Starting phenix.real_space_refine on Wed Nov 19 14:46:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vfg_31952/11_2025/7vfg_31952.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vfg_31952/11_2025/7vfg_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vfg_31952/11_2025/7vfg_31952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vfg_31952/11_2025/7vfg_31952.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vfg_31952/11_2025/7vfg_31952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vfg_31952/11_2025/7vfg_31952.map" } 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-2.0-5881/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: 10.18, per 1000 atoms: 0.41 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: 1.86 Conformation dependent library (CDL) restraints added in 1.8 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: 1.25 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: 5.58 Time building geometry restraints manager: 2.55 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: 0.02 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 30.200 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- 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 : 1.032 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: 0.8558 (mp) REVERT: F 524 GLN cc_start: 0.7852 (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: 0.7742 (m) cc_final: 0.7534 (t) REVERT: D 379 THR cc_start: 0.7695 (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: 0.8031 (mmmt) cc_final: 0.7789 (mmmt) REVERT: D 453 TYR cc_start: 0.7548 (t80) cc_final: 0.7337 (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: 0.7797 (m-30) cc_final: 0.7325 (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: 0.7077 (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: 0.7769 (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: 0.1808 time to fit residues: 232.9068 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 : 0.909 ------------------------------------------------------------------------------- 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 : 0.879 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: 0.7835 (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: 0.7795 (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: 0.6311 (ttp80) cc_final: 0.5921 (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: 0.7267 (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: 0.1686 time to fit residues: 113.1034 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 : 1.026 ------------------------------------------------------------------------------- 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 : 0.792 Fit side-chains revert: symmetry clash REVERT: E 104 ASN cc_start: 0.7233 (m-40) cc_final: 0.5454 (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: 0.7635 (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: 0.6997 (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: 0.8285 (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: 0.8354 (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: 0.8563 (t) cc_final: 0.8029 (p) REVERT: B 147 THR cc_start: 0.8287 (m) cc_final: 0.7860 (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: 0.1581 time to fit residues: 95.1758 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 : 1.009 ------------------------------------------------------------------------------- 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 : 1.007 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 165 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7664 (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: 0.8518 (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: 0.7977 (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: 0.6042 (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: 0.1617 time to fit residues: 89.5981 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 : 1.095 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.114363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.090306 restraints weight = 102346.