Starting phenix.real_space_refine on Thu Mar 5 19:54:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vfg_31952/03_2026/7vfg_31952.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vfg_31952/03_2026/7vfg_31952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vfg_31952/03_2026/7vfg_31952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vfg_31952/03_2026/7vfg_31952.map" model { file = "/net/cci-nas-00/data/ceres_data/7vfg_31952/03_2026/7vfg_31952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vfg_31952/03_2026/7vfg_31952.cif" } resolution = 3.87 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= 1.000 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 78 5.16 5 C 16032 2.51 5 N 4074 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25044 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Chain: "F" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Chain: "D" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Chain: "C" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Chain: "A" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Chain: "B" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS E 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 94 " occ=0.50 residue: pdb=" N ACYS F 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS F 94 " occ=0.50 residue: pdb=" N ACYS D 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 94 " occ=0.50 residue: pdb=" N ACYS C 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 94 " occ=0.50 residue: pdb=" N ACYS A 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 94 " occ=0.50 residue: pdb=" N ACYS B 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 94 " occ=0.50 Time building chain proxies: 9.99, per 1000 atoms: 0.40 Number of scatterers: 25044 At special positions: 0 Unit cell: (178.08, 110.88, 106.4, 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 78 16.00 O 4860 8.00 N 4074 7.00 C 16032 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: 1.92 Conformation dependent library (CDL) restraints added in 1.9 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6036 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 72 sheets defined 19.8% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.553A pdb=" N ASP E 163 " --> pdb=" O THR E 160 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL E 164 " --> pdb=" O PRO E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 160 through 164' Processing helix chain 'E' and resid 165 through 170 removed outlier: 3.621A pdb=" N SER E 170 " --> pdb=" O THR E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 189 Processing helix chain 'E' and resid 198 through 206 Processing helix chain 'E' and resid 279 through 295 removed outlier: 4.037A pdb=" N ASP E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 394 removed outlier: 3.797A pdb=" N THR E 393 " --> pdb=" O ASN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 401 removed outlier: 4.042A pdb=" N TRP E 400 " --> pdb=" O PRO E 396 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR E 401 " --> pdb=" O VAL E 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 396 through 401' Processing helix chain 'E' and resid 413 through 418 Processing helix chain 'E' and resid 458 through 469 Processing helix chain 'E' and resid 495 through 499 Processing helix chain 'E' and resid 516 through 521 Processing helix chain 'F' and resid 89 through 94 Processing helix chain 'F' and resid 112 through 119 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.894A pdb=" N VAL F 164 " --> pdb=" O PRO F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 189 Processing helix chain 'F' and resid 198 through 206 Processing helix chain 'F' and resid 279 through 295 removed outlier: 4.162A pdb=" N ASP F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP F 294 " --> pdb=" O ARG F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 394 removed outlier: 3.821A pdb=" N THR F 393 " --> pdb=" O ASN F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 401 removed outlier: 4.161A pdb=" N TRP F 400 " --> pdb=" O PRO F 396 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR F 401 " --> pdb=" O VAL F 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 396 through 401' Processing helix chain 'F' and resid 413 through 418 Processing helix chain 'F' and resid 458 through 469 Processing helix chain 'F' and resid 516 through 521 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.882A pdb=" N VAL D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 189 Processing helix chain 'D' and resid 198 through 206 Processing helix chain 'D' and resid 279 through 295 removed outlier: 4.271A pdb=" N ASP D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 394 removed outlier: 3.871A pdb=" N THR D 393 " --> pdb=" O ASN D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 removed outlier: 4.108A pdb=" N TRP D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 401' Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 495 through 499 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 112 through 119 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.553A pdb=" N ASP C 163 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C 164 " --> pdb=" O PRO C 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 160 through 164' Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.616A pdb=" N SER C 170 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 279 through 295 removed outlier: 4.038A pdb=" N ASP C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 394 removed outlier: 3.795A pdb=" N THR C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 removed outlier: 4.040A pdb=" N TRP C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 401' Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 495 through 499 Processing helix chain 'C' and resid 516 through 521 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.896A pdb=" N VAL A 164 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.164A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.819A pdb=" N THR A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 4.161A pdb=" N TRP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 401' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.882A pdb=" N VAL B 164 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 279 through 295 removed outlier: 4.268A pdb=" N ASP B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 394 removed outlier: 3.869A pdb=" N THR B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.106A pdb=" N TRP B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 401' Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'B' and resid 516 through 521 Processing sheet with id=AA1, first strand: chain 'E' and resid 32 through 40 removed outlier: 4.231A pdb=" N ILE E 215 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS E 68 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TYR E 217 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU E 66 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU E 69 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 152 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 32 through 40 removed outlier: 4.231A pdb=" N ILE E 215 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS E 68 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TYR E 217 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU E 66 " --> pdb=" O TYR E 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 42 through 44 removed outlier: 6.285A pdb=" N SER E 102 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 78 through 79 removed outlier: 6.805A pdb=" N VAL E 78 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 139 through 141 removed outlier: 3.845A pdb=" N GLY E 82 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 227 through 236 removed outlier: 4.489A pdb=" N GLN E 522 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN E 530 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER E 254 " --> pdb=" O ASN E 530 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU E 532 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA E 252 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA E 252 " --> pdb=" O ILE E 492 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 492 " --> pdb=" O ALA E 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 475 through 478 removed outlier: 3.827A pdb=" N ARG E 475 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA E 252 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU E 532 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER E 254 " --> pdb=" O ASN E 530 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN E 530 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN E 522 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 243 through 246 removed outlier: 3.669A pdb=" N ARG E 442 " --> pdb=" O VAL E 508 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR E 453 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE E 447 " --> pdb=" O VAL E 451 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL E 451 " --> pdb=" O PHE E 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 269 through 270 Processing sheet with id=AB1, first strand: chain 'E' and resid 296 through 299 