o \ r (resid 337 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 38 or (resid 339 through 342 and (name N or name CA or name C or name O or name \ CB )) or (resid 352 and (name N or name CA or name C or name O or name CB )) or \ resid 353 through 361 or (resid 362 and (name N or name CA or name C or name O o \ r name CB )) or resid 363 through 388 or (resid 389 and (name N or name CA or na \ me C or name O or name CB )) or resid 390 through 408 or (resid 409 through 413 \ and (name N or name CA or name C or name O or name CB )) or resid 414 through 42 \ 1 or (resid 422 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 33 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 through 191 or (re \ sid 192 and (name N or name CA or name C or name O or name CB )) or resid 193 th \ rough 200 or (resid 201 and (name N or name CA or name C or name O or name CB )) \ or resid 202 through 204 or (resid 205 and (name N or name CA or name C or name \ O or name CB )) or resid 206 through 256 or (resid 257 and (name N or name CA o \ r name C or name O or name CB )) or resid 258 through 287 or (resid 288 and (nam \ e N or name CA or name C or name O or name CB )) or resid 289 through 290 or (re \ sid 291 and (name N or name CA or name C or name O or name CB )) or resid 292 th \ rough 294 or (resid 295 and (name N or name CA or name C or name O or name CB )) \ or resid 296 through 317 or (resid 318 through 320 and (name N or name CA or na \ me C or name O or name CB )) or resid 321 through 388 or (resid 389 and (name N \ or name CA or name C or name O or name CB )) or resid 390 through 408 or (resid \ 409 through 413 and (name N or name CA or name C or name O or name CB )) or resi \ d 414 through 421 or (resid 422 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'I' and (resid 33 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 through 81 or (res \ id 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throu \ gh 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) or \ resid 118 through 141 or (resid 142 and (name N or name CA or name C or name O \ or name CB )) or resid 143 through 191 or (resid 192 and (name N or name CA or n \ ame C or name O or name CB )) or resid 193 through 204 or (resid 205 and (name N \ or name CA or name C or name O or name CB )) or resid 206 through 256 or (resid \ 257 and (name N or name CA or name C or name O or name CB )) or resid 258 throu \ gh 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) or \ resid 289 through 290 or (resid 291 and (name N or name CA or name C or name O \ or name CB )) or resid 292 through 293 or (resid 294 through 295 and (name N or \ name CA or name C or name O or name CB )) or resid 296 through 317 or (resid 318 \ through 320 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 21 through 342 or resid 352 through 361 or (resid 362 and (name N or name CA or \ name C or name O or name CB )) or resid 363 through 408 or (resid 409 through 41 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 414 through \ 421 or (resid 422 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and (resid 33 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 through 81 or (res \ id 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throu \ gh 141 or (resid 142 and (name N or name CA or name C or name O or name CB )) or \ resid 143 through 191 or (resid 192 and (name N or name CA or name C or name O \ or name CB )) or resid 193 through 200 or (resid 201 and (name N or name CA or n \ ame C or name O or name CB )) or resid 202 through 204 or (resid 205 and (name N \ or name CA or name C or name O or name CB )) or resid 206 through 256 or (resid \ 257 and (name N or name CA or name C or name O or name CB )) or resid 258 throu \ gh 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) or \ resid 289 through 290 or (resid 291 and (name N or name CA or name C or name O \ or name CB )) or resid 292 through 293 or (resid 294 through 295 and (name N or \ name CA or name C or name O or name CB )) or resid 296 through 317 or (resid 318 \ through 320 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 21 through 342 or resid 352 through 408 or (resid 409 through 413 and (name N or \ name CA or name C or name O or name CB )) or resid 414 through 422)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.470 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: 0.010 Extract box with map and model: 1.000 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.110 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 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 : 0.003 0.090 30102 Z= 0.177 Angle : 0.511 8.170 41006 Z= 0.306 Chirality : 0.043 0.348 4386 Planarity : 0.004 0.032 5410 Dihedral : 7.752 82.264 10822 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.70 (0.12), residues: 3869 helix: 0.18 (0.13), residues: 1227 sheet: -0.29 (0.17), residues: 824 loop : -0.92 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 54 TYR 0.012 0.001 TYR J 392 PHE 0.012 0.001 PHE G 165 TRP 0.003 0.001 TRP G 294 HIS 0.001 0.000 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.18 (30102) covalent geometry : angle 0.51073 / 0.31 (41006) hydrogen bonds : bond 0.17911 / 11.73 ( 1251) hydrogen bonds : angle 6.66449 / 4.78 ( 4104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 418 time to evaluate : 1.180 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.6241 (ttm) cc_final: 0.5289 (ptt) REVERT: B 194 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8557 (mp) REVERT: B 367 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7382 (ttp80) REVERT: C 191 ASN cc_start: 0.8391 (m-40) cc_final: 0.8162 (m-40) REVERT: C 321 ILE cc_start: 0.8865 (mt) cc_final: 0.8583 (mp) REVERT: D 302 ASN cc_start: 0.8707 (m-40) cc_final: 0.8462 (m110) REVERT: D 321 ILE cc_start: 0.9113 (mt) cc_final: 0.8898 (mp) REVERT: D 379 TYR cc_start: 0.8649 (p90) cc_final: 0.8341 (p90) REVERT: E 321 ILE cc_start: 0.8864 (mt) cc_final: 0.8637 (mp) REVERT: G 245 MET cc_start: 0.7579 (ttm) cc_final: 0.7363 (ttp) REVERT: J 42 MET cc_start: 0.6714 (ttm) cc_final: 0.6315 (mtp) REVERT: J 245 MET cc_start: 0.7589 (ttm) cc_final: 0.7344 (ttp) outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 0.8885 time to fit residues: 421.8911 Evaluate side-chains 212 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 159 HIS A 361 ASN B 57 GLN B 159 HIS B 205 GLN B 236 ASN B 264 HIS C 57 GLN C 113 GLN C 159 HIS C 187 GLN D 57 GLN D 159 HIS E 57 GLN E 159 HIS E 205 GLN F 57 GLN F 159 HIS F 205 GLN G 57 GLN G 159 HIS G 187 GLN G 205 GLN G 295 ASN H 57 GLN H 159 HIS H 205 GLN H 236 ASN I 57 GLN I 159 HIS I 291 GLN J 57 GLN J 159 HIS J 205 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.071406 restraints weight = 38556.012| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.58 r_work: 0.2608 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 30102 Z= 0.267 Angle : 0.611 10.030 41006 Z= 0.321 Chirality : 0.049 0.201 4386 Planarity : 0.004 0.039 5410 Dihedral : 4.289 59.520 4201 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.93 % Allowed : 7.04 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.29 (0.13), residues: 3869 helix: 1.27 (0.14), residues: 1226 sheet: -0.11 (0.17), residues: 814 loop : -0.31 (0.13), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 85 TYR 0.017 0.002 TYR I 74 PHE 0.017 0.003 PHE I 165 TRP 0.022 0.002 TRP A 294 HIS 0.004 0.001 HIS I 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.27 (30102) covalent geometry : angle 0.61134 / 0.32 (41006) hydrogen bonds : bond 0.05258 / 3.48 ( 1251) hydrogen bonds : angle 5.32356 / 3.84 ( 4104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 1.175 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: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8647 (mttt) cc_final: 0.8425 (mtpp) REVERT: A 194 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8339 (mp) REVERT: B 42 MET cc_start: 0.5556 (ttm) cc_final: 0.4734 (ptt) REVERT: B 97 ASP cc_start: 0.8801 (t0) cc_final: 0.8547 (t0) REVERT: B 130 LYS cc_start: 0.8671 (mttt) cc_final: 0.8419 (mtpp) REVERT: B 194 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8692 (mp) REVERT: B 367 ARG cc_start: 0.7961 (ttm170) cc_final: 0.7481 (ttp80) REVERT: C 245 MET cc_start: 0.8118 (ttm) cc_final: 0.7661 (tpp) REVERT: D 130 LYS cc_start: 0.8692 (mttt) cc_final: 0.8438 (mtpp) REVERT: D 194 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8770 (mp) REVERT: D 245 MET cc_start: 0.8410 (mtp) cc_final: 0.7844 (tpp) REVERT: D 367 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7661 (mtp180) REVERT: D 379 TYR cc_start: 0.8910 (p90) cc_final: 0.8639 (p90) REVERT: E 42 MET cc_start: 0.5295 (mtp) cc_final: 0.4932 (ptt) REVERT: E 97 ASP cc_start: 0.8839 (t0) cc_final: 0.8533 (t0) REVERT: E 130 LYS cc_start: 0.8708 (mttt) cc_final: 0.8437 (mtpp) REVERT: E 367 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7518 (mtp-110) REVERT: F 96 GLU cc_start: 0.8531 (pm20) cc_final: 0.8310 (pm20) REVERT: F 245 MET cc_start: 0.8791 (ttp) cc_final: 0.8536 (mmp) REVERT: F 375 LYS cc_start: 0.8901 (mttm) cc_final: 0.8613 (mttm) REVERT: G 198 VAL cc_start: 0.8590 (t) cc_final: 0.8244 (m) REVERT: G 245 MET cc_start: 0.8661 (ttm) cc_final: 0.8454 (mmm) REVERT: G 318 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8514 (mmtp) REVERT: H 97 ASP cc_start: 0.8941 (t0) cc_final: 0.8726 (t70) REVERT: H 318 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8725 (mttp) REVERT: H 375 LYS cc_start: 0.8848 (mttm) cc_final: 0.8587 (mttm) REVERT: I 172 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8395 (pp20) REVERT: I 375 LYS cc_start: 0.8860 (mttm) cc_final: 0.8554 (mttm) REVERT: J 96 GLU cc_start: 0.8488 (pm20) cc_final: 0.8253 (pm20) REVERT: J 245 MET cc_start: 0.8684 (ttm) cc_final: 0.8444 (mmp) REVERT: J 318 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8743 (mtmp) outliers start: 28 outliers final: 2 residues processed: 220 average time/residue: 0.9122 time to fit residues: 228.1393 Evaluate side-chains 205 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain G residue 318 LYS Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 318 LYS Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain J residue 318 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 232 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 31 optimal weight: 50.0000 chunk 219 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 187 optimal weight: 40.