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.095156 restraints weight = 46242.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098357 restraints weight = 23236.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098938 restraints weight = 14828.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099102 restraints weight = 13757.720| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25602 Z= 0.172 Angle : 0.599 16.718 34860 Z= 0.304 Chirality : 0.049 0.187 4038 Planarity : 0.004 0.044 4446 Dihedral : 4.314 30.473 3466 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.67 % Allowed : 19.69 % Favored : 78.64 % 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: -0.12 (0.15), residues: 3156 helix: -0.97 (0.22), residues: 498 sheet: 0.39 (0.17), residues: 954 loop : 0.07 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 498 TYR 0.017 0.002 TYR D 258 PHE 0.035 0.002 PHE E 202 TRP 0.023 0.003 TRP A 108 HIS 0.005 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00401 (25602) covalent geometry : angle 0.59895 (34860) hydrogen bonds : bond 0.03796 ( 874) hydrogen bonds : angle 5.16116 ( 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 324 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: E 25 ASP cc_start: 0.7527 (m-30) cc_final: 0.6939 (p0) REVERT: E 104 ASN cc_start: 0.6907 (m-40) cc_final: 0.5299 (t0) REVERT: E 137 ASP cc_start: 0.7769 (m-30) cc_final: 0.7248 (m-30) REVERT: E 177 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8476 (tttt) REVERT: E 199 PHE cc_start: 0.7957 (t80) cc_final: 0.7714 (t80) REVERT: E 455 GLU cc_start: 0.7234 (pt0) cc_final: 0.6876 (pt0) REVERT: E 500 LYS cc_start: 0.6408 (mtpt) cc_final: 0.5974 (mmtm) REVERT: F 83 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7489 (mtp85) REVERT: F 193 ARG cc_start: 0.8530 (pmt170) cc_final: 0.7852 (pmt170) REVERT: F 233 ARG cc_start: 0.6338 (ttp80) cc_final: 0.6117 (ttt90) REVERT: F 297 ILE cc_start: 0.7428 (mt) cc_final: 0.7122 (mm) REVERT: D 55 SER cc_start: 0.8535 (t) cc_final: 0.8035 (p) REVERT: D 147 THR cc_start: 0.8538 (m) cc_final: 0.8066 (p) REVERT: D 287 TYR cc_start: 0.7572 (t80) cc_final: 0.7290 (t80) REVERT: D 331 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7453 (mmtp) REVERT: D 439 ILE cc_start: 0.8188 (pt) cc_final: 0.7961 (tp) REVERT: D 453 TYR cc_start: 0.7668 (t80) cc_final: 0.7302 (t80) REVERT: D 504 SER cc_start: 0.8863 (m) cc_final: 0.8576 (p) REVERT: C 104 ASN cc_start: 0.6902 (m-40) cc_final: 0.5306 (t0) REVERT: C 137 ASP cc_start: 0.7775 (m-30) cc_final: 0.7250 (m-30) REVERT: C 177 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8465 (ttmt) REVERT: C 199 PHE cc_start: 0.7952 (t80) cc_final: 0.7711 (t80) REVERT: C 339 MET cc_start: 0.8040 (mmm) cc_final: 0.7619 (mmm) REVERT: C 455 GLU cc_start: 0.7250 (pt0) cc_final: 0.6897 (pt0) REVERT: C 500 LYS cc_start: 0.6426 (mtpt) cc_final: 0.6008 (mmtm) REVERT: A 248 GLU cc_start: 0.7311 (tt0) cc_final: 0.6951 (tt0) REVERT: A 297 ILE cc_start: 0.7421 (mt) cc_final: 0.7113 (mm) REVERT: A 357 PHE cc_start: 0.6278 (t80) cc_final: 0.5934 (t80) REVERT: B 55 SER cc_start: 0.8524 (t) cc_final: 0.8037 (p) REVERT: B 147 THR cc_start: 0.8545 (m) cc_final: 0.8067 (p) REVERT: B 331 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7480 (mmtp) REVERT: B 441 SER cc_start: 0.8901 (p) cc_final: 0.8685 (t) REVERT: B 504 SER cc_start: 0.8883 (m) cc_final: 0.8612 (p) outliers start: 48 outliers final: 37 residues processed: 319 average time/residue: 0.1548 time to fit residues: 81.2697 Evaluate side-chains 298 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 212 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** C 136 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.089920 restraints weight = 93274.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.092890 restraints weight = 47889.