removed outlier: 3.542A pdb=" N SER E 299 " --> pdb=" O SER E 340 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER E 340 " --> pdb=" O SER E 299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 320 through 323 removed outlier: 5.066A pdb=" N SER E 366 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE E 365 " --> pdb=" O HIS E 386 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N HIS E 386 " --> pdb=" O PHE E 365 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA E 367 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE E 384 " --> pdb=" O ALA E 367 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR E 369 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG E 378 " --> pdb=" O SER E 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 349 through 350 Processing sheet with id=AB4, first strand: chain 'F' and resid 32 through 40 removed outlier: 4.258A pdb=" N ILE F 215 " --> pdb=" O HIS F 68 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS F 68 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR F 217 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU F 66 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU F 69 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER F 152 " --> pdb=" O LEU F 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 32 through 40 removed outlier: 4.258A pdb=" N ILE F 215 " --> pdb=" O HIS F 68 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS F 68 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR F 217 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU F 66 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 42 through 44 removed outlier: 7.228A pdb=" N ASN F 96 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLU F 111 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL F 98 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU F 109 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE F 100 " --> pdb=" O ILE F 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 78 through 79 removed outlier: 6.924A pdb=" N VAL F 78 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.757A pdb=" N GLY F 82 " --> pdb=" O GLY F 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 227 through 236 removed outlier: 3.543A pdb=" N SER F 227 " --> pdb=" O VAL F 535 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL F 535 " --> pdb=" O SER F 227 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN F 530 " --> pdb=" O SER F 254 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER F 254 " --> pdb=" O ASN F 530 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU F 532 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA F 252 " --> pdb=" O LEU F 532 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 475 through 478 removed outlier: 3.900A pdb=" N ARG F 475 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA F 252 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU F 532 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER F 254 " --> pdb=" O ASN F 530 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN F 530 " --> pdb=" O SER F 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 243 through 246 removed outlier: 3.591A pdb=" N ARG F 442 " --> pdb=" O VAL F 508 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 443 " --> pdb=" O GLU F 455 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR F 453 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE F 447 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL F 451 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 269 through 270 Processing sheet with id=AC4, first strand: chain 'F' and resid 296 through 299 removed outlier: 3.704A pdb=" N SER F 299 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER F 340 " --> pdb=" O SER F 299 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 320 through 323 removed outlier: 6.554A pdb=" N ASP F 327 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE F 368 " --> pdb=" O ASP F 327 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR F 329 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY F 370 " --> pdb=" O TYR F 329 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS F 331 " --> pdb=" O GLY F 370 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TYR F 372 " --> pdb=" O LYS F 331 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP F 333 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE F 365 " --> pdb=" O HIS F 386 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N HIS F 386 " --> pdb=" O PHE F 365 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA F 367 " --> pdb=" O ILE F 384 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE F 384 " --> pdb=" O ALA F 367 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR F 369 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG F 378 " --> pdb=" O SER F 373 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 349 through 350 Processing sheet with id=AC7, first strand: chain 'D' and resid 32 through 40 removed outlier: 4.441A pdb=" N ILE D 215 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS D 68 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR D 217 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU D 66 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU D 69 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER D 152 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 32 through 40 removed outlier: 4.441A pdb=" N ILE D 215 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS D 68 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR D 217 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU D 66 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.663A pdb=" N ILE D 178 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN D 96 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU D 111 " --> pdb=" O ASN D 96 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL D 98 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE D 100 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 78 through 79 removed outlier: 6.777A pdb=" N VAL D 78 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AD3, first strand: chain 'D' and resid 227 through 236 removed outlier: 3.600A pdb=" N SER D 227 " --> pdb=" O VAL D 535 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D 530 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER D 254 " --> pdb=" O ASN D 530 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU D 532 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA D 252 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 252 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 475 through 478 removed outlier: 3.865A pdb=" N ARG D 475 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA D 252 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU D 532 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER D 254 " --> pdb=" O ASN D 530 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D 530 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 243 through 246 removed outlier: 3.864A pdb=" N ARG D 442 " --> pdb=" O VAL D 508 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 453 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE D 447 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AD7, first strand: chain 'D' and resid 296 through 299 removed outlier: 3.636A pdb=" N SER D 299 " --> pdb=" O SER D 340 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 320 through 323 removed outlier: 6.314A pdb=" N ASP D 327 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE D 368 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR D 329 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLY D 370 " --> pdb=" O TYR D 329 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS D 331 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR D 372 " --> pdb=" O LYS D 331 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP D 333 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE D 365 " --> pdb=" O HIS D 386 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N HIS D 386 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA D 367 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE D 384 " --> pdb=" O ALA D 367 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR D 369 " --> pdb=" O ALA D 382 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 349 through 350 Processing sheet with id=AE1, first strand: chain 'C' and resid 32 through 40 removed outlier: 4.234A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU C 69 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 152 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 32 through 40 removed outlier: 4.234A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.285A pdb=" N SER C 102 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.803A pdb=" N VAL C 78 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 139 through 141 removed outlier: 3.839A pdb=" N GLY C 82 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 227 through 236 removed outlier: 4.491A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 530 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C 252 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 492 " --> pdb=" O ALA C 