Starting phenix.real_space_refine on Thu Sep 18 12:44:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9krf_62310/09_2025/9krf_62310.cif Found real_map, /net/cci-nas-00/data/ceres_data/9krf_62310/09_2025/9krf_62310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9krf_62310/09_2025/9krf_62310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9krf_62310/09_2025/9krf_62310.map" model { file = "/net/cci-nas-00/data/ceres_data/9krf_62310/09_2025/9krf_62310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9krf_62310/09_2025/9krf_62310.cif" } resolution = 2.8 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= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 49 5.16 5 C 10542 2.51 5 N 2828 2.21 5 O 3318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16744 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 2354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Conformer: "B" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} bond proxies already assigned to first conformer: 2387 Chain: "A" Number of atoms: 2354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Conformer: "B" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} bond proxies already assigned to first conformer: 2387 Chain: "B" Number of atoms: 2354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Conformer: "B" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} bond proxies already assigned to first conformer: 2387 Chain: "C" Number of atoms: 2354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Conformer: "B" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} bond proxies already assigned to first conformer: 2387 Chain: "D" Number of atoms: 2354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Conformer: "B" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} bond proxies already assigned to first conformer: 2387 Chain: "E" Number of atoms: 2354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Conformer: "B" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} bond proxies already assigned to first conformer: 2387 Chain: "F" Number of atoms: 2354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Conformer: "B" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} bond proxies already assigned to first conformer: 2387 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.14, per 1000 atoms: 0.43 Number of scatterers: 16744 At special positions: 0 Unit cell: (111.32, 109.48, 115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 7 15.00 O 3318 8.00 N 2828 7.00 C 10542 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: 1.52 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3808 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 29 sheets defined 4.4% alpha, 45.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'G' and resid 1 through 6 Processing helix chain 'G' and resid 217 through 223 removed outlier: 4.180A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 217 through 223 removed outlier: 4.173A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 Processing helix chain 'B' and resid 217 through 223 removed outlier: 4.148A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 Processing helix chain 'C' and resid 217 through 223 removed outlier: 4.152A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 6 Processing helix chain 'D' and resid 217 through 223 removed outlier: 4.200A pdb=" N SER D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 6 Processing helix chain 'E' and resid 217 through 223 removed outlier: 4.162A pdb=" N SER E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 6 Processing helix chain 'F' and resid 217 through 223 removed outlier: 4.184A pdb=" N SER F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 21 through 22 removed outlier: 3.522A pdb=" N LYS G 21 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET G 34 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 21 through 22 removed outlier: 3.522A pdb=" N LYS G 21 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA G 229 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR G 101 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL G 231 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 70 through 71 removed outlier: 3.740A pdb=" N LYS G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER G 76 " --> pdb=" O LEU G 258 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP G 254 " --> pdb=" O PRO G 81 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR G 256 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA G 79 " --> pdb=" O TYR G 256 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 153 through 157 removed outlier: 3.743A pdb=" N VAL G 86 " --> pdb=" O TRP G 167 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N SER G 82 " --> pdb=" O PHE G 171 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA G 79 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR G 256 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP G 254 " --> pdb=" O PRO G 81 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 251 through 260 current: chain 'G' and resid 279 through 285 Processing sheet with id=AA5, first strand: chain 'G' and resid 109 through 127 removed outlier: 7.278A pdb=" N THR G 109 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL G 149 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS G 147 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN G 139 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS A 110 " --> pdb=" O GLN G 150 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 109 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL A 149 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 147 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN A 139 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 110 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N THR B 109 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL B 149 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 147 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 139 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS C 147 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN C 139 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS D 110 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR D 109 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL D 149 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS D 147 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN D 139 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS E 110 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR E 109 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL E 149 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS E 147 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN E 139 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 110 " --> pdb=" O GLN E 150 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR F 109 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL F 149 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS F 147 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN F 139 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G 110 " --> pdb=" O GLN F 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 21 through 22 removed outlier: 3.508A pdb=" N LYS A 21 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 34 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 21 through 22 removed outlier: 3.508A pdb=" N LYS A 21 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 229 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR A 101 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 231 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 70 through 71 removed outlier: 3.735A pdb=" N LYS A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 76 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP A 254 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR A 256 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA A 79 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 157 removed outlier: 3.850A pdb=" N VAL A 86 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N SER A 82 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA A 79 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR A 256 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP A 254 " --> pdb=" O PRO A 81 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 251 through 260 current: chain 'A' and resid 280 through 285 Processing sheet with id=AB1, first strand: chain 'B' and resid 21 through 22 removed outlier: 3.516A pdb=" N LYS B 21 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 34 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 21 through 22 removed outlier: 3.516A pdb=" N LYS B 21 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 229 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR B 101 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 231 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 70 through 71 removed outlier: 3.723A pdb=" N LYS B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 76 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP B 254 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR B 256 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALA B 79 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 153 through 157 removed outlier: 3.797A