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.124205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.070984 restraints weight = 38373.683| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.57 r_work: 0.2599 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30102 Z= 0.219 Angle : 0.563 5.906 41006 Z= 0.294 Chirality : 0.047 0.181 4386 Planarity : 0.004 0.034 5410 Dihedral : 4.313 57.288 4201 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.23 % Allowed : 8.14 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.60 (0.13), residues: 3869 helix: 1.58 (0.15), residues: 1233 sheet: -0.11 (0.17), residues: 786 loop : -0.09 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 54 TYR 0.012 0.002 TYR H 66 PHE 0.014 0.002 PHE G 165 TRP 0.013 0.002 TRP A 294 HIS 0.003 0.001 HIS D 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (30102) covalent geometry : angle 0.56282 / 0.29 (41006) hydrogen bonds : bond 0.04878 / 3.23 ( 1251) hydrogen bonds : angle 5.14670 / 3.71 ( 4104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.903 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8626 (mttt) cc_final: 0.8402 (mtpp) REVERT: A 194 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8391 (mp) REVERT: A 329 ASP cc_start: 0.8686 (m-30) cc_final: 0.8344 (m-30) REVERT: A 370 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7739 (mtm180) REVERT: A 373 GLU cc_start: 0.8559 (tp30) cc_final: 0.8284 (tp30) REVERT: B 97 ASP cc_start: 0.8829 (t0) cc_final: 0.8534 (t0) REVERT: B 130 LYS cc_start: 0.8668 (mttt) cc_final: 0.8405 (mtpp) REVERT: B 173 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8697 (mm110) REVERT: B 194 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8717 (mp) REVERT: B 367 ARG cc_start: 0.7983 (ttm170) cc_final: 0.7375 (ttp80) REVERT: C 194 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8476 (mp) REVERT: C 245 MET cc_start: 0.8170 (ttm) cc_final: 0.7653 (tpp) REVERT: C 367 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7820 (mtp180) REVERT: C 370 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8198 (ptp90) REVERT: D 130 LYS cc_start: 0.8672 (mttt) cc_final: 0.8400 (mtpp) REVERT: D 245 MET cc_start: 0.8442 (mtp) cc_final: 0.7871 (tpp) REVERT: D 367 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7673 (mtp180) REVERT: E 97 ASP cc_start: 0.8844 (t0) cc_final: 0.8565 (t0) REVERT: E 130 LYS cc_start: 0.8700 (mttt) cc_final: 0.8434 (mtpp) REVERT: E 286 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7630 (t70) REVERT: F 96 GLU cc_start: 0.8508 (pm20) cc_final: 0.8278 (pm20) REVERT: F 194 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8887 (mp) REVERT: F 245 MET cc_start: 0.8748 (ttp) cc_final: 0.8496 (mmp) REVERT: F 375 LYS cc_start: 0.8918 (mttm) cc_final: 0.8636 (mttp) REVERT: F 389 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.7958 (pp-130) REVERT: G 42 MET cc_start: 0.5639 (ttm) cc_final: 0.5311 (ptt) REVERT: G 97 ASP cc_start: 0.8900 (t0) cc_final: 0.8625 (t0) REVERT: G 194 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9045 (mp) REVERT: G 245 MET cc_start: 0.8630 (ttm) cc_final: 0.8430 (mmm) REVERT: G 318 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8572 (mmtp) REVERT: H 97 ASP cc_start: 0.8947 (t0) cc_final: 0.8688 (t70) REVERT: H 375 LYS cc_start: 0.8822 (mttm) cc_final: 0.8559 (mttm) REVERT: I 42 MET cc_start: 0.6000 (ttt) cc_final: 0.5738 (ptp) REVERT: I 97 ASP cc_start: 0.8954 (t0) cc_final: 0.8664 (t0) REVERT: I 172 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8390 (pp20) REVERT: I 294 TRP cc_start: 0.8038 (OUTLIER) cc_final: 0.6493 (p90) REVERT: I 375 LYS cc_start: 0.8868 (mttm) cc_final: 0.8533 (mttm) REVERT: J 96 GLU cc_start: 0.8550 (pm20) cc_final: 0.8296 (pm20) REVERT: J 97 ASP cc_start: 0.8945 (t0) cc_final: 0.8703 (t0) REVERT: J 245 MET cc_start: 0.8673 (ttm) cc_final: 0.8443 (mmt) outliers start: 37 outliers final: 8 residues processed: 219 average time/residue: 0.8948 time to fit residues: 223.5496 Evaluate side-chains 217 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 294 TRP Chi-restraints excluded: chain F residue 318 LYS Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 294 TRP Chi-restraints excluded: chain G residue 318 LYS Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 294 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 247 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 276 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN H 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.072317 restraints weight = 38087.908| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.56 r_work: 0.2629 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30102 Z= 0.148 Angle : 0.515 5.784 41006 Z= 0.268 Chirality : 0.044 0.175 4386 Planarity : 0.004 0.033 5410 Dihedral : 4.138 56.709 4201 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.17 % Allowed : 8.51 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.80 (0.13), residues: 3869 helix: 1.81 (0.15), residues: 1237 sheet: -0.18 (0.18), residues: 767 loop : 0.08 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.010 0.001 TYR G 66 PHE 0.013 0.002 PHE J 165 TRP 0.009 0.001 TRP A 294 HIS 0.002 0.001 HIS J 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (30102) covalent geometry : angle 0.51503 / 0.27 (41006) hydrogen bonds : bond 0.04221 / 2.79 ( 1251) hydrogen bonds : angle 4.89206 / 3.52 ( 4104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 1.208 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8560 (mttt) cc_final: 0.8332 (mtpp) REVERT: A 194 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8375 (mp) REVERT: A 321 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8690 (mp) REVERT: B 97 ASP cc_start: 0.8820 (t0) cc_final: 0.8480 (t0) REVERT: B 130 LYS cc_start: 0.8603 (mttt) cc_final: 0.8338 (mtpp) REVERT: B 173 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8688 (mm110) REVERT: B 194 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8641 (mp) REVERT: B 321 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8720 (mp) REVERT: B 