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.828A pdb=" N ARG C 475 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 530 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 243 through 246 removed outlier: 3.666A pdb=" N ARG C 442 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 453 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE C 447 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AF1, first strand: chain 'C' and resid 296 through 299 removed outlier: 3.538A pdb=" N SER C 299 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 340 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 320 through 323 removed outlier: 5.062A pdb=" N SER C 366 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE C 365 " --> pdb=" O HIS C 386 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N HIS C 386 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA C 367 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE C 384 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR C 369 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 378 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AF4, first strand: chain 'A' and resid 32 through 40 removed outlier: 4.258A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A 69 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 152 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 32 through 40 removed outlier: 4.258A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 42 through 44 removed outlier: 7.224A pdb=" N ASN A 96 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU A 111 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 98 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU A 109 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 100 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.923A pdb=" N VAL A 78 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 139 through 141 removed outlier: 3.761A pdb=" N GLY A 82 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 227 through 236 removed outlier: 3.539A pdb=" N SER A 227 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 535 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 530 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.900A pdb=" N ARG A 475 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 530 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.590A pdb=" N ARG A 442 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 443 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 453 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE A 447 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AG4, first strand: chain 'A' and resid 296 through 299 removed outlier: 3.702A pdb=" N SER A 299 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 340 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 320 through 323 removed outlier: 6.562A pdb=" N ASP A 327 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE A 368 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR A 329 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLY A 370 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS A 331 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N TYR A 372 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP A 333 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 365 " --> pdb=" O HIS A 386 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N HIS A 386 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA A 367 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE A 384 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR A 369 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 378 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AG7, first strand: chain 'B' and resid 32 through 40 removed outlier: 4.441A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU B 69 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 152 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 32 through 40 removed outlier: 4.441A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.663A pdb=" N ILE B 178 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN B 96 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU B 111 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 98 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU B 109 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 100 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.780A pdb=" N VAL B 78 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AH3, first strand: chain 'B' and resid 227 through 236 removed outlier: 3.602A pdb=" N SER B 227 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 530 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 252 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.862A pdb=" N ARG B 475 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 530 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 243 through 246 removed outlier: 3.868A pdb=" N ARG B 442 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 453 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE B 447 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AH7, first strand: chain 'B' and resid 296 through 299 removed outlier: 3.641A pdb=" N SER B 299 " --> pdb=" O SER B 340 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.301A pdb=" N ASP B 327 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE B 368 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR B 329 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLY B 370 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS B 331 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N TYR B 372 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASP B 333 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE B 365 " --> pdb=" O HIS B 386 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N HIS B 386 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA B 367 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE B 384 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B 369 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 349 through 350 984 hydrogen bonds defined for protein. 2610 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: 4.82 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7975 1.34 - 1.46: 4322 1.46 - 1.57: 13179 1.57 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 25602 Sorted by residual: bond pdb=" N ASP E 25 " pdb=" CA ASP E 25 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.24e-02 6.50e+03 5.22e+00 bond pdb=" N ASP C 25 " pdb=" CA ASP C 25 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.24e-02 6.50e+03 5.11e+00 bond pdb=" C PHE C 481 " pdb=" N THR C 482 " ideal model delta sigma weight residual 1.340 1.258 0.082 5.87e-02 2.90e+02 1.95e+00 bond pdb=" C PHE E 481 " pdb=" N THR E 482 " ideal model delta sigma weight residual 1.340 1.259 0.081 5.87e-02 2.90e+02 1.90e+00 bond pdb=" CG LYS A 93 " pdb=" CD LYS A 93 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.80e+00 ... (remaining 25597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 34128 2.30 - 4.59: 682 4.59 - 6.89: 36 6.89 - 9.18: 12 9.18 - 11.48: 2 Bond angle restraints: 34860 Sorted by residual: angle pdb=" C ARG D 233 " pdb=" CA ARG D 233 " pdb=" CB ARG D 233 " ideal model delta sigma weight residual 109.65 115.26 -5.61 1.75e+00 3.27e-01 1.03e+01 angle pdb=" C ARG B 233 " pdb=" CA ARG B 233 " pdb=" CB ARG B 233 " ideal model delta sigma weight residual 109.65 115.25 -5.60 1.75e+00 3.27e-01 1.02e+01 angle pdb=" N GLY E 409 " pdb=" CA GLY E 409 " pdb=" C GLY E 409 " ideal model delta sigma weight residual 113.18 120.34 -7.16 2.37e+00 1.78e-01 9.12e+00 angle pdb=" N GLY C 409 " pdb=" CA GLY C 409 " pdb=" C GLY C 409 " ideal model delta sigma weight residual 113.18 120.27 -7.09 2.37e+00 1.78e-01 8.94e+00 angle pdb=" C THR D 201 " pdb=" N PHE D 202 " pdb=" CA PHE D 202 " ideal model delta sigma weight residual 120.28 116.47 3.81 1.34e+00 5.57e-01 8.08e+00 ... (remaining 34855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 13837 17.32 - 34.64: 1256 34.64 - 51.96: 192 51.96 - 69.28: 47 69.28 - 86.60: 22 Dihedral angle restraints: 15354 sinusoidal: 5964 harmonic: 9390 Sorted by residual: dihedral pdb=" CA ARG B 353 " pdb=" C ARG B 353 " pdb=" N LYS B 354 " pdb=" CA LYS B 354 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ARG D 353 " pdb=" C ARG D 353 " pdb=" N LYS D 354 " pdb=" CA LYS D 354 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ARG E 353 " pdb=" C ARG E 353 " pdb=" N LYS E 354 " pdb=" CA LYS E 354 " ideal model delta harmonic sigma weight residual -180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 15351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2466 0.043 - 0.086: 1094 0.086 - 0.129: 424 0.129 - 0.172: 44 0.172 - 0.215: 10 Chirality restraints: 4038 Sorted by residual: chirality pdb=" CA TYR F 62 " pdb=" N TYR F 62 " pdb=" C TYR F 62 " pdb=" CB TYR F 62 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA TYR A 62 " pdb=" N TYR A 62 " pdb=" C TYR A 62 " pdb=" CB TYR A 62 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PRO F 144 " pdb=" N PRO F 144 " pdb=" C PRO F 144 " pdb=" CB PRO F 144 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 4035 not shown) Planarity restraints: 