pdb=" N VAL B 86 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N SER B 82 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALA B 79 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR B 256 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP B 254 " --> pdb=" O PRO B 81 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 251 through 260 current: chain 'B' and resid 279 through 285 Processing sheet with id=AB5, first strand: chain 'C' and resid 21 through 22 removed outlier: 3.506A pdb=" N LYS C 21 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 34 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 21 through 22 removed outlier: 3.506A pdb=" N LYS C 21 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA C 229 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR C 101 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 231 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.731A pdb=" N LYS C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 76 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP C 254 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR C 256 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ALA C 79 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 153 through 157 removed outlier: 3.856A pdb=" N VAL C 86 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N SER C 82 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ALA C 79 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR C 256 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP C 254 " --> pdb=" O PRO C 81 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 251 through 260 current: chain 'C' and resid 280 through 285 Processing sheet with id=AB9, first strand: chain 'D' and resid 21 through 22 removed outlier: 3.511A pdb=" N LYS D 21 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET D 34 " --> pdb=" O ASP D 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 21 through 22 removed outlier: 3.511A pdb=" N LYS D 21 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA D 229 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR D 101 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 231 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 70 through 71 removed outlier: 3.743A pdb=" N LYS D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER D 76 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP D 254 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR D 256 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA D 79 " --> pdb=" O TYR D 256 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 157 removed outlier: 3.781A pdb=" N VAL D 86 " --> pdb=" O TRP D 167 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N SER D 82 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA D 79 " --> pdb=" O TYR D 256 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR D 256 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP D 254 " --> pdb=" O PRO D 81 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 251 through 260 current: chain 'D' and resid 280 through 285 Processing sheet with id=AC4, first strand: chain 'E' and resid 21 through 22 removed outlier: 3.538A pdb=" N LYS E 21 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET E 34 " --> pdb=" O ASP E 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 21 through 22 removed outlier: 3.538A pdb=" N LYS E 21 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA E 229 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR E 101 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL E 231 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 70 through 71 removed outlier: 3.758A pdb=" N LYS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 76 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP E 254 " --> pdb=" O PRO E 81 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR E 256 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ALA E 79 " --> pdb=" O TYR E 256 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 153 through 157 removed outlier: 3.724A pdb=" N VAL E 86 " --> pdb=" O TRP E 167 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N SER E 82 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ALA E 79 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR E 256 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP E 254 " --> pdb=" O PRO E 81 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 251 through 260 current: chain 'E' and resid 279 through 285 Processing sheet with id=AC8, first strand: chain 'F' and resid 21 through 22 removed outlier: 3.525A pdb=" N LYS F 21 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET F 34 " --> pdb=" O ASP