367 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7493 (ttp80) REVERT: C 245 MET cc_start: 0.8137 (ttm) cc_final: 0.7624 (tpp) REVERT: C 367 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7737 (mtp180) REVERT: C 370 ARG cc_start: 0.8671 (mtp85) cc_final: 0.8350 (ptp90) REVERT: D 130 LYS cc_start: 0.8608 (mttt) cc_final: 0.8330 (mtpp) REVERT: D 367 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7682 (mtp180) REVERT: E 97 ASP cc_start: 0.8844 (t0) cc_final: 0.8541 (t0) REVERT: E 130 LYS cc_start: 0.8637 (mttt) cc_final: 0.8368 (mtpp) REVERT: E 286 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7577 (t70) REVERT: E 321 ILE cc_start: 0.8896 (mt) cc_final: 0.8646 (mp) REVERT: F 96 GLU cc_start: 0.8490 (pm20) cc_final: 0.8207 (pm20) REVERT: F 245 MET cc_start: 0.8707 (ttp) cc_final: 0.8457 (mmt) REVERT: F 375 LYS cc_start: 0.8915 (mttm) cc_final: 0.8702 (mttp) REVERT: G 97 ASP cc_start: 0.8899 (t0) cc_final: 0.8582 (t0) REVERT: G 194 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9011 (mp) REVERT: G 245 MET cc_start: 0.8601 (ttm) cc_final: 0.8398 (mmm) REVERT: G 318 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8548 (mmtp) REVERT: H 96 GLU cc_start: 0.8610 (pm20) cc_final: 0.8376 (pm20) REVERT: H 97 ASP cc_start: 0.8928 (t0) cc_final: 0.8654 (t70) REVERT: H 375 LYS cc_start: 0.8811 (mttm) cc_final: 0.8579 (mttp) REVERT: I 97 ASP cc_start: 0.8935 (t0) cc_final: 0.8615 (t0) REVERT: I 172 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8436 (pp20) REVERT: I 294 TRP cc_start: 0.8027 (OUTLIER) cc_final: 0.6491 (p90) REVERT: I 367 ARG cc_start: 0.8728 (ttp80) cc_final: 0.8459 (ttp-110) REVERT: I 375 LYS cc_start: 0.8871 (mttm) cc_final: 0.8652 (mttp) REVERT: J 96 GLU cc_start: 0.8573 (pm20) cc_final: 0.8288 (pm20) REVERT: J 97 ASP cc_start: 0.8912 (t0) cc_final: 0.8658 (t0) REVERT: J 245 MET cc_start: 0.8647 (ttm) cc_final: 0.8401 (mmp) outliers start: 35 outliers final: 7 residues processed: 220 average time/residue: 0.8554 time to fit residues: 214.8792 Evaluate side-chains 217 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 294 TRP Chi-restraints excluded: chain G residue 318 LYS Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 294 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 161 optimal weight: 0.9990 chunk 376 optimal weight: 10.0000 chunk 314 optimal weight: 3.9990 chunk 283 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 ASN C 264 HIS F 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.125944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.073154 restraints weight = 38241.805| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.55 r_work: 0.2646 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30102 Z= 0.126 Angle : 0.495 5.768 41006 Z= 0.257 Chirality : 0.044 0.170 4386 Planarity : 0.004 0.033 5410 Dihedral : 4.000 55.590 4201 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.07 % Allowed : 8.77 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.95 (0.13), residues: 3869 helix: 1.97 (0.15), residues: 1237 sheet: -0.17 (0.18), residues: 768 loop : 0.17 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 319 TYR 0.009 0.001 TYR J 66 PHE 0.012 0.001 PHE B 314 TRP 0.008 0.001 TRP C 76 HIS 0.002 0.000 HIS J 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (30102) covalent geometry : angle 0.49538 / 0.26 (41006) hydrogen bonds : bond 0.03898 / 2.58 ( 1251) hydrogen bonds : angle 4.72447 / 3.40 ( 4104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 1.253 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8529 (mttt) cc_final: 0.8308 (mtpp) REVERT: A 194 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8385 (mp) REVERT: A 321 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8673 (mp) REVERT: B 97 ASP cc_start: 0.8806 (t0) cc_final: 0.8439 (t0) REVERT: B 130 LYS cc_start: 0.8585 (mttt) cc_final: 0.8322 (mtpp) REVERT: B 194 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8640 (mp) REVERT: B 367 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7496 (ttp80) REVERT: C 194 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8424 (mp) REVERT: C 245 MET cc_start: 0.8130 (ttm) cc_final: 0.7607 (tpp) REVERT: C 367 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7735 (mtp180) REVERT: C 370 ARG cc_start: 0.8642 (mtp85) cc_final: 0.8255 (ptp90) REVERT: D 130 LYS cc_start: 0.8572 (mttt) cc_final: 0.8310 (mtpp) REVERT: D 367 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7685 (mtp180) REVERT: E 97 ASP cc_start: 0.8839 (t0) cc_final: 0.8613 (t70) REVERT: E 130 LYS cc_start: 0.8623 (mttt) cc_final: 0.8362 (mtpp) REVERT: E 194 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8628 (mp) REVERT: E 286 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7592 (t70) REVERT: F 96 GLU cc_start: 0.8507 (pm20) cc_final: 0.8202 (pm20) REVERT: F 194 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8856 (mp) REVERT: F 245 MET cc_start: 0.8681 (ttp) cc_final: 0.8434 (mmt) REVERT: F 375 LYS cc_start: 0.8907 (mttm) cc_final: 0.8657 (mttp) REVERT: G 97 ASP cc_start: 0.8898 (t0) cc_final: 0.8541 (t0) REVERT: G 194 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8984 (mp) REVERT: H 96 GLU cc_start: 0.8631 (pm20) cc_final: 0.8316 (pm20) REVERT: H 97 ASP cc_start: 0.8927 (t0) cc_final: 0.8635 (t70) REVERT: H 370 ARG cc_start: 0.8305 (ptp90) cc_final: 0.8085 (ptp90) REVERT: H 375 LYS cc_start: 0.8811 (mttm) cc_final: 0.8543 (mttp) REVERT: I 97 ASP cc_start: 0.8923 (t0) cc_final: 0.8571 (t0) REVERT: I 172 GLU cc_start: 