4446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 200 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.87e+00 pdb=" C GLU B 200 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU B 200 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 201 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 200 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C GLU D 200 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU D 200 " 0.019 2.00e-02 2.50e+03 pdb=" N THR D 201 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 200 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C GLU F 200 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU F 200 " -0.018 2.00e-02 2.50e+03 pdb=" N THR F 201 " -0.016 2.00e-02 2.50e+03 ... (remaining 4443 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1579 2.73 - 3.27: 22898 3.27 - 3.81: 37687 3.81 - 4.36: 45259 4.36 - 4.90: 79821 Nonbonded interactions: 187244 Sorted by model distance: nonbonded pdb=" OG SER C 356 " pdb=" N PHE C 357 " model vdw 2.182 3.120 nonbonded pdb=" OG SER E 356 " pdb=" N PHE E 357 " model vdw 2.182 3.120 nonbonded pdb=" O ILE F 390 " pdb=" OG1 THR F 393 " model vdw 2.217 3.040 nonbonded pdb=" O ILE A 390 " pdb=" OG1 THR A 393 " model vdw 2.218 3.040 nonbonded pdb=" OE2 GLU D 444 " pdb=" NH1 ARG D 446 " model vdw 2.247 3.120 ... (remaining 187239 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'B' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'C' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'D' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'E' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'F' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 28.530 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 25602 Z= 0.291 Angle : 0.788 11.477 34860 Z= 0.445 Chirality : 0.054 0.215 4038 Planarity : 0.005 0.050 4446 Dihedral : 13.861 86.599 9318 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.45 % Allowed : 10.44 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.13), residues: 3156 helix: -2.37 (0.18), residues: 438 sheet: -0.17 (0.15), residues: 984 loop : -0.71 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 461 TYR 0.026 0.003 TYR D 36 PHE 0.025 0.003 PHE D 427 TRP 0.024 0.004 TRP E 400 HIS 0.009 0.002 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00659 (25602) covalent geometry : angle 0.78837 (34860) hydrogen bonds : bond 0.22523 ( 874) hydrogen bonds : angle 8.05623 ( 2610) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 830 time to evaluate : 1.011 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: E 73 LEU cc_start: 0.8918 (mt) cc_final: 0.8717 (mt) REVERT: E 104 ASN cc_start: 0.7071 (m-40) cc_final: 0.5147 (t0) REVERT: E 137 ASP cc_start: 0.7748 (m-30) cc_final: 0.7263 (m-30) REVERT: E 199 PHE cc_start: 0.8123 (t80) cc_final: 0.7907 (t80) REVERT: E 206 PHE cc_start: 0.6835 (t80) cc_final: 0.6596 (t80) REVERT: E 345 THR cc_start: 0.8603 (p) cc_final: 0.8211 (t) REVERT: E 371 THR cc_start: 0.7409 (m) cc_final: 0.7131 (p) REVERT: E 485 ILE cc_start: 0.8618 (mm) cc_final: 0.8298 (mm) REVERT: E 486 PHE cc_start: 0.7508 (m-80) cc_final: 0.7258 (m-80) REVERT: E 500 LYS cc_start: 0.6858 (mtpt) cc_final: 0.6205 (mmtp) REVERT: F 25 ASP cc_start: 0.6552 (OUTLIER) cc_final: 0.6330 (p0) REVERT: F 134 GLU cc_start: 0.7291 (tp30) cc_final: 0.6520 (tp30) REVERT: F 165 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7669 (mm-30) REVERT: F 193 ARG cc_start: 0.8497 (pmt170) cc_final: 0.8276 (pmt170) REVERT: F 223 GLN cc_start: 0.7377 (mm-40) cc_final: 0.7042 (mp10) REVERT: F 297 ILE cc_start: 0.8020 (mt) cc_final: 0.7637 (mm) REVERT: F 423 ILE cc_start: 0.8793 (mt) cc_final: 0.8559 (mp) REVERT: F 524 GLN cc_start: 0.7853 (mt0) cc_final: 0.7651 (mp10) REVERT: D 40 SER cc_start: 0.7586 (t) cc_final: 0.7072 (p) REVERT: D 242 PRO cc_start: 0.9006 (Cg_endo) cc_final: 0.8636 (Cg_exo) REVERT: D 243 THR cc_start: 0.8646 (p) cc_final: 0.8031 (m) REVERT: D 278 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6558 (tt0) REVERT: D 328 VAL cc_start: 0.7776 (t) cc_final: 0.7541 (p) REVERT: D 331 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7817 (tppp) REVERT: D 371 THR cc_start: 0.7741 (m) cc_final: 0.7534 (t) REVERT: D 379 THR cc_start: 0.7696 (m) cc_final: 0.7440 (p) REVERT: D 431 ILE cc_start: 0.8223 (pt) cc_final: 0.7588 (mt) REVERT: D 434 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7788 (mmmt) REVERT: D 453 TYR cc_start: 0.7548 (t80) cc_final: 0.7336 (t80) REVERT: D 503 LEU cc_start: 0.9236 (mt) cc_final: 0.8742 (mm) REVERT: C 73 LEU cc_start: 0.8911 (mt) cc_final: 0.8710 (mt) REVERT: C 104 ASN cc_start: 0.7055 (m-40) cc_final: 0.5140 (t0) REVERT: C 137 ASP cc_start: 0.7798 (m-30) cc_final: 0.7326 (m-30) REVERT: C 199 PHE cc_start: 0.8117 (t80) cc_final: 0.7874 (t80) REVERT: C 206 PHE cc_start: 0.6845 (t80) cc_final: 0.6594 (t80) REVERT: C 345 THR cc_start: 0.8594 (p) cc_final: 0.8205 (t) REVERT: C 363 LYS cc_start: 0.7260 (mtpp) cc_final: 0.7041 (tptt) REVERT: C 485 ILE cc_start: 0.8629 (mm) cc_final: 0.8309 (mm) REVERT: C 486 PHE cc_start: 0.7543 (m-80) cc_final: 0.7289 (m-80) REVERT: C 500 LYS cc_start: 0.6848 (mtpt) cc_final: 0.6213 (mmtp) REVERT: A 25 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.5860 (t0) REVERT: A 134 GLU cc_start: 0.7318 (tp30) cc_final: 0.6529 (tp30) REVERT: A 159 LYS cc_start: 0.8306 (tttt) cc_final: 0.8065 (tptp) REVERT: A 165 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 223 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7078 (mp10) REVERT: A 297 ILE cc_start: 0.8025 (mt) cc_final: 0.7644 (mm) REVERT: A 423 ILE cc_start: 0.8793 (mt) cc_final: 0.8548 (mp) REVERT: B 40 SER cc_start: 0.7596 (t) cc_final: 0.7087 (p) REVERT: B 242 PRO cc_start: 0.9008 (Cg_endo) cc_final: 0.8688 (Cg_exo) REVERT: B 278 GLN cc_start: 0.7084 (mm-40) cc_final: 0.6557 (tt0) REVERT: B 328 VAL cc_start: 0.7768 (t) cc_final: 0.7533 (p) REVERT: B 331 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7815 (tppp) REVERT: B 371 THR cc_start: 0.7727 (m) cc_final: 0.7514 (t) REVERT: B 379 THR cc_start: 0.7713 (m) cc_final: 0.7444 (p) REVERT: B 431 ILE cc_start: 0.8228 (pt) cc_final: 0.7599 (mt) REVERT: B 434 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7801 (mmmt) REVERT: B 503 LEU cc_start: 0.9240 (mt) cc_final: 0.8743 (mm) outliers start: 13 outliers final: 6 residues processed: 840 average time/residue: 0.1879 time to fit residues: 242.6496 Evaluate side-chains 353 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 345 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 90 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 516 HIS F 456 ASN D 27 GLN C 516 HIS A 456 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093194 restraints weight = 94243.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097344 restraints weight = 46985.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099111 restraints weight = 25002.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099849 restraints weight = 19282.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100190 restraints weight = 17124.300| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25602 Z= 0.132 Angle : 0.634 12.407 34860 Z= 0.327 Chirality : 0.051 0.355 4038 Planarity : 0.004 0.049 4446 Dihedral : 4.556 26.377 3472 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.01 % Allowed : 16.81 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.14), residues: 3156 helix: -1.29 (0.21), residues: 468 sheet: 0.48 (0.16), residues: 978 loop : -0.28 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 498 TYR 0.030 0.001 TYR F 287 PHE 0.017 0.001 PHE E 381 TRP 0.021 0.003 TRP C 108 HIS 0.007 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00289 (25602) covalent geometry : angle 0.63401 (34860) hydrogen bonds : bond 0.04223 ( 874) hydrogen bonds : angle 5.78196 ( 2610) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 395 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 ASN cc_start: 0.7075 (m-40) cc_final: 0.5378 (t0) REVERT: E 137 ASP cc_start: 0.7762 (m-30) cc_final: 0.7270 (m-30) REVERT: E 199 PHE cc_start: 0.7969 (t80) cc_final: 0.7572 (t80) REVERT: E 206 PHE cc_start: 0.6941 (t80) cc_final: 0.6724 (t80) REVERT: E 339 MET cc_start: 0.7847 (mmm) cc_final: 0.7605 (mmm) REVERT: E 345 THR cc_start: 0.8503 (p) cc_final: 0.8214 (t) REVERT: E 455 GLU cc_start: 0.7273 (pt0) cc_final: 0.6994 (pt0) REVERT: E 486 PHE cc_start: 0.7674 (m-80) cc_final: 0.7398 (m-80) REVERT: E 500 LYS cc_start: 0.6368 (mtpt) cc_final: 0.5835 (mmtp) REVERT: F 134 GLU cc_start: 0.7542 (tp30) cc_final: 0.6785 (tp30) REVERT: F 165 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7702 (mm-30) REVERT: F 193 ARG cc_start: 0.8514 (pmt170) cc_final: 0.8274 (pmt170) REVERT: F 233 ARG cc_start: 0.6313 (ttp80) cc_final: 0.5933 (ttt90) REVERT: F 297 ILE cc_start: 0.7834 (mt) cc_final: 0.7509 (mm) REVERT: F 384 ILE cc_start: 0.7216 (mm) cc_final: 0.6912 (mm) REVERT: D 40 SER cc_start: 0.7843 (t) cc_final: 0.7045 (p) REVERT: D 55 SER cc_start: 0.8543 (t) cc_final: 0.7914 (p) REVERT: D 242 PRO cc_start: 0.8967 (Cg_endo) cc_final: 0.8627 (Cg_exo) REVERT: D 331 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7796 (tppp) REVERT: D 453 TYR cc_start: 