F 29 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 21 through 22 removed outlier: 3.525A pdb=" N LYS F 21 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA F 229 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR F 101 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL F 231 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 70 through 71 removed outlier: 3.736A pdb=" N LYS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER F 76 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP F 254 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR F 256 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ALA F 79 " --> pdb=" O TYR F 256 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 153 through 157 removed outlier: 3.784A pdb=" N VAL F 86 " --> pdb=" O TRP F 167 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N SER F 82 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ALA F 79 " --> pdb=" O TYR F 256 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR F 256 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP F 254 " --> pdb=" O PRO F 81 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 251 through 260 current: chain 'F' and resid 280 through 285 545 hydrogen bonds defined for protein. 1464 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: 3.14 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2978 1.32 - 1.44: 4565 1.44 - 1.56: 9453 1.56 - 1.68: 14 1.68 - 1.80: 98 Bond restraints: 17108 Sorted by residual: bond pdb=" C SER C 159 " pdb=" N PRO C 160 " ideal model delta sigma weight residual 1.335 1.324 0.011 8.70e-03 1.32e+04 1.70e+00 bond pdb=" C SER G 159 " pdb=" N PRO G 160 " ideal model delta sigma weight residual 1.335 1.324 0.011 8.70e-03 1.32e+04 1.68e+00 bond pdb=" C SER A 159 " pdb=" N PRO A 160 " ideal model delta sigma weight residual 1.335 1.324 0.011 8.70e-03 1.32e+04 1.65e+00 bond pdb=" C SER D 159 " pdb=" N PRO D 160 " ideal model delta sigma weight residual 1.335 1.324 0.011 8.70e-03 1.32e+04 1.51e+00 bond pdb=" C SER B 159 " pdb=" N PRO B 160 " ideal model delta sigma weight residual 1.335 1.325 0.010 8.70e-03 1.32e+04 1.44e+00 ... (remaining 17103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 22042 0.99 - 1.98: 909 1.98 - 2.98: 115 2.98 - 3.97: 54 3.97 - 4.96: 8 Bond angle restraints: 23128 Sorted by residual: angle pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta sigma weight residual 121.80 117.23 4.57 2.44e+00 1.68e-01 3.51e+00 angle pdb=" N GLY C 166 " pdb=" CA GLY C 166 " pdb=" C GLY C 166 " ideal model delta sigma weight residual 110.80 113.93 -3.13 1.71e+00 3.42e-01 3.35e+00 angle pdb=" N GLY G 166 " pdb=" CA GLY G 166 " pdb=" C GLY G 166 " ideal model delta sigma weight residual 110.80 113.92 -3.12 1.71e+00 3.42e-01 3.33e+00 angle pdb=" N GLY F 166 " pdb=" CA GLY F 166 " pdb=" C GLY F 166 " ideal model delta sigma weight residual 110.80 113.91 -3.11 1.71e+00 3.42e-01 3.31e+00 angle pdb=" CA TYR A 102 " pdb=" CB TYR A 102 " pdb=" CG TYR A 102 " ideal model delta sigma weight residual 113.90 110.77 3.13 1.80e+00 3.09e-01 3.02e+00 ... (remaining 23123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 10135 35.78 - 71.55: 99 71.55 - 107.33: 7 107.33 - 143.11: 0 143.11 - 178.88: 7 Dihedral angle restraints: 10248 sinusoidal: 4284 harmonic: 5964 Sorted by residual: dihedral pdb=" O5 P1O D 301 " pdb=" C7 P1O D 301 " pdb=" C8 P1O D 301 " pdb=" O7 P1O D 301 " ideal model delta sinusoidal sigma weight residual 56.91 -121.97 178.88 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 P1O F 301 " pdb=" C7 P1O F 301 " pdb=" C8 P1O F 301 " pdb=" O7 P1O F 301 " ideal model delta sinusoidal sigma weight residual 56.91 -121.91 178.82 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 P1O E 301 " pdb=" C7 P1O E 301 " pdb=" C8 P1O E 301 " pdb=" O7 P1O E 301 " ideal model delta sinusoidal sigma weight residual 56.91 -121.70 178.61 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1409 0.025 - 0.049: 580 0.049 - 0.074: 216 0.074 - 0.098: 78 0.098 - 0.123: 160 Chirality restraints: 2443 Sorted by residual: chirality pdb=" CA ILE F 98 " pdb=" N ILE F 98 " pdb=" C ILE F 98 " pdb=" CB ILE F 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE B 98 " pdb=" N ILE B 98 " pdb=" C ILE B 98 " pdb=" CB ILE B 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA ILE A 98 " pdb=" N ILE A 98 " pdb=" C ILE A 98 " pdb=" CB ILE A 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 2440 not shown) Planarity restraints: 2961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 180 " -0.014 5.00e-02 4.00e+02 2.19e-02 7.65e-01 pdb=" N PRO C 181 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 180 " 0.014 5.00e-02 