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.094684 restraints weight = 28587.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095701 restraints weight = 22155.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.096028 restraints weight = 19242.490| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25602 Z= 0.233 Angle : 0.668 17.046 34860 Z= 0.341 Chirality : 0.051 0.175 4038 Planarity : 0.005 0.049 4446 Dihedral : 4.672 28.014 3464 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.40 % Allowed : 19.21 % Favored : 78.39 % 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: -0.46 (0.15), residues: 3156 helix: -1.18 (0.22), residues: 498 sheet: 0.26 (0.17), residues: 924 loop : -0.24 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 461 TYR 0.033 0.002 TYR B 287 PHE 0.033 0.002 PHE E 202 TRP 0.018 0.003 TRP A 108 HIS 0.010 0.002 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00546 (25602) covalent geometry : angle 0.66782 (34860) hydrogen bonds : bond 0.04288 ( 874) hydrogen bonds : angle 5.42542 ( 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 348 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 279 time to evaluate : 1.031 Fit side-chains REVERT: E 25 ASP cc_start: 0.7540 (m-30) cc_final: 0.6969 (p0) REVERT: E 104 ASN cc_start: 0.6827 (m-40) cc_final: 0.5076 (t0) REVERT: E 137 ASP cc_start: 0.7889 (m-30) cc_final: 0.7389 (m-30) REVERT: E 455 GLU cc_start: 0.7397 (pt0) cc_final: 0.7053 (pt0) REVERT: F 193 ARG cc_start: 0.8560 (pmt170) cc_final: 0.7910 (pmt170) REVERT: F 297 ILE cc_start: 0.7260 (mt) cc_final: 0.6882 (mm) REVERT: F 357 PHE cc_start: 0.6269 (t80) cc_final: 0.5923 (t80) REVERT: D 55 SER cc_start: 0.8552 (t) cc_final: 0.8072 (p) REVERT: D 147 THR cc_start: 0.8589 (m) cc_final: 0.8031 (p) REVERT: D 269 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8098 (ttmm) REVERT: D 331 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7476 (mmtp) REVERT: D 332 ILE cc_start: 0.8334 (mm) cc_final: 0.7559 (tt) REVERT: D 439 ILE cc_start: 0.8251 (pt) cc_final: 0.7943 (tp) REVERT: D 453 TYR cc_start: 0.7717 (t80) cc_final: 0.7399 (t80) REVERT: D 504 SER cc_start: 0.8898 (m) cc_final: 0.8516 (p) REVERT: C 25 ASP cc_start: 0.7543 (m-30) cc_final: 0.6957 (p0) REVERT: C 104 ASN cc_start: 0.6836 (m-40) cc_final: 0.5086 (t0) REVERT: C 137 ASP cc_start: 0.7903 (m-30) cc_final: 0.7395 (m-30) REVERT: C 339 MET cc_start: 0.8147 (mmm) cc_final: 0.7886 (mmm) REVERT: C 455 GLU cc_start: 0.7439 (pt0) cc_final: 0.7074 (pt0) REVERT: A 297 ILE cc_start: 0.7260 (mt) cc_final: 0.6888 (mm) REVERT: A 357 PHE cc_start: 0.6229 (t80) cc_final: 0.5802 (t80) REVERT: B 28 ILE cc_start: 0.8645 (mm) cc_final: 0.8348 (mt) REVERT: B 55 SER cc_start: 0.8553 (t) cc_final: 0.8055 (p) REVERT: B 147 THR cc_start: 0.8592 (m) cc_final: 0.8053 (p) REVERT: B 293 ASP cc_start: 0.5993 (OUTLIER) cc_final: 0.5770 (m-30) REVERT: B 331 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7506 (mmtp) REVERT: B 332 ILE cc_start: 0.8427 (mm) cc_final: 0.7709 (tt) REVERT: B 504 SER cc_start: 0.8878 (m) cc_final: 0.8518 (p) outliers start: 69 outliers final: 55 residues processed: 339 average time/residue: 0.1486 time to fit residues: 84.3323 Evaluate side-chains 308 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 252 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 503 LEU 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 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 477 LEU 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 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 361 ILE 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 503 LEU Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 50 ASN 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 291 LEU Chi-restraints excluded: chain B residue 293 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 235 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 260 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 293 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** F 524 GLN D 355 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.092450 restraints weight = 76151.