0.8814 (pt0) cc_final: 0.8472 (pp20) REVERT: I 294 TRP cc_start: 0.8052 (OUTLIER) cc_final: 0.6542 (p90) REVERT: I 375 LYS cc_start: 0.8866 (mttm) cc_final: 0.8606 (mttp) REVERT: J 96 GLU cc_start: 0.8598 (pm20) cc_final: 0.8296 (pm20) REVERT: J 97 ASP cc_start: 0.8918 (t0) cc_final: 0.8652 (t0) REVERT: J 245 MET cc_start: 0.8640 (ttm) cc_final: 0.8406 (mmt) outliers start: 32 outliers final: 11 residues processed: 222 average time/residue: 0.8109 time to fit residues: 206.7254 Evaluate side-chains 223 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 294 TRP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 294 TRP Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 294 TRP Chi-restraints excluded: chain J residue 73 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 285 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 109 optimal weight: 50.0000 chunk 75 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 361 optimal weight: 6.9990 chunk 297 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN G 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.069502 restraints weight = 38392.881| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.54 r_work: 0.2572 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 30102 Z= 0.312 Angle : 0.600 5.948 41006 Z= 0.314 Chirality : 0.049 0.178 4386 Planarity : 0.004 0.031 5410 Dihedral : 4.557 55.637 4201 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.30 % Allowed : 8.71 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.70 (0.13), residues: 3869 helix: 1.64 (0.15), residues: 1233 sheet: -0.07 (0.17), residues: 800 loop : 0.01 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 85 TYR 0.012 0.002 TYR J 66 PHE 0.020 0.002 PHE E 201 TRP 0.013 0.002 TRP H 249 HIS 0.004 0.001 HIS D 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.31 (30102) covalent geometry : angle 0.59950 / 0.31 (41006) hydrogen bonds : bond 0.05229 / 3.46 ( 1251) hydrogen bonds : angle 5.17120 / 3.73 ( 4104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 1.212 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8729 (mttt) cc_final: 0.8494 (mtpp) REVERT: A 194 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8481 (mp) REVERT: A 370 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7285 (mtm-85) REVERT: B 130 LYS cc_start: 0.8743 (mttt) cc_final: 0.8494 (mtpp) REVERT: B 367 ARG cc_start: 0.8059 (ttm170) cc_final: 0.7528 (ttp80) REVERT: C 194 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8581 (mp) REVERT: C 367 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7896 (mtp180) REVERT: C 370 ARG cc_start: 0.8697 (mtp85) cc_final: 0.8362 (ptp90) REVERT: D 130 LYS cc_start: 0.8767 (mttt) cc_final: 0.8510 (mtpp) REVERT: D 367 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7716 (mtp180) REVERT: D 370 ARG cc_start: 0.8586 (mtp85) cc_final: 0.8367 (ptp90) REVERT: E 42 MET cc_start: 0.5262 (mtp) cc_final: 0.5009 (ptt) REVERT: E 97 ASP cc_start: 0.8895 (t0) cc_final: 0.8629 (t70) REVERT: E 130 LYS cc_start: 0.8775 (mttt) cc_final: 0.8571 (mtpp) REVERT: E 194 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8735 (mp) REVERT: E 286 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7682 (t70) REVERT: F 96 GLU cc_start: 0.8576 (pm20) cc_final: 0.8285 (pm20) REVERT: F 194 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.8969 (mp) REVERT: F 245 MET cc_start: 0.8770 (ttp) cc_final: 0.8544 (mmt) REVERT: F 318 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8812 (mttp) REVERT: F 375 LYS cc_start: 0.8889 (mttm) cc_final: 0.8593 (mttp) REVERT: F 389 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.7978 (pp-130) REVERT: G 42 MET cc_start: 0.5638 (ttm) cc_final: 0.5247 (ptt) REVERT: G 97 ASP cc_start: 0.8971 (t0) cc_final: 0.8717 (t0) REVERT: G 194 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9117 (mp) REVERT: G 318 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8620 (mmtp) REVERT: H 96 GLU cc_start: 0.8645 (pm20) cc_final: 0.8263 (pm20) REVERT: H 367 ARG cc_start: 0.8743 (ttp80) cc_final: 0.8517 (ttp-110) REVERT: H 389 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8564 (pp-130) REVERT: I 97 ASP cc_start: 0.8963 (t0) cc_final: 0.8730 (t0) REVERT: I 172 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8482 (pp20) REVERT: I 294 TRP cc_start: 0.8106 (OUTLIER) cc_final: 0.6458 (p90) REVERT: I 375 LYS cc_start: 0.8833 (mttm) cc_final: 0.8523 (mttp) REVERT: J 96 GLU cc_start: 0.8621 (pm20) cc_final: 0.8327 (pm20) outliers start: 39 outliers final: 13 residues processed: 214 average time/residue: 0.8478 time to fit residues: 206.9111 Evaluate side-chains 220 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 367 ARG Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 294 TRP Chi-restraints excluded: chain F residue 318 LYS Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 294 TRP Chi-restraints excluded: chain G residue 318 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 389 MET Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 294 TRP Chi-restraints excluded: chain J residue 73 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 10 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 276 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 364 optimal weight: 0.6980 chunk 355 optimal weight: 4.9990 chunk 294 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 371 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN J 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.125913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.073414 