4.00e+02 2.07e-02 6.89e-01 pdb=" N PRO A 181 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 180 " 0.014 5.00e-02 4.00e+02 2.07e-02 6.87e-01 pdb=" N PRO G 181 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO G 181 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO G 181 " 0.012 5.00e-02 4.00e+02 ... (remaining 2958 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3279 2.77 - 3.30: 15775 3.30 - 3.83: 25393 3.83 - 4.37: 30953 4.37 - 4.90: 56857 Nonbonded interactions: 132257 Sorted by model distance: nonbonded pdb=" N GLU D 70 " pdb=" OE1 GLU D 70 " model vdw 2.237 3.120 nonbonded pdb=" N GLU A 70 " pdb=" OE1 GLU A 70 " model vdw 2.241 3.120 nonbonded pdb=" N GLU G 70 " pdb=" OE1 GLU G 70 " model vdw 2.244 3.120 nonbonded pdb=" OG1 THR A 129 " pdb=" NZ LYS A 131 " model vdw 2.246 3.120 nonbonded pdb=" OG1 THR E 129 " pdb=" NZ LYS E 131 " model vdw 2.248 3.120 ... (remaining 132252 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: 0.06 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.100 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 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 : 0.005 0.027 17108 Z= 0.234 Angle : 0.484 4.959 23128 Z= 0.260 Chirality : 0.042 0.123 2443 Planarity : 0.003 0.022 2961 Dihedral : 12.531 178.882 6440 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.76 % Allowed : 6.76 % Favored : 91.48 % 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 aren not related in a simple way. whole: -0.92 (0.19), residues: 2058 helix: None (None), residues: 0 sheet: -0.37 (0.17), residues: 987 loop : -0.75 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 104 TYR 0.012 0.001 TYR E 65 PHE 0.010 0.001 PHE F 224 TRP 0.007 0.001 TRP E 80 HIS 0.003 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00533 (17108) covalent geometry : angle 0.48353 (23128) hydrogen bonds : bond 0.25464 ( 524) hydrogen bonds : angle 11.13125 ( 1464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 630 time to evaluate : 0.659 Fit side-chains REVERT: G 29 ASP cc_start: 0.5015 (t0) cc_final: 0.4525 (t70) REVERT: G 30 LYS cc_start: 0.5602 (mttt) cc_final: 0.5338 (tptp) REVERT: G 38 VAL cc_start: 0.6319 (m) cc_final: 0.6046 (p) REVERT: G 44 ASP cc_start: 0.7029 (p0) cc_final: 0.6780 (t0) REVERT: G 64 GLN cc_start: 0.5850 (mm-40) cc_final: 0.5480 (mm110) REVERT: G 82 SER cc_start: 0.7064 (t) cc_final: 0.6694 (p) REVERT: G 87 GLN cc_start: 0.6041 (pt0) cc_final: 0.5646 (pt0) REVERT: G 136 ILE cc_start: 0.5133 (mm) cc_final: 0.4578 (pt) REVERT: G 154 LYS cc_start: 0.7002 (ttpp) cc_final: 0.6591 (ptmm) REVERT: G 186 SER cc_start: 0.5185 (t) cc_final: 0.4469 (p) REVERT: G 191 TYR cc_start: 0.5331 (m-10) cc_final: 0.5049 (m-80) REVERT: G 200 ARG cc_start: 0.5588 (mtt180) cc_final: 0.5144 (mtp85) REVERT: G 205 LYS cc_start: 0.4217 (ttmm) cc_final: 0.3407 (tttm) REVERT: G 227 ASP cc_start: 0.5986 (t0) cc_final: 0.5212 (m-30) REVERT: G 250 GLU cc_start: 0.5700 (pt0) cc_final: 0.4950 (pp20) REVERT: G 254 ASP cc_start: 0.6845 (m-30) cc_final: 0.6377 (m-30) REVERT: G 257 GLN cc_start: 0.5405 (mt0) cc_final: 0.4980 (mt0) REVERT: G 268 THR cc_start: 0.5783 (m) cc_final: 0.5453 (t) REVERT: G 276 ASP cc_start: 0.5462 (OUTLIER) cc_final: 0.4904 (m-30) REVERT: G 280 GLU cc_start: 0.6958 (tt0) cc_final: 0.6384 (tt0) REVERT: G 287 GLU cc_start: 0.6508 (tt0) cc_final: 0.6173 (mm-30) REVERT: G 289 GLU cc_start: 0.5102 (mt-10) cc_final: 0.4797 (mt-10) REVERT: A 29 ASP cc_start: 0.4768 (t0) cc_final: 0.4471 (t70) REVERT: A 30 LYS cc_start: 0.6094 (mttt) cc_final: 0.5791 (tttp) REVERT: A 38 VAL cc_start: 0.6744 (m) cc_final: 0.6522 (p) REVERT: A 49 ASN cc_start: 0.6076 (t0) cc_final: 0.5833 (t0) REVERT: A 82 SER cc_start: 0.7094 (t) cc_final: 0.6782 (p) REVERT: A 87 GLN cc_start: 0.6255 (pt0) cc_final: 0.5885 (pt0) REVERT: A 113 MET cc_start: 0.6131 (ttp) cc_final: 0.5865 (ttm) REVERT: A 136 ILE cc_start: 0.5067 (mm) cc_final: 0.4573 (pt) REVERT: A 145 THR cc_start: 0.6833 (m) cc_final: 0.6308 (t) REVERT: A 152 ASP cc_start: 0.5089 (m-30) cc_final: 0.4770 (t0) REVERT: A 186 SER cc_start: 0.5247 (t) cc_final: 0.4665 (m) REVERT: A 205 LYS cc_start: 0.4146 (ttmm) cc_final: 0.3432 (tmtt) REVERT: A 227 ASP cc_start: 0.5820 (t0) cc_final: 0.5080 (m-30) REVERT: A 250 GLU cc_start: 0.5694 (pt0) cc_final: 0.4921 (pp20) REVERT: A 254 ASP cc_start: 0.7266 (m-30) cc_final: 0.6424 (m-30) REVERT: A 255 ASP cc_start: 0.6219 (t0) cc_final: 0.5828 (t70) REVERT: A 257 GLN cc_start: 0.5230 (mt0) cc_final: 0.4889 (mt0) REVERT: A 268 THR cc_start: 0.5824 (m) cc_final: 0.5401 (t) REVERT: A 276 ASP cc_start: 0.5262 (OUTLIER) cc_final: 0.4596 (m-30) REVERT: A 280 GLU cc_start: 0.6863 (tt0) cc_final: 