0.7573 (t80) cc_final: 0.7299 (t80) REVERT: D 504 SER cc_start: 0.8514 (m) cc_final: 0.8266 (p) REVERT: C 104 ASN cc_start: 0.7080 (m-40) cc_final: 0.5386 (t0) REVERT: C 137 ASP cc_start: 0.7758 (m-30) cc_final: 0.7268 (m-30) REVERT: C 199 PHE cc_start: 0.7973 (t80) cc_final: 0.7582 (t80) REVERT: C 206 PHE cc_start: 0.6934 (t80) cc_final: 0.6717 (t80) REVERT: C 279 ASP cc_start: 0.7143 (t0) cc_final: 0.6671 (t0) REVERT: C 339 MET cc_start: 0.7841 (mmm) cc_final: 0.7589 (mmm) REVERT: C 345 THR cc_start: 0.8498 (p) cc_final: 0.8196 (t) REVERT: C 363 LYS cc_start: 0.7718 (mtpp) cc_final: 0.7198 (tptt) REVERT: C 455 GLU cc_start: 0.7282 (pt0) cc_final: 0.6985 (pt0) REVERT: C 486 PHE cc_start: 0.7702 (m-80) cc_final: 0.7412 (m-80) REVERT: C 500 LYS cc_start: 0.6438 (mtpt) cc_final: 0.5984 (mmtp) REVERT: A 134 GLU cc_start: 0.7623 (tp30) cc_final: 0.6819 (tp30) REVERT: A 159 LYS cc_start: 0.8390 (tttt) cc_final: 0.8076 (tptp) REVERT: A 165 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7681 (mm-30) REVERT: A 233 ARG cc_start: 0.6310 (ttp80) cc_final: 0.5920 (ttt90) REVERT: A 297 ILE cc_start: 0.7842 (mt) cc_final: 0.7515 (mm) REVERT: A 384 ILE cc_start: 0.7221 (mm) cc_final: 0.6919 (mm) REVERT: B 20 ASN cc_start: 0.7546 (t0) cc_final: 0.7266 (t0) REVERT: B 40 SER cc_start: 0.7855 (t) cc_final: 0.7108 (p) REVERT: B 55 SER cc_start: 0.8538 (t) cc_final: 0.7920 (p) REVERT: B 242 PRO cc_start: 0.8967 (Cg_endo) cc_final: 0.8642 (Cg_exo) REVERT: B 331 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7802 (tppp) REVERT: B 442 ARG cc_start: 0.7695 (ttt180) cc_final: 0.7348 (ttt-90) REVERT: B 504 SER cc_start: 0.8562 (m) cc_final: 0.8290 (p) outliers start: 29 outliers final: 16 residues processed: 422 average time/residue: 0.1693 time to fit residues: 114.0076 Evaluate side-chains 332 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 316 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 296 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 138 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 234 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 241 optimal weight: 0.2980 chunk 35 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 456 ASN D 240 ASN A 456 ASN B 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.090185 restraints weight = 94038.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.093986 restraints weight = 50192.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.096577 restraints weight = 27867.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.096923 restraints weight = 20908.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097336 restraints weight = 18149.201| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25602 Z= 0.167 Angle : 0.608 15.026 34860 Z= 0.313 Chirality : 0.050 0.258 4038 Planarity : 0.004 0.051 4446 Dihedral : 4.483 27.757 3467 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.95 % Allowed : 17.92 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.14), residues: 3156 helix: -1.33 (0.21), residues: 504 sheet: 0.61 (0.16), residues: 918 loop : -0.09 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 461 TYR 0.017 0.002 TYR D 258 PHE 0.025 0.002 PHE E 381 TRP 0.022 0.003 TRP B 400 HIS 0.005 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00391 (25602) covalent geometry : angle 0.60763 (34860) hydrogen bonds : bond 0.04066 ( 874) hydrogen bonds : angle 5.37985 ( 2610) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 322 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: E 104 ASN cc_start: 0.7233 (m-40) cc_final: 0.5453 (t0) REVERT: E 137 ASP cc_start: 0.7708 (m-30) cc_final: 0.7193 (m-30) REVERT: E 199 PHE cc_start: 0.7990 (t80) cc_final: 0.7551 (t80) REVERT: E 455 GLU cc_start: 0.7144 (pt0) cc_final: 0.6860 (pt0) REVERT: E 486 PHE cc_start: 0.7663 (m-80) cc_final: 0.7441 (m-80) REVERT: E 500 LYS cc_start: 0.6531 (mtpt) cc_final: 0.5912 (mmtp) REVERT: F 134 GLU cc_start: 0.7662 (tp30) cc_final: 0.6896 (tp30) REVERT: F 165 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7636 (mm-30) REVERT: F 193 ARG cc_start: 0.8523 (pmt170) cc_final: 0.8046 (pmt170) REVERT: F 233 ARG cc_start: 0.6357 (ttp80) cc_final: 0.6082 (ttt90) REVERT: F 248 GLU cc_start: 0.7212 (tt0) cc_final: 0.6996 (tt0) REVERT: F 297 ILE cc_start: 0.7719 (mt) cc_final: 0.7388 (mm) REVERT: F 547 MET cc_start: 0.6072 (ppp) cc_final: 0.5854 (ppp) REVERT: D 55 SER cc_start: 0.8604 (t) cc_final: 0.8058 (p) REVERT: D 147 THR cc_start: 0.8284 (m) cc_final: 0.7840 (p) REVERT: D 211 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7601 (tm-30) REVERT: D 242 PRO cc_start: 0.8894 (Cg_endo) cc_final: 0.8608 (Cg_exo) REVERT: D 287 TYR cc_start: 0.7609 (t80) cc_final: 0.7182 (t80) REVERT: D 331 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7655 (mmtp) REVERT: D 439 ILE cc_start: 0.8219 (pt) cc_final: 0.7935 (tp) REVERT: D 453 TYR cc_start: 0.7613 (t80) cc_final: 0.7233 (t80) REVERT: D 504 SER cc_start: 0.8713 (m) cc_final: 0.8355 (p) REVERT: C 104 ASN cc_start: 0.7237 (m-40) cc_final: 0.5455 (t0) REVERT: C 137 ASP cc_start: 0.7723 (m-30) cc_final: 0.7202 (m-30) REVERT: C 199 PHE cc_start: 0.7987 (t80) cc_final: 0.7557 (t80) REVERT: C 363 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7200 (tptt) REVERT: C 455 GLU cc_start: 0.7160 (pt0) cc_final: 0.6891 (pt0) REVERT: C 486 PHE cc_start: 0.7660 (m-80) cc_final: 0.7443 (m-80) REVERT: C 500 LYS cc_start: 0.6588 (mtpt) cc_final: 0.5997 (mmtp) REVERT: A 134 GLU cc_start: 0.7689 (tp30) cc_final: 0.6893 (tp30) REVERT: A 159 LYS cc_start: 0.8342 (tttt) cc_final: 0.8096 (tptp) REVERT: A 165 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7626 (mm-30) REVERT: A 233 ARG cc_start: 0.6346 (ttp80) cc_final: 0.6053 (ttt90) REVERT: A 248 GLU cc_start: 0.7203 (tt0) cc_final: 0.6990 (tt0) REVERT: A 297 ILE cc_start: 0.7723 (mt) cc_final: 0.7393 (mm) REVERT: A 547 MET cc_start: 0.6074 (ppp) cc_final: 0.5866 (ppp) REVERT: B 55 SER cc_start: 0.8564 (t) cc_final: 0.8029 (p) REVERT: B 147 THR cc_start: 0.8287 (m) cc_final: 0.7861 (p) REVERT: B 242 PRO cc_start: 0.8900 (Cg_endo) cc_final: 0.8628 (Cg_exo) REVERT: B 287 TYR cc_start: 0.7525 (t80) cc_final: 0.7239 (t80) REVERT: B 331 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7684 (mmtp) REVERT: B 504 SER cc_start: 0.8748 (m) cc_final: 0.8365 (p) outliers start: 56 outliers final: 40 residues processed: 371 average time/residue: 0.1601 time to fit residues: 96.8041 Evaluate side-chains 303 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 256 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 249 optimal weight: 0.7980 chunk 215 optimal weight: 0.4980 chunk 189 optimal weight: 0.5980 chunk 272 optimal weight: 0.0170 chunk 288 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 344 HIS E 408 ASN E 472 ASN C 344 HIS C 408 ASN C 472 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093564 restraints weight = 80445.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097241 restraints weight = 44192.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099316 restraints weight = 24196.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100626 restraints weight = 18280.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101110 restraints weight = 15529.504| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25602 Z= 0.104 Angle : 0.543 16.188 34860 Z= 0.277 Chirality : 0.048 0.209 4038 Planarity : 0.004 0.050 4446 Dihedral : 4.126 27.293 3467 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.36 % Allowed : 19.31 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.15), residues: 3156 helix: -0.93 (0.23), residues: 498 sheet: 0.51 (0.17), residues: 948 loop : 0.14 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 498 TYR 0.013 0.001 TYR E 283 PHE 0.019 0.001 PHE C 381 TRP 0.015 0.002 TRP C 108 HIS 0.005 0.001 HIS E 516 Details of bonding type rmsd covalent geometry : bond 0.00227 (25602) covalent geometry : angle 0.54300 (34860) hydrogen bonds : bond 0.03262 ( 874) hydrogen bonds : angle 5.07407 ( 2610) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 313 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 104 ASN cc_start: 0.7181 (m-40) cc_final: 0.5498 (t0) REVERT: E 137 ASP cc_start: 0.7543 (m-30) cc_final: 0.7057 (m-30) REVERT: E 177 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8584 (tttt) REVERT: E 199 PHE cc_start: 0.7981 (t80) cc_final: 0.7492 (t80) REVERT: E 339 MET cc_start: 0.7972 (mmm) cc_final: 0.7708 (mmt) REVERT: E 455 GLU cc_start: 0.7063 (pt0) cc_final: 0.6750 (pt0) REVERT: E 500 LYS cc_start: 0.6384 (mtpt) cc_final: 0.5920 (mmtp) REVERT: F 134 GLU cc_start: 0.7463 (tp30) cc_final: 0.6703 (tp30) REVERT: F 193 ARG cc_start: 0.8505 (pmt170) cc_final: 0.7924 (pmt170) REVERT: F 233 ARG cc_start: 0.6355 (ttp80) cc_final: 0.6051 (ttt90) REVERT: F 297 ILE cc_start: 0.7720 (mt) cc_final: 0.7321 (mm) REVERT: F 547 MET cc_start: 0.6306 (ppp) cc_final: 0.6036 (ppp) REVERT: D 55 SER cc_start: 0.8519 (t) cc_final: 0.8024 (p) REVERT: D 331 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7584 (mmtp) REVERT: D 439 ILE cc_start: 0.8151 (pt) cc_final: 0.7886 (tp) REVERT: D 453 TYR cc_start: 0.7709 (t80) cc_final: 0.7316 (t80) REVERT: D 504 SER cc_start: 0.8758 (m) cc_final: 0.8463 (p) REVERT: D 516 HIS cc_start: 0.7192 (t-90) cc_final: 0.6933 (t70) REVERT: C 104 ASN cc_start: 0.7183 (m-40) cc_final: 0.5484 (t0) REVERT: C 137 ASP cc_start: 0.7555 (m-30) cc_final: 0.7063 (m-30) REVERT: C 177 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8447 (tttt) REVERT: C 199 PHE cc_start: 0.7973 (t80) cc_final: 0.7489 (t80) REVERT: C 339 MET cc_start: 0.7976 (mmm) cc_final: 0.7697 (mmt) REVERT: C 363 LYS cc_start: 0.7835 (mtpp) cc_final: 0.7053 (tptt) REVERT: C 455 GLU cc_start: 0.7093 (pt0) cc_final: 0.6774 (pt0) REVERT: C 500 LYS cc_start: 0.6396 (mtpt) cc_final: 0.5992 (mmtp) REVERT: A 134 GLU cc_start: 0.7487 (tp30) cc_final: 0.6727 (tp30) REVERT: A 159 LYS cc_start: 0.8340 (tttt) cc_final: 0.8074 (tptp) REVERT: A 165 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7662 (tp30) REVERT: A 233 ARG cc_start: 0.6353 (ttp80) cc_final: 0.6032 (ttt90) REVERT: A 297 ILE cc_start: 0.7719 (mt) cc_final: 0.7325 (mm) REVERT: A 547 MET cc_start: 0.6318 (ppp) cc_final: 0.6041 (ppp) REVERT: B 55 SER cc_start: 0.8481 (t) cc_final: 0.7989 (p) REVERT: B 287 TYR cc_start: 0.7360 (t80) cc_final: 0.7122 (t80) REVERT: B 331 LYS cc_start: 0.7948 (mmtt) cc_final: 0.7509 (mmtp) REVERT: B 332 ILE cc_start: 0.8079 (mm) cc_final: 0.7579 (tt) REVERT: B 441 SER cc_start: 0.8800 (p) cc_final: 0.8494 (t) REVERT: B 504 SER cc_start: 0.8766 (m) cc_final: 0.8395 (p) REVERT: B 516 HIS cc_start: 0.7184 (t-90) cc_final: 0.6919 (t70) outliers start: 39 outliers final: 31 residues processed: 342 average time/residue: 0.1624 time to fit residues: 90.2478 Evaluate side-chains 293 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 213 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 309 optimal weight: 0.0170 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN E 334 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 ASN ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 334 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.091411 restraints weight = 102463.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.094356 restraints weight = 51133.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.096548 restraints weight = 30489.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097530 restraints weight = 22249.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098012 restraints weight = 19508.241| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25602 Z= 0.171 Angle : 0.604 16.638 34860 Z= 0.307 Chirality : 0.049 0.176 4038 Planarity : 0.004 0.044 4446 Dihedral : 4.348 30.503 3466 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.74 % Allowed : 19.55 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.15), residues: 3156 helix: -0.99 (0.22), residues: 498 sheet: 0.38 (0.17), residues: 954 loop : 0.06 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 498 TYR 0.018 0.002 TYR D 258 PHE 0.034 0.002 PHE E 202 TRP 0.025 0.003 TRP A 108 HIS 0.005 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00399 (25602) covalent geometry : angle 0.60375 (34860) hydrogen bonds : bond 0.03853 ( 874) hydrogen bonds : angle 5.17841 ( 2610) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 1.093 Fit side-chains REVERT: E 25 ASP cc_start: 0.7555 (m-30) cc_final: 0.6940 (p0) REVERT: E 104 ASN cc_start: 0.6915 (m-40) cc_final: 0.5310 (t0) REVERT: E 137 ASP cc_start: 0.7803 (m-30) cc_final: 0.7287 (m-30) REVERT: E 177 LYS cc_start: 0.8950 (ttmt) cc_final: 0.8502 (ttmt) REVERT: E 199 PHE cc_start: 0.7947 (t80) cc_final: 0.7703 (t80) REVERT: E 339 MET cc_start: 0.8040 (mmm) cc_final: 0.7640 (mmm) REVERT: E 455 GLU cc_start: 0.7226 (pt0) cc_final: 0.6876 (pt0) REVERT: E 500 LYS cc_start: 0.6417 (mtpt) cc_final: 0.5960 (mmtm) REVERT: F 83 ARG cc_start: 0.7741 (mtm-85) cc_final: 0.7509 (mtp85) REVERT: F 248 GLU cc_start: 0.7367 (tt0) cc_final: 0.7006 (tt0) REVERT: F 297 ILE cc_start: 0.7443 (mt) cc_final: 0.7129 (mm) REVERT: D 55 SER cc_start: 0.8531 (t) cc_final: 0.8019 (p) REVERT: D 147 THR cc_start: 0.8555 (m) cc_final: 0.8095 (p) REVERT: D 287 TYR cc_start: 0.7582 (t80) cc_final: 0.7307 (t80) REVERT: D 331 LYS cc_start: 0.7930 (mmtt) cc_final: 0.7478 (mmtp) REVERT: D 439 ILE cc_start: 0.8190 (pt) cc_final: 0.7962 (tp) REVERT: D 453 TYR cc_start: 0.7646 (t80) cc_final: 0.7263 (t80) REVERT: D 504 SER cc_start: 0.8872 (m) cc_final: 0.8573 (p) REVERT: C 104 ASN cc_start: 0.6918 (m-40) cc_final: 0.5320 (t0) REVERT: C 137 ASP cc_start: 0.7814 (m-30) cc_final: 0.7296 (m-30) REVERT: C 177 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8481 (ttmt) REVERT: C 199 PHE cc_start: 0.7921 (t80) cc_final: 0.7696 (t80) REVERT: C 339 MET cc_start: 0.8041 (mmm) cc_final: 0.7621 (mmm) REVERT: C 455 GLU cc_start: 0.7251 (pt0) cc_final: 0.6895 (pt0) REVERT: C 500 LYS cc_start: 0.6440 (mtpt) cc_final: 0.5999 (mmtm) REVERT: A 248 GLU cc_start: 0.7357 (tt0) cc_final: 0.6994 (tt0) REVERT: A 297 ILE cc_start: 0.7435 (mt) cc_final: 0.7119 (mm) REVERT: A 357 PHE cc_start: 0.6256 (t80) cc_final: 0.5907 (t80) REVERT: B 55 SER cc_start: 0.8531 (t) cc_final: 0.8034 (p) REVERT: B 147 THR cc_start: 0.8560 (m) cc_final: 0.8094 (p) REVERT: B 331 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7498 (mmtp) REVERT: B 441 SER cc_start: 0.8917 (p) cc_final: 0.8670 (t) REVERT: B 504 SER cc_start: 0.8881 (m) cc_final: 0.8598 (p) outliers start: 50 outliers final: 38 residues processed: 324 average time/residue: 0.1451 time to fit residues: 78.0811 Evaluate side-chains 300 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 239 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN C 136 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091257 restraints weight = 92059.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094384 restraints weight = 51155.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.096957 restraints weight = 28496.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097592 restraints weight = 20352.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098518 restraints weight = 17843.990| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25602 Z= 0.156 Angle : 0.592 16.749 34860 Z= 0.299 Chirality : 0.049 0.159 4038 Planarity : 0.004 0.044 4446 Dihedral : 4.251 22.285 3464 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.95 % Allowed : 19.69 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.15), residues: 3156 helix: -0.97 (0.22), residues: 498 sheet: 0.44 (0.17), residues: 924 loop : -0.05 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 498 TYR 0.027 0.001 TYR B 287 PHE 0.033 0.001 PHE E 202 TRP 0.019 0.002 TRP A 108 HIS 0.005 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00366 (25602) covalent geometry : angle 0.59238 (34860) hydrogen bonds : bond 0.03637 ( 874) hydrogen bonds : angle 5.13807 ( 2610) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 25 ASP cc_start: 0.7475 (m-30) cc_final: 0.6866 (p0) REVERT: E 104 ASN cc_start: 0.6833 (m-40) cc_final: 0.5380 (t0) REVERT: E 137 ASP cc_start: 0.7796 (m-30) cc_final: 0.7266 (m-30) REVERT: E 199 PHE cc_start: 0.7981 (t80) cc_final: 0.7749 (t80) REVERT: E 339 MET cc_start: 0.8083 (mmm) cc_final: 0.7667 (mmm) REVERT: E 349 MET cc_start: 0.6762 (mpp) cc_final: 0.6542 (mpp) REVERT: E 455 GLU cc_start: 0.7246 (pt0) cc_final: 0.6901 (pt0) REVERT: F 193 ARG cc_start: 0.8511 (pmt170) cc_final: 0.7819 (pmt170) REVERT: F 297 ILE cc_start: 0.7345 (mt) cc_final: 0.6999 (mm) REVERT: F 357 PHE cc_start: 0.6288 (t80) cc_final: 0.5952 (t80) REVERT: D 55 SER cc_start: 0.8522 (t) cc_final: 0.8035 (p) REVERT: D 147 THR cc_start: 0.8572 (m) cc_final: 0.8070 (p) REVERT: D 287 TYR cc_start: 0.7678 (t80) cc_final: 0.7387 (t80) REVERT: D 331 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7476 (mmtp) REVERT: D 439 ILE cc_start: 0.8222 (pt) cc_final: 0.7934 (tp) REVERT: D 453 TYR cc_start: 0.7673 (t80) cc_final: 0.7326 (t80) REVERT: D 504 SER cc_start: 0.8911 (m) cc_final: 0.8529 (p) REVERT: C 25 ASP cc_start: 0.7478 (m-30) cc_final: 0.6869 (p0) REVERT: C 104 ASN cc_start: 0.6852 (m-40) cc_final: 0.5375 (t0) REVERT: C 137 ASP cc_start: 0.7803 (m-30) cc_final: 0.7288 (m-30) REVERT: C 199 PHE cc_start: 0.7979 (t80) cc_final: 0.7748 (t80) REVERT: C 339 MET cc_start: 0.8087 (mmm) cc_final: 0.7745 (mmm) REVERT: C 349 MET cc_start: 0.6808 (mpp) cc_final: 0.6531 (mpp) REVERT: C 455 GLU cc_start: 0.7271 (pt0) cc_final: 0.6918 (pt0) REVERT: A 83 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7424 (mtp85) REVERT: A 297 ILE cc_start: 0.7339 (mt) cc_final: 0.6993 (mm) REVERT: A 357 PHE cc_start: 0.6256 (t80) cc_final: 0.5916 (t80) REVERT: B 28 ILE cc_start: 0.8619 (mm) cc_final: 0.8338 (mt) REVERT: B 55 SER cc_start: 0.8525 (t) cc_final: 0.8015 (p) REVERT: B 147 THR cc_start: 0.8583 (m) cc_final: 0.8090 (p) REVERT: B 331 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7431 (mmtp) REVERT: B 332 ILE cc_start: 0.8378 (mm) cc_final: 0.7683 (tt) REVERT: B 504 SER cc_start: 0.8904 (m) cc_final: 0.8605 (p) outliers start: 56 outliers final: 47 residues processed: 324 average time/residue: 0.1456 time to fit residues: 79.0831 Evaluate side-chains 301 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 254 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 472 ASN Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 235 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN E 221 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 GLN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.091228 restraints weight = 76636.