restraints weight = 38269.598| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.55 r_work: 0.2654 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30102 Z= 0.108 Angle : 0.490 6.266 41006 Z= 0.255 Chirality : 0.043 0.168 4386 Planarity : 0.004 0.034 5410 Dihedral : 3.932 15.499 4199 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.07 % Allowed : 9.01 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.94 (0.13), residues: 3869 helix: 1.94 (0.15), residues: 1237 sheet: -0.17 (0.18), residues: 768 loop : 0.18 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 319 TYR 0.008 0.001 TYR J 66 PHE 0.017 0.001 PHE E 201 TRP 0.009 0.001 TRP C 76 HIS 0.001 0.000 HIS J 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (30102) covalent geometry : angle 0.49014 / 0.26 (41006) hydrogen bonds : bond 0.03704 / 2.45 ( 1251) hydrogen bonds : angle 4.68802 / 3.37 ( 4104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 1.213 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.5524 (ttm) cc_final: 0.4396 (ptt) REVERT: A 130 LYS cc_start: 0.8534 (mttt) cc_final: 0.8305 (mtpp) REVERT: B 130 LYS cc_start: 0.8597 (mttt) cc_final: 0.8336 (mtpp) REVERT: B 367 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7454 (ttp80) REVERT: C 367 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7753 (mtp180) REVERT: C 370 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8298 (ptp90) REVERT: D 130 LYS cc_start: 0.8577 (mttt) cc_final: 0.8302 (mtpp) REVERT: D 367 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7658 (mtp180) REVERT: D 370 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8340 (ptp90) REVERT: E 97 ASP cc_start: 0.8838 (t0) cc_final: 0.8569 (t70) REVERT: E 130 LYS cc_start: 0.8605 (mttt) cc_final: 0.8357 (mtpp) REVERT: E 286 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7556 (t70) REVERT: F 96 GLU cc_start: 0.8531 (pm20) cc_final: 0.8215 (pm20) REVERT: F 245 MET cc_start: 0.8669 (ttp) cc_final: 0.8420 (mmp) REVERT: F 375 LYS cc_start: 0.8886 (mttm) cc_final: 0.8580 (mttp) REVERT: G 97 ASP cc_start: 0.8923 (t0) cc_final: 0.8562 (t0) REVERT: G 194 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8986 (mp) REVERT: G 318 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8533 (mmtp) REVERT: G 370 ARG cc_start: 0.8325 (ptp90) cc_final: 0.8095 (ptp-110) REVERT: H 96 GLU cc_start: 0.8629 (pm20) cc_final: 0.8219 (pm20) REVERT: H 367 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8492 (ttp-110) REVERT: I 97 ASP cc_start: 0.8964 (t0) cc_final: 0.8626 (t0) REVERT: I 172 GLU cc_start: 0.8821 (pt0) cc_final: 0.8478 (pp20) REVERT: I 294 TRP cc_start: 0.8014 (OUTLIER) cc_final: 0.6475 (p90) REVERT: I 367 ARG cc_start: 0.8735 (ttp80) cc_final: 0.8439 (ttp-110) REVERT: I 375 LYS cc_start: 0.8843 (mttm) cc_final: 0.8531 (mttp) REVERT: J 96 GLU cc_start: 0.8586 (pm20) cc_final: 0.8173 (pm20) outliers start: 32 outliers final: 10 residues processed: 217 average time/residue: 0.8556 time to fit residues: 212.3251 Evaluate side-chains 213 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 294 TRP Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 294 TRP Chi-restraints excluded: chain G residue 318 LYS Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 294 TRP Chi-restraints excluded: chain J residue 73 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 294 optimal weight: 0.6980 chunk 341 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 156 optimal weight: 30.0000 chunk 101 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 332 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.070522 restraints weight = 38031.600| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.53 r_work: 0.2587 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30102 Z= 0.211 Angle : 0.553 6.366 41006 Z= 0.289 Chirality : 0.046 0.172 4386 Planarity : 0.004 0.051 5410 Dihedral : 4.234 16.700 4199 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.87 % Allowed : 9.17 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.86 (0.13), residues: 3869 helix: 1.79 (0.15), residues: 1237 sheet: -0.02 (0.18), residues: 764 loop : 0.10 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 319 TYR 0.011 0.002 TYR F 66 PHE 0.025 0.002 PHE E 201 TRP 0.010 0.001 TRP H 249 HIS 0.002 0.001 HIS C 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (30102) covalent geometry : angle 0.55307 / 0.29 (41006) hydrogen bonds : bond 0.04625 / 3.06 ( 1251) hydrogen bonds : angle 4.98430 / 3.59 ( 4104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.324 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8580 (mttt) cc_final: 0.8328 (mtpp) REVERT: A 194 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8370 (mp) REVERT: B 130 LYS cc_start: 0.8605 (mttt) cc_final: 0.8337 (mtpp) REVERT: B 367 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7451 (ttp80) REVERT: B 370 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7803 (mtp180) REVERT: C 194 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8460 (mp) REVERT: C 321 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8688 (mp) REVERT: C 367 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7752 (mtp180) REVERT: C 370 ARG cc_start: 0.8660 (mtp85) cc_final: 0.8274 (ptp90) REVERT: D 130 LYS cc_start: 0.8620 (mttt) cc_final: 0.8337 (mtpp) REVERT: D 367 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7675 (mtp180) REVERT: D 370 ARG cc_start: 0.8608 (mtp85) cc_final: 0.8379 (ptp90) REVERT: E 97 ASP cc_start: 0.8845 (t0) cc_final: 0.8548 (t70) REVERT: E 130 LYS cc_start: 0.8645 (mttt) cc_final: 0.8379 (mtpp) REVERT: E 245 MET cc_start: 0.8416 (ttp) cc_final: 0.7666 (mmp) REVERT: E 286 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7592 (t70) REVERT: F 96 GLU cc_start: 0.8543 (pm20) cc_final: 0.8217 (pm20) REVERT: F 245 MET cc_start: 0.8686 (ttp) cc_final: 0.8394 (mmt) REVERT: G 42 MET cc_start: 0.5581 (ttm) cc_final: 0.5191 (ptt) REVERT: G 97 ASP cc_start: 0.8937 (t0) cc_final: 0.8608 (t0) REVERT: G 194 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9017 (mp) REVERT: G 318 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8539 (mmtp) REVERT: G 367 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8441 (ttp-110) REVERT: G 370 ARG cc_start: 0.8342 (ptp90) cc_final: 0.8134 (ptp-110) REVERT: H 96 GLU cc_start: 0.8646 (pm20) cc_final: 0.8214 (pm20) REVERT: H 367 ARG cc_start: 0.8691 (ttp80) cc_final: 0.8465 (ttp-110) REVERT: I 97 ASP cc_start: 0.8960 (t0) cc_final: 0.8653 (t0) REVERT: I 172 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8461 (pp20) REVERT: I 294 TRP cc_start: 0.7999 (OUTLIER) cc_final: 0.6346 (p90) REVERT: I 367 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8379 (ttp-110) REVERT: I 375 LYS cc_start: 0.8822 (mttm) cc_final: 0.8502 (mttp) REVERT: J 96 GLU cc_start: 0.8605 (pm20) cc_final: 0.8257 (pm20) outliers start: 26 outliers final: 11 residues processed: 209 average time/residue: 0.9001 time to fit residues: 214.4705 Evaluate side-chains 213 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 367 ARG Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 294 TRP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 294 TRP Chi-restraints excluded: chain G residue 318 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 294 TRP Chi-restraints excluded: chain J residue 73 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 323 optimal weight: 0.5980 chunk 327 optimal weight: 0.8980 chunk 338 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 162 optimal weight: 0.0870 chunk 105 optimal weight: 10.0000 chunk 191 optimal weight: 0.4980 chunk 297 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.074373 restraints weight = 38061.180| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.55 r_work: 0.2667 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 30102 Z= 0.099 Angle : 0.488 6.659 41006 Z= 0.254 Chirality : 0.043 0.167 4386 Planarity : 0.004 0.051 5410 Dihedral : 3.782 15.317 4199 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.70 % Allowed : 9.44 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.03 (0.13), residues: 3869 helix: 2.00 (0.15), residues: 1237 sheet: -0.13 (0.18), residues: 768 loop : 0.25 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 319 TYR 0.008 0.001 TYR H 66 PHE 0.024 0.001 PHE E 201 TRP 0.012 0.001 TRP E 294 HIS 0.001 0.000 HIS J 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (30102) covalent geometry : angle 0.48800 / 0.25 (41006) hydrogen bonds : bond 0.03472 / 2.30 ( 1251) hydrogen bonds : angle 4.58308 / 3.30 ( 4104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.213 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: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.5543 (ttm) cc_final: 0.4351 (ptt) REVERT: A 130 LYS cc_start: 0.8479 (mttt) cc_final: 0.8252 (mtpp) REVERT: A 194 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8310 (mp) REVERT: B 130 LYS cc_start: 0.8538 (mttt) cc_final: 0.8281 (mtpp) REVERT: B 367 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7453 (ttp80) REVERT: C 194 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8373 (mp) REVERT: C 321 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8671 (mp) REVERT: C 367 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7727 (mtp180) REVERT: C 370 ARG cc_start: 0.8599 (mtp85) cc_final: 0.8245 (ptp90) REVERT: D 130 LYS cc_start: 0.8521 (mttt) cc_final: 0.8251 (mtpp) REVERT: D 367 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7725 (mtp180) REVERT: D 370 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8347 (ptp90) REVERT: E 97 ASP cc_start: 0.8825 (t0) cc_final: 0.8544 (t70) REVERT: E 130 LYS cc_start: 0.8570 (mttt) cc_final: 0.8315 (mtpp) REVERT: E 194 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8576 (mp) REVERT: E 286 ASP cc_start: 0.7976 (m-30) cc_final: 0.7512 (t70) REVERT: F 96 GLU cc_start: 0.8540 (pm20) cc_final: 0.8211 (pm20) REVERT: F 245 MET cc_start: 0.8619 (ttp) cc_final: 0.8361 (mmt) REVERT: F 370 ARG cc_start: 0.8357 (ptp90) cc_final: 0.8069 (ptp-110) REVERT: G 97 ASP cc_start: 0.8933 (t0) cc_final: 0.8529 (t0) REVERT: G 194 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8931 (mp) REVERT: G 367 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8459 (ttp-110) REVERT: G 370 ARG cc_start: 0.8368 (ptp90) cc_final: 0.8099 (ptp-170) REVERT: H 96 GLU cc_start: 0.8631 (pm20) cc_final: 0.8202 (pm20) REVERT: H 367 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8466 (ttp-110) REVERT: I 97 ASP cc_start: 0.8957 (t0) cc_final: 0.8620 (t0) REVERT: I 172 GLU cc_start: 0.8834 (pt0) cc_final: 0.8490 (pp20) REVERT: I 294 TRP cc_start: 0.7972 (OUTLIER) cc_final: 0.6414 (p90) REVERT: I 367 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8393 (ttp-110) REVERT: I 375 LYS cc_start: 0.8844 (mttm) cc_final: 0.8522 (mttp) REVERT: J 42 MET cc_start: 0.5981 (mtp) cc_final: 0.5354 (ptt) REVERT: J 96 GLU cc_start: 0.8566 (pm20) cc_final: 0.8230 (pm20) REVERT: J 97 ASP cc_start: 0.8939 (t70) cc_final: 0.8733 (t70) outliers start: 21 outliers final: 8 residues processed: 216 average time/residue: 0.9066 time to fit residues: 223.2579 Evaluate side-chains 214 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain F residue 294 TRP Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 294 TRP Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 294 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 37 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 250 optimal weight: 0.9990 chunk 25 optimal weight: 0.0570 chunk 361 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.073550 restraints weight = 37911.669| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.54 r_work: 0.2649 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30102 Z= 0.113 Angle : 0.506 7.624 41006 Z= 0.262 Chirality : 0.043 0.180 4386 Planarity : 0.004 0.054 5410 Dihedral : 3.821 14.909 4199 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.53 % Allowed : 9.61 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.08 (0.13), residues: 3869 helix: 2.03 (0.15), residues: 1237 sheet: -0.09 (0.19), residues: 768 loop : 0.29 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 319 TYR 0.008 0.001 TYR H 232 PHE 0.021 0.001 PHE E 201 TRP 0.014 0.001 TRP E 294 HIS 0.001 0.000 HIS J 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (30102) covalent geometry : angle 0.50606 / 0.26 (41006) hydrogen bonds : bond 0.03676 / 2.43 ( 1251) hydrogen bonds : angle 4.60534 / 3.31 ( 4104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7738 Ramachandran restraints generated. 3869 Oldfield, 0 Emsley, 3869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 1.179 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: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.5593 (ttm) cc_final: 0.4380 (ptt) REVERT: A 130 LYS cc_start: 0.8481 (mttt) cc_final: 0.8257 (mtpp) REVERT: B 130 LYS cc_start: 0.8541 (mttt) cc_final: 0.8288 (mtpp) REVERT: B 367 ARG cc_start: 0.7987 (ttm170) cc_final: 0.7440 (ttp80) REVERT: C 321 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8656 (mp) REVERT: C 367 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7730 (mtp180) REVERT: C 370 ARG cc_start: 0.8606 (mtp85) cc_final: 0.8240 (ptp90) REVERT: C 379 TYR cc_start: 0.8855 (p90) cc_final: 0.8629 (p90) REVERT: D 130 LYS cc_start: 0.8523 (mttt) cc_final: 0.8254 (mtpp) REVERT: D 367 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7667 (mtp180) REVERT: D 370 ARG cc_start: 0.8564 (mtp85) cc_final: 0.8169 (ptp90) REVERT: E 97 ASP cc_start: 0.8819 (t0) cc_final: 0.8530 (t70) REVERT: E 130 LYS cc_start: 0.8573 (mttt) cc_final: 0.8318 (mtpp) REVERT: E 286 ASP cc_start: 0.7974 (m-30) cc_final: 0.7534 (t70) REVERT: F 96 GLU cc_start: 0.8541 (pm20) cc_final: 0.8211 (pm20) REVERT: F 245 MET cc_start: 0.8639 (ttp) cc_final: 0.8367 (mmp) REVERT: G 97 ASP cc_start: 0.8931 (t0) cc_final: 0.8546 (t0) REVERT: G 194 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8942 (mp) REVERT: G 367 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8450 (ttp-110) REVERT: G 370 ARG cc_start: 0.8368 (ptp90) cc_final: 0.8077 (ptp-170) REVERT: H 42 MET cc_start: 0.6084 (ptt) cc_final: 0.5871 (ptp) REVERT: H 96 GLU cc_start: 0.8647 (pm20) cc_final: 0.8208 (pm20) REVERT: H 367 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8460 (ttp-110) REVERT: I 97 ASP cc_start: 0.8960 (t0) cc_final: 0.8599 (t0) REVERT: I 172 GLU cc_start: 0.8828 (pt0) cc_final: 0.8477 (pp20) REVERT: I 294 TRP cc_start: 0.7958 (OUTLIER) cc_final: 0.6419 (p90) REVERT: I 367 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8377 (ttp-110) REVERT: I 375 LYS cc_start: 0.8846 (mttm) cc_final: 0.8532 (mttp) REVERT: J 42 MET cc_start: 0.5953 (mtp) cc_final: 0.5372 (ptt) REVERT: J 96 GLU cc_start: 0.8570 (pm20) cc_final: 0.8229 (pm20) outliers start: 16 outliers final: 8 residues processed: 205 average time/residue: 0.9011 time to fit residues: 210.1006 Evaluate side-chains 208 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain F residue 294 TRP Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 294 TRP Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 294 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 293 optimal weight: 1.9990 chunk 344 optimal weight: 9.9990 chunk 334 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 148 optimal weight: 50.0000 chunk 274 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 280 optimal weight: 0.2980 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.071002 restraints weight = 38129.739| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.56 r_work: 0.2591 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30102 Z= 0.192 Angle : 0.551 8.268 41006 Z= 0.287 Chirality : 0.045 0.180 4386 Planarity : 0.004 0.056 5410 Dihedral : 4.154 16.261 4199 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.67 % Allowed : 9.41 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.95 (0.13), residues: 3869 helix: 1.83 (0.15), residues: 1237 sheet: -0.06 (0.18), residues: 771 loop : 0.23 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 319 TYR 0.010 0.001 TYR F 66 PHE 0.019 0.002 PHE E 201 TRP 0.010 0.001 TRP A 294 HIS 0.002 0.001 HIS D 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (30102) covalent geometry : angle 0.55115 / 0.29 (41006) hydrogen bonds : bond 0.04483 / 2.96 ( 1251) hydrogen bonds : angle 4.91807 / 3.53 ( 4104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18744.25 seconds wall clock time: 317 minutes 58.56 seconds (19078.56 seconds total)