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.097045 restraints weight = 41719.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099594 restraints weight = 21998.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100632 restraints weight = 14804.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100918 restraints weight = 13961.951| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25602 Z= 0.107 Angle : 0.556 17.182 34860 Z= 0.281 Chirality : 0.048 0.155 4038 Planarity : 0.004 0.046 4446 Dihedral : 4.117 22.674 3464 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.60 % Allowed : 20.32 % Favored : 78.08 % 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: -0.18 (0.15), residues: 3156 helix: -0.85 (0.23), residues: 498 sheet: 0.46 (0.17), residues: 918 loop : -0.10 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 475 TYR 0.016 0.001 TYR E 283 PHE 0.032 0.001 PHE B 206 TRP 0.020 0.002 TRP F 108 HIS 0.005 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00245 (25602) covalent geometry : angle 0.55587 (34860) hydrogen bonds : bond 0.03240 ( 874) hydrogen bonds : angle 5.00155 ( 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 331 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: E 81 MET cc_start: 0.6082 (tpp) cc_final: 0.5687 (tpp) REVERT: E 104 ASN cc_start: 0.6795 (m-40) cc_final: 0.5071 (t0) REVERT: E 137 ASP cc_start: 0.7720 (m-30) cc_final: 0.7177 (m-30) REVERT: E 177 LYS cc_start: 0.9081 (ttmt) cc_final: 0.8644 (tttt) REVERT: E 345 THR cc_start: 0.8248 (p) cc_final: 0.7956 (t) REVERT: E 455 GLU cc_start: 0.7182 (pt0) cc_final: 0.6587 (pt0) REVERT: F 193 ARG cc_start: 0.8463 (pmt170) cc_final: 0.7852 (pmt170) REVERT: F 248 GLU cc_start: 0.7344 (tt0) cc_final: 0.7131 (tt0) REVERT: F 297 ILE cc_start: 0.7262 (mt) cc_final: 0.6827 (mm) REVERT: F 357 PHE cc_start: 0.6162 (t80) cc_final: 0.5906 (t80) REVERT: F 443 LEU cc_start: 0.8364 (tt) cc_final: 0.8126 (tp) REVERT: D 28 ILE cc_start: 0.8621 (mm) cc_final: 0.8316 (mt) REVERT: D 55 SER cc_start: 0.8478 (t) cc_final: 0.8030 (p) REVERT: D 147 THR cc_start: 0.8537 (m) cc_final: 0.7912 (p) REVERT: D 269 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8089 (ttmm) REVERT: D 331 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7532 (mmtp) REVERT: D 439 ILE cc_start: 0.8169 (pt) cc_final: 0.7884 (tp) REVERT: D 453 TYR cc_start: 0.7793 (t80) cc_final: 0.7567 (t80) REVERT: D 504 SER cc_start: 0.8884 (m) cc_final: 0.8499 (p) REVERT: C 81 MET cc_start: 0.6093 (tpp) cc_final: 0.5695 (tpp) REVERT: C 104 ASN cc_start: 0.6784 (m-40) cc_final: 0.5075 (t0) REVERT: C 107 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8405 (tp) REVERT: C 137 ASP cc_start: 0.7734 (m-30) cc_final: 0.7169 (m-30) REVERT: C 345 THR cc_start: 0.8257 (p) cc_final: 0.7989 (t) REVERT: C 455 GLU cc_start: 0.7186 (pt0) cc_final: 0.6557 (pt0) REVERT: A 83 ARG cc_start: 0.7939 (mtp85) cc_final: 0.7321 (mtp85) REVERT: A 134 GLU cc_start: 0.7655 (tp30) cc_final: 0.7042 (tp30) REVERT: A 297 ILE cc_start: 0.7233 (mt) cc_final: 0.6812 (mm) REVERT: A 357 PHE cc_start: 0.6169 (t80) cc_final: 0.5833 (t80) REVERT: A 443 LEU cc_start: 0.8403 (tt) cc_final: 0.8147 (tp) REVERT: B 28 ILE cc_start: 0.8609 (mm) cc_final: 0.8303 (mt) REVERT: B 55 SER cc_start: 0.8490 (t) cc_final: 0.8015 (p) REVERT: B 147 THR cc_start: 0.8553 (m) cc_final: 0.8043 (p) REVERT: B 269 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8081 (ttmm) REVERT: B 331 LYS cc_start: 0.7976 (mmtt) cc_final: 0.7500 (mmtp) REVERT: B 332 ILE cc_start: 0.8367 (mm) cc_final: 0.7667 (tt) REVERT: B 504 SER cc_start: 0.8871 (m) cc_final: 0.8613 (p) outliers start: 46 outliers final: 39 residues processed: 327 average time/residue: 0.1504 time to fit residues: 81.4139 Evaluate side-chains 299 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 227 SER 