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.095879 restraints weight = 41818.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098147 restraints weight = 22378.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099061 restraints weight = 15598.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.099323 restraints weight = 14550.535| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25602 Z= 0.143 Angle : 0.574 17.037 34860 Z= 0.291 Chirality : 0.049 0.148 4038 Planarity : 0.004 0.048 4446 Dihedral : 4.169 21.686 3464 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.95 % Allowed : 20.01 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.15), residues: 3156 helix: -0.87 (0.23), residues: 498 sheet: 0.44 (0.17), residues: 918 loop : -0.12 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 475 TYR 0.024 0.001 TYR B 287 PHE 0.031 0.001 PHE E 202 TRP 0.018 0.002 TRP A 108 HIS 0.005 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00334 (25602) covalent geometry : angle 0.57382 (34860) hydrogen bonds : bond 0.03493 ( 874) hydrogen bonds : angle 5.03787 ( 2610) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 MET cc_start: 0.6141 (tpp) cc_final: 0.5719 (tpp) REVERT: E 104 ASN cc_start: 0.6817 (m-40) cc_final: 0.5086 (t0) REVERT: E 107 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8412 (tp) REVERT: E 137 ASP cc_start: 0.7778 (m-30) cc_final: 0.7257 (m-30) REVERT: E 199 PHE cc_start: 0.7876 (t80) cc_final: 0.7669 (t80) REVERT: E 339 MET cc_start: 0.8154 (mmm) cc_final: 0.7934 (mmm) REVERT: E 455 GLU cc_start: 0.7209 (pt0) cc_final: 0.6862 (pt0) REVERT: F 83 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7347 (mtp85) REVERT: F 193 ARG cc_start: 0.8507 (pmt170) cc_final: 0.7860 (pmt170) REVERT: F 297 ILE cc_start: 0.7304 (mt) cc_final: 0.6873 (mm) REVERT: F 357 PHE cc_start: 0.6280 (t80) cc_final: 0.5921 (t80) REVERT: F 443 LEU cc_start: 0.8372 (tt) cc_final: 0.8124 (tp) REVERT: F 516 HIS cc_start: 0.8038 (t-90) cc_final: 0.7828 (t-90) REVERT: D 28 ILE cc_start: 0.8642 (mm) cc_final: 0.8345 (mt) REVERT: D 55 SER cc_start: 0.8494 (t) cc_final: 0.8039 (p) REVERT: D 147 THR cc_start: 0.8544 (m) cc_final: 0.7983 (p) REVERT: D 269 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8075 (ttmm) REVERT: D 331 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7427 (mmtp) REVERT: D 332 ILE cc_start: 0.8443 (mm) cc_final: 0.7810 (tt) REVERT: D 453 TYR cc_start: 0.7731 (t80) cc_final: 0.7448 (t80) REVERT: D 504 SER cc_start: 0.8896 (m) cc_final: 0.8507 (p) REVERT: C 81 MET cc_start: 0.6136 (tpp) cc_final: 0.5738 (tpp) REVERT: C 104 ASN cc_start: 0.6980 (m-40) cc_final: 0.5214 (t0) REVERT: C 107 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8428 (tp) REVERT: C 137 ASP cc_start: 0.7787 (m-30) cc_final: 0.7241 (m-30) REVERT: C 199 PHE cc_start: 0.7883 (t80) cc_final: 0.7680 (t80) REVERT: C 339 MET cc_start: 0.8132 (mmm) cc_final: 0.7919 (mmm) REVERT: C 455 GLU cc_start: 0.7237 (pt0) cc_final: 0.6882 (pt0) REVERT: A 134 GLU cc_start: 0.7760 (tp30) cc_final: 0.7130 (tp30) REVERT: A 297 ILE cc_start: 0.7307 (mt) cc_final: 0.6892 (mm) REVERT: A 357 PHE cc_start: 0.6250 (t80) cc_final: 0.5824 (t80) REVERT: A 443 LEU cc_start: 0.8399 (tt) cc_final: 0.8142 (tp) REVERT: A 516 HIS cc_start: 0.8038 (t-90) cc_final: 0.7823 (t-90) REVERT: B 28 ILE cc_start: 0.8626 (mm) cc_final: 0.8315 (mt) REVERT: B 55 SER cc_start: 0.8498 (t) cc_final: 0.8009 (p) REVERT: B 147 THR cc_start: 0.8598 (m) cc_final: 0.8071 (p) REVERT: B 269 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8072 (ttmm) REVERT: B 331 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7498 (mmtp) REVERT: B 332 ILE cc_start: 0.8371 (mm) cc_final: 0.7666 (tt) REVERT: B 504 SER cc_start: 0.8893 (m) cc_final: 0.8607 (p) outliers start: 56 outliers final: 49 residues processed: 329 average time/residue: 0.1505 time to fit residues: 82.7416 Evaluate side-chains 306 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 472 ASN Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 455 GLU Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 227 optimal weight: 5.9990 chunk 80 optimal weight: 40.0000 chunk 126 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 291 optimal weight: 0.0470 chunk 174 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 334 ASN B 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.091217 restraints weight = 88097.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094031 restraints weight = 47880.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.095942 restraints weight = 28434.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097101 restraints weight = 21475.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.097452 restraints weight = 18341.236| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25602 Z= 0.159 Angle : 0.588 17.628 34860 Z= 0.299 Chirality : 0.049 0.161 4038 Planarity : 0.004 0.049 4446 Dihedral : 4.254 22.115 3464 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.95 % Allowed : 20.81 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.15), residues: 3156 helix: -0.91 (0.23), residues: 498 sheet: 0.32 (0.17), residues: 924 loop : -0.16 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 498 TYR 0.026 0.001 TYR B 287 PHE 0.027 0.002 PHE B 206 TRP 0.017 0.002 TRP A 108 HIS 0.005 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00371 (25602) covalent geometry : angle 0.58777 (34860) hydrogen bonds : bond 0.03606 ( 874) hydrogen bonds : angle 5.09628 ( 2610) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 260 time to evaluate : 0.998 Fit side-chains REVERT: E 81 MET cc_start: 0.6109 (tpp) cc_final: 0.5676 (tpp) REVERT: E 104 ASN cc_start: 0.6919 (m-40) cc_final: 0.5243 (t0) REVERT: E 107 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8396 (tp) REVERT: E 137 ASP cc_start: 0.7863 (m-30) cc_final: 0.7319 (m-30) REVERT: E 199 PHE cc_start: 0.7885 (t80) cc_final: 0.7672 (t80) REVERT: E 345 THR cc_start: 0.8179 (p) cc_final: 0.7877 (t) REVERT: E 455 GLU cc_start: 0.7241 (pt0) cc_final: 0.6905 (pt0) REVERT: F 83 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7346 (mtp85) REVERT: F 134 GLU cc_start: 0.7843 (tp30) cc_final: 0.7238 (tp30) REVERT: F 193 ARG cc_start: 0.8499 (pmt170) cc_final: 0.7848 (pmt170) REVERT: F 357 PHE cc_start: 0.6145 (t80) cc_final: 0.5801 (t80) REVERT: F 443 LEU cc_start: 0.8395 (tt) cc_final: 0.8149 (tp) REVERT: D 55 SER cc_start: 0.8521 (t) cc_final: 0.8055 (p) REVERT: D 147 THR cc_start: 0.8587 (m) cc_final: 0.8055 (p) REVERT: D 269 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8110 (ttmm) REVERT: D 331 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7520 (mmtp) REVERT: D 332 ILE cc_start: 0.8472 (mm) cc_final: 0.7789 (tt) REVERT: D 439 ILE cc_start: 0.8146 (pt) cc_final: 0.7833 (tp) REVERT: D 453 TYR cc_start: 0.7726 (t80) cc_final: 0.7450 (t80) REVERT: D 504 SER cc_start: 0.8909 (m) cc_final: 0.8496 (p) REVERT: C 81 MET cc_start: 0.6097 (tpp) cc_final: 0.5677 (tpp) REVERT: C 104 ASN cc_start: 0.6843 (m-40) cc_final: 0.5179 (t0) REVERT: C 107 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8411 (tp) REVERT: C 137 ASP cc_start: 0.7867 (m-30) cc_final: 0.7288 (m-30) REVERT: C 199 PHE cc_start: 0.7991 (t80) cc_final: 0.7768 (t80) REVERT: C 455 GLU cc_start: 0.7274 (pt0) cc_final: 0.6934 (pt0) REVERT: A 134 GLU cc_start: 0.7868 (tp30) cc_final: 0.7280 (tp30) REVERT: A 357 PHE cc_start: 0.6236 (t80) cc_final: 0.5794 (t80) REVERT: A 443 LEU cc_start: 0.8418 (tt) cc_final: 0.8159 (tp) REVERT: B 28 ILE cc_start: 0.8652 (mm) cc_final: 0.8369 (mt) REVERT: B 55 SER cc_start: 0.8545 (t) cc_final: 0.8074 (p) REVERT: B 147 THR cc_start: 0.8586 (m) cc_final: 0.8070 (p) REVERT: B 269 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8101 (ttmm) REVERT: B 331 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7548 (mmtp) REVERT: B 332 ILE cc_start: 0.8417 (mm) cc_final: 0.7701 (tt) REVERT: B 504 SER cc_start: 0.8908 (m) cc_final: 0.8618 (p) outliers start: 56 outliers final: 50 residues processed: 311 average time/residue: 0.1439 time to fit residues: 75.4998 Evaluate side-chains 304 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 472 ASN Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 295 optimal weight: 8.9990 chunk 310 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.090932 restraints weight = 85450.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.094370 restraints weight = 47361.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.096879 restraints weight = 26410.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097427 restraints weight = 19006.