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 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 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 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 355 ASN 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 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: 6.9990 chunk 80 optimal weight: 0.0040 chunk 126 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 291 optimal weight: 0.0000 chunk 174 optimal weight: 6.9990 chunk 242 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- 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 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 334 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.090479 restraints weight = 88316.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.093788 restraints weight = 49595.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095871 restraints weight = 27537.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.096866 restraints weight = 20594.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097652 restraints weight = 17834.202| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25602 Z= 0.171 Angle : 0.604 17.867 34860 Z= 0.306 Chirality : 0.049 0.148 4038 Planarity : 0.004 0.046 4446 Dihedral : 4.293 22.273 3464 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.81 % Allowed : 20.77 % Favored : 77.42 % 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: -0.33 (0.15), residues: 3156 helix: -0.97 (0.23), residues: 498 sheet: 0.30 (0.17), residues: 924 loop : -0.17 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 83 TYR 0.029 0.002 TYR B 287 PHE 0.028 0.002 PHE E 202 TRP 0.016 0.002 TRP A 108 HIS 0.010 0.002 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00402 (25602) covalent geometry : angle 0.60438 (34860) hydrogen bonds : bond 0.03691 ( 874) hydrogen bonds : angle 5.14477 ( 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: 52 poor density : 264 time to evaluate : 1.133 Fit side-chains REVERT: E 81 MET cc_start: 0.6056 (tpp) cc_final: 0.5629 (tpp) REVERT: E 104 ASN cc_start: 0.6913 (m-40) cc_final: 0.5261 (t0) REVERT: E 137 ASP cc_start: 0.7892 (m-30) cc_final: 0.7368 (m-30) REVERT: E 177 LYS cc_start: 0.9130 (ttmt) cc_final: 0.8877 (ttmm) REVERT: E 345 THR cc_start: 0.8234 (p) cc_final: 0.7960 (t) REVERT: E 455 GLU cc_start: 0.7259 (pt0) cc_final: 0.6918 (pt0) REVERT: F 83 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7594 (mtp85) REVERT: F 134 GLU cc_start: 0.7805 (tp30) cc_final: 0.7225 (tp30) REVERT: F 297 ILE cc_start: 0.7187 (mt) cc_final: 0.6744 (mm) REVERT: F 357 PHE cc_start: 0.6196 (t80) cc_final: 0.5862 (t80) REVERT: F 443 LEU cc_start: 0.8406 (tt) cc_final: 0.8165 (tp) REVERT: D 28 ILE cc_start: 0.8636 (mm) cc_final: 0.8348 (mt) REVERT: D 55 SER cc_start: 0.8494 (t) cc_final: 0.8006 (p) REVERT: D 147 THR cc_start: 0.8595 (m) cc_final: 0.8023 (p) REVERT: D 269 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8085 (ttmm) REVERT: D 331 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7652 (mmtp) REVERT: D 355 ASN cc_start: 0.7650 (m110) cc_final: 0.6792 (t0) REVERT: D 439 ILE cc_start: 0.8156 (pt) cc_final: 0.7846 (tp) REVERT: D 453 TYR cc_start: 0.7748 (t80) cc_final: 0.7482 (t80) REVERT: D 504 SER cc_start: 0.8935 (m) cc_final: 0.8559 (p) REVERT: C 81 MET cc_start: 0.6078 (tpp) cc_final: 0.5671 (tpp) REVERT: C 104 ASN cc_start: 0.6905 (m-40) cc_final: 0.5245 (t0) REVERT: C 107 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8402 (tp) REVERT: C 137 ASP cc_start: 0.7866 (m-30) cc_final: 0.7344 (m-30) REVERT: C 345 THR cc_start: 0.8243 (p) cc_final: 0.7978 (t) REVERT: C 455 GLU cc_start: 0.7274 (pt0) cc_final: 0.6949 (pt0) REVERT: A 83 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7357 (mtp85) REVERT: A 134 GLU cc_start: 0.7838 (tp30) cc_final: 0.7286 (tp30) REVERT: A 297 ILE cc_start: 0.7198 (mt) cc_final: 0.6768 (mm) REVERT: A 357 PHE cc_start: 0.6138 (t80) cc_final: 0.5819 (t80) REVERT: A 443 LEU cc_start: 0.8409 (tt) cc_final: 0.8169 (tp) REVERT: B 28 ILE cc_start: 0.8644 (mm) cc_final: 0.8363 (mt) REVERT: B 55 SER cc_start: 0.8497 (t) cc_final: 0.8019 (p) REVERT: B 147 THR cc_start: 0.8593 (m) cc_final: 0.8151 (p) REVERT: B 331 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7480 (mmtp) REVERT: B 332 ILE cc_start: 0.8384 (mm) cc_final: 0.7675 (tt) REVERT: B 504 SER cc_start: 0.8894 (m) cc_final: 0.8632 (p) outliers start: 52 outliers final: 45 residues processed: 309 average time/residue: 0.1426 time to fit residues: 75.0689 Evaluate side-chains 299 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 24 VAL 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 341 VAL 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 441 SER Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 518 ILE 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 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 541 VAL 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 265 ASN 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 Chi-restraints excluded: chain B residue 518 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 295 optimal weight: 9.9990 chunk 310 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 278 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 304 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 227 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** F 516 HIS ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.092470 restraints weight = 84534.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097362 restraints weight = 44602.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099882 restraints weight = 22168.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100343 restraints weight = 15413.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100923 restraints weight = 14917.716| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25602 Z= 0.107 Angle : 0.569 16.900 34860 Z= 0.285 Chirality : 0.048 0.321 4038 Planarity : 0.004 0.045 4446 Dihedral : 4.070 19.311 3464 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.32 % Allowed : 21.64 % Favored : 77.04 % 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: -0.14 (0.15), residues: 3156 helix: -0.75 (0.24), residues: 474 sheet: 0.43 (0.18), residues: 918 loop : -0.08 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 83 TYR 0.020 0.001 TYR D 287 PHE 0.028 0.001 PHE E 202 TRP 0.018 0.002 TRP F 108 HIS 0.009 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00244 (25602) covalent geometry : angle 0.56867 (34860) hydrogen bonds : bond 0.03165 ( 874) hydrogen bonds : angle 4.94461 ( 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 311 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 0.829 Fit side-chains REVERT: E 81 MET cc_start: 0.6026 (tpp) cc_final: 0.5608 (tpp) REVERT: E 104 ASN cc_start: 0.6879 (m-40) cc_final: 0.5247 (t0) REVERT: E 137 ASP cc_start: 0.7798 (m-30) cc_final: 0.7229 (m-30) REVERT: E 177 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8850 (ttmm) REVERT: E 345 THR cc_start: 0.8263 (p) cc_final: 0.8011 (t) REVERT: E 455 GLU cc_start: 0.7169 (pt0) cc_final: 0.6854 (pt0) REVERT: F 83 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7551 (mtp85) REVERT: F 134 GLU cc_start: 0.7714 (tp30) cc_final: 0.7125 (tp30) REVERT: F 193 ARG cc_start: 0.8475 (pmt170) cc_final: 0.7840 (pmt170) REVERT: F 357 PHE cc_start: 0.6340 (t80) cc_final: 0.6031 (t80) REVERT: F 443 LEU cc_start: 0.8406 (tt) cc_final: 0.8162 (tp) REVERT: D 28 ILE cc_start: 0.8632 (mm) cc_final: 0.8324 (mt) REVERT: D 55 SER cc_start: 0.8471 (t) cc_final: 0.8011 (p) REVERT: D 147 THR cc_start: 0.8585 (m) cc_final: 0.8081 (p) REVERT: D 269 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8087 (ttmm) REVERT: D 331 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7593 (mmtp) REVERT: D 355 ASN cc_start: 0.7617 (m110) cc_final: 0.6832 (t0) REVERT: D 453 TYR cc_start: 0.7786 (t80) cc_final: 0.7553 (t80) REVERT: D 504 SER cc_start: 0.8921 (m) cc_final: 0.8542 (p) REVERT: C 81 MET cc_start: 0.6162 (tpp) cc_final: 0.5755 (tpp) REVERT: C 104 ASN cc_start: 0.6891 (m-40) cc_final: 0.5249 (t0) REVERT: C 107 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8382 (tp) REVERT: C 137 ASP cc_start: 0.7798 (m-30) cc_final: 0.7257 (m-30) REVERT: C 345 THR cc_start: 0.8229 (p) cc_final: 0.7957 (t) REVERT: C 455 GLU cc_start: 0.7194 (pt0) cc_final: 0.6889 (pt0) REVERT: A 83 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7291 (mtp85) REVERT: A 134 GLU cc_start: 0.7766 (tp30) cc_final: 0.7197 (tp30) REVERT: A 357 PHE cc_start: 0.6130 (t80) cc_final: 0.5823 (t80) REVERT: A 443 LEU cc_start: 0.8403 (tt) cc_final: 0.8174 (tp) REVERT: B 28 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8343 (mt) REVERT: B 55 SER cc_start: 0.8472 (t) cc_final: 0.7980 (p) REVERT: B 147 THR cc_start: 0.8593 (m) cc_final: 0.8117 (p) REVERT: B 331 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7501 (mmtp) REVERT: B 332 ILE cc_start: 0.8334 (mm) cc_final: 0.7635 (tt) REVERT: B 355 ASN cc_start: 0.7573 (m110) cc_final: 0.6773 (t0) REVERT: B 504 SER cc_start: 0.8890 (m) cc_final: 0.8628 (p) outliers start: 38 outliers final: 35 residues processed: 305 average time/residue: 0.1461 time to fit residues: 75.5062 Evaluate side-chains 295 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 258 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 355 ASN Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 219 VAL 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 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 541 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 ILE 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 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 274 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 220 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.092611 restraints weight = 85691.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096609 restraints weight = 46215.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099185 restraints weight = 24964.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099985 restraints weight = 18080.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100572 restraints weight = 15808.210| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25602 Z= 0.109 Angle : 0.566 17.858 34860 Z= 0.284 Chirality : 0.048 0.155 4038 Planarity : 0.004 0.049 4446 Dihedral : 3.971 20.399 3464 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.43 % Allowed : 21.43 % Favored : 77.14 % 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: -0.10 (0.15), residues: 3156 helix: -0.67 (0.24), residues: 474 sheet: 0.45 (0.18), residues: 918 loop : -0.06 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 83 TYR 0.021 0.001 TYR B 287 PHE 0.027 0.001 PHE E 202 TRP 0.016 0.002 TRP A 108 HIS 0.009 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00253 (25602) covalent geometry : angle 0.56588 (34860) hydrogen bonds : bond 0.03098 ( 874) hydrogen bonds : angle 4.87044 ( 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 313 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: E 81 MET cc_start: 0.6016 (tpp) cc_final: 0.5608 (tpp) REVERT: E 104 ASN cc_start: 0.6794 (m-40) cc_final: 0.5210 (t0) REVERT: E 137 ASP cc_start: 0.7797 (m-30) cc_final: 0.7232 (m-30) REVERT: E 177 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8841 (ttmm) REVERT: E 198 ASP cc_start: 0.8166 (t0) cc_final: 0.7911 (t0) REVERT: E 345 THR cc_start: 0.8258 (p) cc_final: 0.7983 (t) REVERT: E 455 GLU cc_start: 0.7168 (pt0) cc_final: 0.6870 (pt0) REVERT: F 83 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7573 (mtp85) REVERT: F 134 GLU cc_start: 0.7745 (tp30) cc_final: 0.7156 (tp30) REVERT: F 193 ARG cc_start: 0.8504 (pmt170) cc_final: 0.7871 (pmt170) REVERT: F 357 PHE cc_start: 0.6270 (t80) cc_final: 0.5925 (t80) REVERT: F 443 LEU cc_start: 0.8428 (tt) cc_final: 0.8169 (tp) REVERT: F 516 HIS cc_start: 0.7719 (t-170) cc_final: 0.7097 (t70) REVERT: D 55 SER cc_start: 0.8479 (t) cc_final: 0.8013 (p) REVERT: D 147 THR cc_start: 0.8596 (m) cc_final: 0.8135 (p) REVERT: D 269 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8092 (ttmm) REVERT: D 331 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7584 (mmtp) REVERT: D 355 ASN cc_start: 0.7481 (m110) cc_final: 0.6708 (t0) REVERT: D 453 TYR cc_start: 0.7763 (t80) cc_final: 0.7520 (t80) REVERT: D 504 SER cc_start: 0.8915 (m) cc_final: 0.8540 (p) REVERT: C 81 MET cc_start: 0.6165 (tpp) cc_final: 0.5752 (tpp) REVERT: C 104 ASN cc_start: 0.6897 (m-40) cc_final: 0.5274 (t0) REVERT: C 107 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8300 (tp) REVERT: C 137 ASP cc_start: 0.7806 (m-30) cc_final: 0.7248 (m-30) REVERT: C 198 ASP cc_start: 0.8109 (t0) cc_final: 0.7865 (t0) REVERT: C 339 MET cc_start: 0.7881 (tpt) cc_final: 0.7448 (tpp) REVERT: C 345 THR cc_start: 0.8237 (p) cc_final: 0.8000 (t) REVERT: C 432 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: C 455 GLU cc_start: 0.7196 (pt0) cc_final: 0.6880 (pt0) REVERT: A 83 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7286 (mtp85) REVERT: A 357 PHE cc_start: 0.6140 (t80) cc_final: 0.5819 (t80) REVERT: A 443 LEU cc_start: 0.8435 (tt) cc_final: 0.8192 (tp) REVERT: B 28 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8308 (mm) REVERT: B 55 SER cc_start: 0.8472 (t) cc_final: 0.7975 (p) REVERT: B 147 THR cc_start: 0.8609 (m) cc_final: 0.8172 (p) REVERT: B 269 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8086 (ttmm) REVERT: B 331 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7502 (mmtp) REVERT: B 332 ILE cc_start: 0.8342 (mm) cc_final: 0.7631 (tt) REVERT: B 355 ASN cc_start: 0.7536 (m110) cc_final: 0.6751 (t0) REVERT: B 504 SER cc_start: 0.8916 (m) cc_final: 0.8633 (p) outliers start: 41 outliers final: 34 residues processed: 307 average time/residue: 0.1554 time to fit residues: 80.3157 Evaluate side-chains 301 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 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 227 SER 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 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 541 VAL Chi-restraints excluded: chain B residue 28 ILE 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 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 33 optimal weight: 0.6980 chunk 306 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 246 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 307 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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** ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.091714 restraints weight = 79827.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096543 restraints weight = 43005.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.098919 restraints weight = 22440.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099918 restraints weight = 15515.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100179 restraints weight = 14831.650| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25602 Z= 0.123 Angle : 0.576 17.863 34860 Z= 0.288 Chirality : 0.048 0.180 4038 Planarity : 0.004 0.054 4446 Dihedral : 3.980 19.450 3464 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.43 % Allowed : 21.64 % 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: -0.11 (0.15), residues: 3156 helix: -0.73 (0.24), residues: 480 sheet: 0.61 (0.17), residues: 948 loop : -0.18 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 83 TYR 0.023 0.001 TYR B 287 PHE 0.029 0.001 PHE E 381 TRP 0.015 0.002 TRP A 108 HIS 0.011 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00288 (25602) covalent geometry : angle 0.57611 (34860) hydrogen bonds : bond 0.03200 ( 874) hydrogen bonds : angle 4.84148 ( 2610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3800.22 seconds wall clock time: 66 minutes 45.79 seconds (4005.79 seconds total)