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097878 restraints weight = 16789.020| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25602 Z= 0.156 Angle : 0.592 16.804 34860 Z= 0.299 Chirality : 0.049 0.151 4038 Planarity : 0.004 0.048 4446 Dihedral : 4.256 22.083 3464 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.88 % Allowed : 21.16 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.15), residues: 3156 helix: -0.91 (0.23), residues: 498 sheet: 0.31 (0.17), residues: 918 loop : -0.21 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 83 TYR 0.024 0.001 TYR B 287 PHE 0.024 0.001 PHE B 206 TRP 0.018 0.002 TRP A 108 HIS 0.005 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00362 (25602) covalent geometry : angle 0.59158 (34860) hydrogen bonds : bond 0.03598 ( 874) hydrogen bonds : angle 5.07389 ( 2610) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 264 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: E 81 MET cc_start: 0.6086 (tpp) cc_final: 0.5684 (tpp) REVERT: E 104 ASN cc_start: 0.6860 (m-40) cc_final: 0.5216 (t0) REVERT: E 107 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8355 (tp) REVERT: E 137 ASP cc_start: 0.7852 (m-30) cc_final: 0.7289 (m-30) REVERT: E 199 PHE cc_start: 0.7872 (t80) cc_final: 0.7664 (t80) REVERT: E 345 THR cc_start: 0.8258 (p) cc_final: 0.7998 (t) REVERT: E 455 GLU cc_start: 0.7235 (pt0) cc_final: 0.6906 (pt0) REVERT: F 83 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7369 (mtp85) REVERT: F 134 GLU cc_start: 0.7802 (tp30) cc_final: 0.7214 (tp30) REVERT: F 193 ARG cc_start: 0.8500 (pmt170) cc_final: 0.7848 (pmt170) REVERT: F 357 PHE cc_start: 0.6147 (t80) cc_final: 0.5808 (t80) REVERT: F 443 LEU cc_start: 0.8400 (tt) cc_final: 0.8154 (tp) REVERT: D 55 SER cc_start: 0.8488 (t) cc_final: 0.8016 (p) REVERT: D 147 THR cc_start: 0.8613 (m) cc_final: 0.8140 (p) REVERT: D 269 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8105 (ttmm) REVERT: D 331 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7486 (mmtp) REVERT: D 332 ILE cc_start: 0.8356 (mm) cc_final: 0.7634 (tt) REVERT: D 439 ILE cc_start: 0.8147 (pt) cc_final: 0.7833 (tp) REVERT: D 453 TYR cc_start: 0.7739 (t80) cc_final: 0.7489 (t80) REVERT: D 504 SER cc_start: 0.8932 (m) cc_final: 0.8545 (p) REVERT: C 59 ARG cc_start: 0.7007 (mmm-85) cc_final: 0.6787 (ttm170) REVERT: C 81 MET cc_start: 0.6074 (tpp) cc_final: 0.5683 (tpp) REVERT: C 104 ASN cc_start: 0.6841 (m-40) cc_final: 0.5208 (t0) REVERT: C 107 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8425 (tp) REVERT: C 137 ASP cc_start: 0.7871 (m-30) cc_final: 0.7314 (m-30) REVERT: C 199 PHE cc_start: 0.7990 (t80) cc_final: 0.7772 (t80) REVERT: C 345 THR cc_start: 0.8214 (p) cc_final: 0.7962 (t) REVERT: C 455 GLU cc_start: 0.7267 (pt0) cc_final: 0.6932 (pt0) REVERT: A 83 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7632 (mtp85) REVERT: A 134 GLU cc_start: 0.7850 (tp30) cc_final: 0.7318 (tp30) REVERT: A 357 PHE cc_start: 0.6221 (t80) cc_final: 0.5791 (t80) REVERT: A 443 LEU cc_start: 0.8414 (tt) cc_final: 0.8158 (tp) REVERT: B 28 ILE cc_start: 0.8666 (mm) cc_final: 0.8378 (mt) REVERT: B 55 SER cc_start: 0.8526 (t) cc_final: 0.8040 (p) REVERT: B 147 THR cc_start: 0.8607 (m) cc_final: 0.8163 (p) REVERT: B 331 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7462 (mmtp) REVERT: B 332 ILE cc_start: 0.8362 (mm) cc_final: 0.7660 (tt) REVERT: B 504 SER cc_start: 0.8913 (m) cc_final: 0.8628 (p) outliers start: 54 outliers final: 49 residues processed: 313 average time/residue: 0.1453 time to fit residues: 76.3767 Evaluate side-chains 303 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 472 ASN Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 274 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 220 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.091276 restraints weight = 85805.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094359 restraints weight = 48026.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097152 restraints weight = 27562.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.097683 restraints weight = 19513.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098168 restraints weight = 16949.221| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 25602 Z= 0.171 Angle : 0.734 59.199 34860 Z= 0.397 Chirality : 0.049 0.316 4038 Planarity : 0.004 0.095 4446 Dihedral : 4.269 22.067 3464 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.98 % Allowed : 21.05 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.15), residues: 3156 helix: -0.79 (0.24), residues: 474 sheet: 0.30 (0.17), residues: 978 loop : -0.21 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG E 59 TYR 0.022 0.001 TYR B 287 PHE 0.023 0.001 PHE B 206 TRP 0.016 0.002 TRP A 108 HIS 0.019 0.002 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00395 (25602) covalent geometry : angle 0.73419 (34860) hydrogen bonds : bond 0.03523 ( 874) hydrogen bonds : angle 5.07166 ( 2610) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: E 81 MET cc_start: 0.6091 (tpp) cc_final: 0.5682 (tpp) REVERT: E 104 ASN cc_start: 0.6859 (m-40) cc_final: 0.5215 (t0) REVERT: E 107 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8351 (tp) REVERT: E 137 ASP cc_start: 0.7821 (m-30) cc_final: 0.7273 (m-30) REVERT: E 199 PHE cc_start: 0.7869 (t80) cc_final: 0.7659 (t80) REVERT: E 345 THR cc_start: 0.8249 (p) cc_final: 0.7990 (t) REVERT: E 455 GLU cc_start: 0.7224 (pt0) cc_final: 0.6891 (pt0) REVERT: F 134 GLU cc_start: 0.7790 (tp30) cc_final: 0.7204 (tp30) REVERT: F 193 ARG cc_start: 0.8494 (pmt170) cc_final: 0.7840 (pmt170) REVERT: F 357 PHE cc_start: 0.6153 (t80) cc_final: 0.5810 (t80) REVERT: F 443 LEU cc_start: 0.8399 (tt) cc_final: 0.8152 (tp) REVERT: D 28 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8319 (mm) REVERT: D 55 SER cc_start: 0.8496 (t) cc_final: 0.8029 (p) REVERT: D 115 LEU cc_start: 0.8052 (tp) cc_final: 0.7802 (tp) REVERT: D 147 THR cc_start: 0.8611 (m) cc_final: 0.8156 (p) REVERT: D 269 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8103 (ttmm) REVERT: D 331 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7489 (mmtp) REVERT: D 332 ILE cc_start: 0.8323 (mm) cc_final: 0.7600 (tt) REVERT: D 439 ILE cc_start: 0.8137 (pt) cc_final: 0.7802 (tp) REVERT: D 453 TYR cc_start: 0.7736 (t80) cc_final: 0.7485 (t80) REVERT: D 504 SER cc_start: 0.8924 (m) cc_final: 0.8537 (p) REVERT: C 59 ARG cc_start: 0.7004 (mmm-85) cc_final: 0.6780 (ttm170) REVERT: C 81 MET cc_start: 0.6074 (tpp) cc_final: 0.5678 (tpp) REVERT: C 104 ASN cc_start: 0.6835 (m-40) cc_final: 0.5204 (t0) REVERT: C 107 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8418 (tp) REVERT: C 137 ASP cc_start: 0.7863 (m-30) cc_final: 0.7310 (m-30) REVERT: C 199 PHE cc_start: 0.7895 (t80) cc_final: 0.7689 (t80) REVERT: C 345 THR cc_start: 0.8208 (p) cc_final: 0.7957 (t) REVERT: C 455 GLU cc_start: 0.7255 (pt0) cc_final: 0.6928 (pt0) REVERT: C 547 MET cc_start: 0.5687 (tpp) cc_final: 0.5348 (mmm) REVERT: A 83 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7622 (mtp85) REVERT: A 134 GLU cc_start: 0.7838 (tp30) cc_final: 0.7308 (tp30) REVERT: A 357 PHE cc_start: 0.6209 (t80) cc_final: 0.5797 (t80) REVERT: A 443 LEU cc_start: 0.8410 (tt) cc_final: 0.8154 (tp) REVERT: B 28 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8373 (mt) REVERT: B 55 SER cc_start: 0.8522 (t) cc_final: 0.8037 (p) REVERT: B 115 LEU cc_start: 0.8044 (tp) cc_final: 0.7827 (tp) REVERT: B 147 THR cc_start: 0.8610 (m) cc_final: 0.8147 (p) REVERT: B 331 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7522 (mmtp) REVERT: B 332 ILE cc_start: 0.8370 (mm) cc_final: 0.7662 (tt) REVERT: B 504 SER cc_start: 0.8898 (m) cc_final: 0.8615 (p) outliers start: 57 outliers final: 53 residues processed: 302 average time/residue: 0.1439 time to fit residues: 73.3014 Evaluate side-chains 308 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 251 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 472 ASN Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 33 optimal weight: 0.0470 chunk 306 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 246 optimal weight: 8.9990 chunk 285 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 150 optimal weight: 0.0470 chunk 190 optimal weight: 0.9990 chunk 307 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.091508 restraints weight = 79683.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.096049 restraints weight = 43499.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098252 restraints weight = 22569.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.099102 restraints weight = 16449.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099591 restraints weight = 14957.425| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 25602 Z= 0.171 Angle : 0.734 59.199 34860 Z= 0.397 Chirality : 0.049 0.316 4038 Planarity : 0.004 0.095 4446 Dihedral : 4.269 22.067 3464 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.98 % Allowed : 21.09 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.15), residues: 3156 helix: -0.79 (0.24), residues: 474 sheet: 0.30 (0.17), residues: 978 loop : -0.21 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG E 59 TYR 0.022 0.001 TYR B 287 PHE 0.023 0.001 PHE B 206 TRP 0.016 0.002 TRP A 108 HIS 0.019 0.002 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00395 (25602) covalent geometry : angle 0.73419 (34860) hydrogen bonds : bond 0.03523 ( 874) hydrogen bonds : angle 5.07166 ( 2610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3740.75 seconds wall clock time: 65 minutes 48.20 seconds (3948.20 seconds total)