0.6201 (tt0) REVERT: A 290 GLU cc_start: 0.5801 (pt0) cc_final: 0.5368 (tt0) REVERT: B 29 ASP cc_start: 0.4893 (t0) cc_final: 0.4639 (t70) REVERT: B 30 LYS cc_start: 0.5960 (mttt) cc_final: 0.5690 (tttp) REVERT: B 32 ASN cc_start: 0.5560 (m110) cc_final: 0.5329 (m110) REVERT: B 44 ASP cc_start: 0.6906 (p0) cc_final: 0.6619 (t0) REVERT: B 64 GLN cc_start: 0.5805 (mm-40) cc_final: 0.5588 (mp10) REVERT: B 82 SER cc_start: 0.7019 (t) cc_final: 0.6577 (p) REVERT: B 87 GLN cc_start: 0.6227 (pt0) cc_final: 0.5846 (pt0) REVERT: B 113 MET cc_start: 0.5993 (ttp) cc_final: 0.5700 (ttm) REVERT: B 145 THR cc_start: 0.6830 (m) cc_final: 0.6281 (t) REVERT: B 152 ASP cc_start: 0.5324 (m-30) cc_final: 0.5091 (t0) REVERT: B 186 SER cc_start: 0.5142 (t) cc_final: 0.4677 (m) REVERT: B 191 TYR cc_start: 0.5161 (m-10) cc_final: 0.4958 (m-80) REVERT: B 200 ARG cc_start: 0.5733 (mtt180) cc_final: 0.5276 (mtp85) REVERT: B 205 LYS cc_start: 0.4065 (ttmm) cc_final: 0.3402 (tttm) REVERT: B 227 ASP cc_start: 0.5947 (t0) cc_final: 0.5163 (m-30) REVERT: B 250 GLU cc_start: 0.5808 (pt0) cc_final: 0.4981 (pp20) REVERT: B 254 ASP cc_start: 0.7136 (m-30) cc_final: 0.6359 (m-30) REVERT: B 255 ASP cc_start: 0.6149 (t0) cc_final: 0.5842 (t70) REVERT: B 257 GLN cc_start: 0.5265 (mt0) cc_final: 0.4681 (mt0) REVERT: B 268 THR cc_start: 0.5905 (m) cc_final: 0.5494 (t) REVERT: B 276 ASP cc_start: 0.5237 (OUTLIER) cc_final: 0.4632 (m-30) REVERT: B 280 GLU cc_start: 0.6826 (tt0) cc_final: 0.6329 (tt0) REVERT: B 287 GLU cc_start: 0.6597 (tt0) cc_final: 0.6150 (mm-30) REVERT: B 290 GLU cc_start: 0.5645 (pt0) cc_final: 0.5279 (pt0) REVERT: C 29 ASP cc_start: 0.4990 (t0) cc_final: 0.4571 (t0) REVERT: C 30 LYS cc_start: 0.6094 (mttt) cc_final: 0.5721 (tptm) REVERT: C 32 ASN cc_start: 0.5564 (m110) cc_final: 0.5128 (m110) REVERT: C 34 MET cc_start: 0.6905 (mtt) cc_final: 0.6638 (mtp) REVERT: C 38 VAL cc_start: 0.6538 (m) cc_final: 0.6223 (p) REVERT: C 49 ASN cc_start: 0.5940 (t0) cc_final: 0.5722 (t0) REVERT: C 56 ARG cc_start: 0.6068 (mtp85) cc_final: 0.5854 (mtp85) REVERT: C 64 GLN cc_start: 0.5759 (mm-40) cc_final: 0.5504 (mm110) REVERT: C 82 SER cc_start: 0.7009 (t) cc_final: 0.6494 (p) REVERT: C 87 GLN cc_start: 0.6163 (pt0) cc_final: 0.5943 (pt0) REVERT: C 89 GLN cc_start: 0.6117 (tt0) cc_final: 0.5905 (tt0) REVERT: C 113 MET cc_start: 0.6163 (ttp) cc_final: 0.5945 (ttm) REVERT: C 145 THR cc_start: 0.6869 (m) cc_final: 0.6259 (t) REVERT: C 164 LYS cc_start: 0.5646 (pttp) cc_final: 0.4938 (ptmm) REVERT: C 186 SER cc_start: 0.5383 (t) cc_final: 0.4654 (p) REVERT: C 205 LYS cc_start: 0.4379 (ttmm) cc_final: 0.3693 (tttm) REVERT: C 227 ASP cc_start: 0.5880 (t0) cc_final: 0.5153 (m-30) REVERT: C 250 GLU cc_start: 0.5702 (pt0) cc_final: 0.4969 (pp20) REVERT: C 254 ASP cc_start: 0.7167 (m-30) cc_final: 0.6491 (m-30) REVERT: C 268 THR cc_start: 0.5569 (m) cc_final: 0.5209 (t) REVERT: C 275 THR cc_start: 0.6910 (p) cc_final: 0.6669 (m) REVERT: C 276 ASP cc_start: 0.5424 (OUTLIER) cc_final: 0.4722 (m-30) REVERT: C 280 GLU cc_start: 0.6912 (tt0) cc_final: 0.6365 (tt0) REVERT: C 281 ARG cc_start: 0.6487 (ttm-80) cc_final: 0.6239 (ttm-80) REVERT: C 283 LYS cc_start: 0.5307 (ttpp) cc_final: 0.5092 (ttmt) REVERT: C 287 GLU cc_start: 0.6654 (tt0) cc_final: 0.6451 (mt-10) REVERT: C 289 GLU cc_start: 0.5173 (mt-10) cc_final: 0.4802 (mt-10) REVERT: D 21 LYS cc_start: 0.5744 (mttp) cc_final: 0.5544 (mttt) REVERT: D 29 ASP cc_start: 0.4760 (t0) cc_final: 0.4231 (t70) REVERT: D 30 LYS cc_start: 0.6030 (mttt) cc_final: 0.5757 (tptp) REVERT: D 32 ASN cc_start: 0.5454 (m110) cc_final: 0.5121 (m110) REVERT: D 34 MET cc_start: 0.6800 (mtt) cc_final: 0.6524 (mtt) REVERT: D 44 ASP cc_start: 0.6982 (p0) cc_final: 0.6747 (t0) REVERT: D 64 GLN cc_start: 0.5933 (mm-40) cc_final: 0.5732 (mm110) REVERT: D 82 SER cc_start: 0.6929 (t) cc_final: 0.6417 (p) REVERT: D 87 GLN cc_start: 0.6189 (pt0) cc_final: 0.5844 (pt0) REVERT: D 89 GLN cc_start: 0.6075 (tt0) cc_final: 0.5757 (tt0) REVERT: D 186 SER cc_start: 0.5481 (t) cc_final: 0.4926 (m) REVERT: D 205 LYS cc_start: 0.4203 (ttmm) cc_final: 0.3542 (tmtt) REVERT: D 227 ASP cc_start: 0.5994 (t0) cc_final: 0.5309 (m-30) REVERT: D 230 THR cc_start: 0.6839 (OUTLIER) cc_final: 0.6598 (t) REVERT: D 250 GLU cc_start: 0.5565 (pt0) cc_final: 0.4758 (pp20) REVERT: D 254 ASP cc_start: 0.7227 (m-30) cc_final: 0.6492 (m-30) REVERT: D 255 ASP cc_start: 0.6089 (t0) cc_final: 0.5658 (t70) REVERT: D 257 GLN cc_start: 0.5333 (mt0) cc_final: 0.4989 (mt0) REVERT: D 268 THR cc_start: 0.5668 (m) cc_final: 0.5297 (t) REVERT: D 276 ASP cc_start: 0.5298 (OUTLIER) cc_final: 0.4778 (m-30) REVERT: D 280 GLU cc_start: 0.7065 (tt0) cc_final: 0.6485 (tt0) REVERT: D 289 GLU cc_start: 0.5326 (mt-10) cc_final: 0.5067 (mt-10) REVERT: E 29 ASP cc_start: 0.4568 (t0) cc_final: 0.4073 (t70) REVERT: E 38 VAL cc_start: 0.6476 (m) cc_final: 0.6255 (p) REVERT: E 44 ASP cc_start: 0.6962 (p0) cc_final: 0.6695 (t0) REVERT: E 56 ARG cc_start: 0.5909 (mtp85) cc_final: 0.5403 (mtt90) REVERT: E 64 GLN cc_start: 0.5655 (mm-40) cc_final: 0.5374 (mm110) REVERT: E 82 SER cc_start: 0.6890 (t) cc_final: 0.6437 (p) REVERT: E 87 GLN cc_start: 0.6295 (pt0) cc_final: 0.5892 (pt0) REVERT: E 113 MET cc_start: 0.6038 (ttp) cc_final: 0.5773 (ttm) REVERT: E 145 THR cc_start: 0.6879 (m) cc_final: 0.6365 (t) REVERT: E 152 ASP cc_start: 0.5122 (m-30) cc_final: 0.4867 (t0) REVERT: E 186 SER cc_start: 0.5289 (t) cc_final: 0.4776 (m) REVERT: E 205 LYS cc_start: 0.4173 (ttmm) cc_final: 0.3293 (tmtt) REVERT: E 227 ASP cc_start: 0.6111 (t0) cc_final: 0.5347 (m-30) REVERT: E 250 GLU cc_start: 0.5667 (pt0) cc_final: 0.4873 (pp20) REVERT: E 254 ASP cc_start: 0.7248 (m-30) cc_final: 0.6665 (m-30) REVERT: E 257 GLN cc_start: 0.5296 (mt0) cc_final: 0.5085 (mt0) REVERT: E 268 THR cc_start: 0.5842 (m) cc_final: 0.5513 (t) REVERT: E 276 ASP cc_start: 0.5204 (OUTLIER) cc_final: 0.4604 (m-30) REVERT: E 280 GLU cc_start: 0.6986 (tt0) cc_final: 0.6360 (tt0) REVERT: E 287 GLU cc_start: 0.6366 (tt0) cc_final: 0.5973 (mm-30) REVERT: E 289 GLU cc_start: 0.5307 (mt-10) cc_final: 0.5093 (mt-10) REVERT: E 290 GLU cc_start: 0.5888 (pt0) cc_final: 0.5336 (pt0) REVERT: F 29 ASP cc_start: 0.4446 (t0) cc_final: 0.4149 (t70) REVERT: F 30 LYS cc_start: 0.5990 (mttt) cc_final: 0.5696 (tttp) REVERT: F 64 GLN cc_start: 0.5924 (mm-40) cc_final: 0.5724 (mm110) REVERT: F 82 SER cc_start: 0.7237 (t) cc_final: 0.6784 (p) REVERT: F 87 GLN cc_start: 0.6185 (pt0) cc_final: 0.5761 (pt0) REVERT: F 89 GLN cc_start: 0.6360 (tt0) cc_final: 0.6045 (tt0) REVERT: F 113 MET cc_start: 0.6091 (ttp) cc_final: 0.5865 (ttm) REVERT: F 145 THR cc_start: 0.6976 (m) cc_final: 0.6452 (t) REVERT: F 152 ASP cc_start: 0.5256 (m-30) cc_final: 0.4955 (t0) REVERT: F 186 SER cc_start: 0.5294 (t) cc_final: 0.4528 (p) REVERT: F 200 ARG cc_start: 0.5689 (mtt180) cc_final: 0.5348 (mtp85) REVERT: F 205 LYS cc_start: 0.4368 (ttmm) cc_final: 0.3580 (tmtt) REVERT: F 227 ASP cc_start: 0.6170 (t0) cc_final: 0.5211 (m-30) REVERT: F 245 ILE cc_start: 0.5435 (mm) cc_final: 0.5231 (tp) REVERT: F 250 GLU cc_start: 0.5639 (pt0) cc_final: 0.4827 (pp20) REVERT: F 254 ASP cc_start: 0.7175 (m-30) cc_final: 0.6652 (m-30) REVERT: F 255 ASP cc_start: 0.6171 (t0) cc_final: 0.5945 (t70) REVERT: F 257 GLN cc_start: 0.5304 (mt0) cc_final: 0.5025 (mt0) REVERT: F 268 THR cc_start: 0.5582 (m) cc_final: 0.5249 (t) REVERT: F 276 ASP cc_start: 0.5445 (OUTLIER) cc_final: 0.4830 (m-30) REVERT: F 280 GLU cc_start: 0.6648 (tt0) cc_final: 0.6395 (tt0) REVERT: F 281 ARG cc_start: 0.6283 (ttm-80) cc_final: 0.6081 (ttm-80) REVERT: F 287 GLU cc_start: 0.6379 (tt0) cc_final: 0.6112 (mm-30) outliers start: 32 outliers final: 16 residues processed: 646 average time/residue: 0.6027 time to fit residues: 434.7763 Evaluate side-chains 402 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 378 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 276 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 49 ASN G 172 ASN G 257 GLN A 64 GLN A 257 GLN B 172 ASN B 257 GLN D 49 ASN D 257 GLN E 49 ASN E 178 ASN E 257 GLN F 49 ASN F 172 ASN F 257 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.154579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127703 restraints weight = 99268.800| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.54 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17108 Z= 0.122 Angle : 0.612 10.919 23128 Z= 0.324 Chirality : 0.046 0.145 2443 Planarity : 0.004 0.027 2961 Dihedral : 14.667 176.780 2491 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.63 % Allowed : 15.88 % Favored : 80.49 % 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 aren not related in a simple way. whole: -0.59 (0.18), residues: 2058 helix: -0.91 (0.84), residues: 42 sheet: 0.35 (0.16), residues: 1078 loop : -1.24 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 281 TYR 0.010 0.001 TYR F 191 PHE 0.011 0.001 PHE B 42 TRP 0.008 0.001 TRP E 260 HIS 0.002 0.000 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00267 (17108) covalent geometry : angle 0.61249 (23128) hydrogen bonds : bond 0.03537 ( 524) hydrogen bonds : angle 6.92625 ( 1464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 413 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: G 136 ILE cc_start: 0.7653 (mm) cc_final: 0.7265 (pp) REVERT: G 205 LYS cc_start: 0.7510 (ttmm) cc_final: 0.6476 (tttm) REVERT: G 257 GLN cc_start: 0.7913 (mt0) cc_final: 0.7627 (mt0) REVERT: G 258 LEU cc_start: 0.7647 (pp) cc_final: 0.7371 (pp) REVERT: G 289 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7149 (mt-10) REVERT: A 56 ARG cc_start: 0.7678 (mtp85) cc_final: 0.7460 (mtp85) REVERT: A 136 ILE cc_start: 0.7722 (mm) cc_final: 0.7359 (pt) REVERT: A 186 SER cc_start: 0.8020 (t) cc_final: 0.7641 (m) REVERT: A 205 LYS cc_start: 0.7329 (ttmm) cc_final: 0.6292 (tmtt) REVERT: A 258 LEU cc_start: 0.7721 (pp) cc_final: 0.7514 (pp) REVERT: A 280 GLU cc_start: 0.7881 (tt0) cc_final: 0.7624 (tt0) REVERT: B 21 LYS cc_start: 0.8144 (mttt) cc_final: 0.7856 (mtpt) REVERT: B 24 ASP cc_start: 0.7468 (t0) cc_final: 0.7255 (t0) REVERT: B 29 ASP cc_start: 0.7722 (t0) cc_final: 0.7413 (t70) REVERT: B 258 LEU cc_start: 0.7678 (pp) cc_final: 0.7391 (pp) REVERT: B 290 GLU cc_start: 0.7251 (pt0) cc_final: 0.7041 (pt0) REVERT: C 21 LYS cc_start: 0.8114 (mttt) cc_final: 0.7832 (mppt) REVERT: C 136 ILE cc_start: 0.7696 (tp) cc_final: 0.7284 (pp) REVERT: C 186 SER cc_start: 0.8027 (t) cc_final: 0.7744 (m) REVERT: C 205 LYS cc_start: 0.7570 (ttmm) cc_final: 0.6594 (tttm) REVERT: C 258 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7505 (pp) REVERT: C 289 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7193 (mt-10) REVERT: D 205 LYS cc_start: 0.7262 (ttmm) cc_final: 0.6366 (tmtt) REVERT: D 257 GLN cc_start: 0.7858 (mt0) cc_final: 0.7615 (mt0) REVERT: D 289 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7212 (mt-10) REVERT: E 30 LYS cc_start: 0.7965 (tttp) cc_final: 0.7693 (ttpt) REVERT: E 56 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7534 (mmm-85) REVERT: E 186 SER cc_start: 0.8031 (t) cc_final: 0.7751 (m) REVERT: E 205 LYS cc_start: 0.7368 (ttmm) cc_final: 0.6447 (tmtt) REVERT: E 257 GLN cc_start: 0.7878 (mt0) cc_final: 0.7608 (mt0) REVERT: E 258 LEU cc_start: 0.7679 (pp) cc_final: 0.7478 (pp) REVERT: E 289 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7039 (mt-10) REVERT: E 290 GLU cc_start: 0.7218 (pt0) cc_final: 0.6903 (pt0) REVERT: F 21 LYS cc_start: 0.8252 (mttt) cc_final: 0.7976 (mtpt) REVERT: F 56 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7587 (mtt90) REVERT: F 205 LYS cc_start: 0.7390 (ttmm) cc_final: 0.6398 (tmtt) REVERT: F 257 GLN cc_start: 0.7783 (mt0) cc_final: 0.7458 (mt0) REVERT: F 277 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7342 (mtp180) REVERT: F 288 LYS cc_start: 0.7863 (tppt) cc_final: 0.7498 (mttm) outliers start: 66 outliers final: 29 residues processed: 466 average time/residue: 0.5734 time to fit residues: 299.6538 Evaluate side-chains 333 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 303 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 153 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 173 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 166 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 49 ASN G 64 GLN A 49 ASN A 64 GLN B 49 ASN B 194 GLN C 32 ASN C 49 ASN C 64 GLN D 32 ASN D 49 ASN D 64 GLN E 49 ASN E 64 GLN F 64 GLN F 178 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.150959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.124482 restraints weight = 76492.093| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.59 r_work: 0.3191 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17108 Z= 0.132 Angle : 0.579 9.365 23128 Z= 0.306 Chirality : 0.045 0.148 2443 Planarity : 0.004 0.034 2961 Dihedral : 14.178 179.102 2466 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.07 % Allowed : 20.82 % Favored : 75.11 % 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 aren not related in a simple way. whole: -0.49 (0.18), residues: 2058 helix: -1.20 (0.81), residues: 42 sheet: 0.51 (0.16), residues: 1078 loop : -1.30 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 281 TYR 0.016 0.002 TYR C 191 PHE 0.009 0.001 PHE F 224 TRP 0.007 0.001 TRP E 260 HIS 0.003 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00307 (17108) covalent geometry : angle 0.57914 (23128) hydrogen bonds : bond 0.03286 ( 524) hydrogen bonds : angle 6.41720 ( 1464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 326 time to evaluate : 0.677 Fit side-chains REVERT: G 136 ILE cc_start: 0.7672 (mm) cc_final: 0.7178 (pp) REVERT: G 198 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7757 (ttmt) REVERT: G 225 SER cc_start: 0.8597 (p) cc_final: 0.8379 (t) REVERT: G 257 GLN cc_start: 0.8358 (mt0) cc_final: 0.8060 (mt0) REVERT: G 258 LEU cc_start: 0.8023 (pp) cc_final: 0.7779 (pp) REVERT: G 289 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7671 (mt-10) REVERT: A 136 ILE cc_start: 0.7683 (mm) cc_final: 0.7345 (pt) REVERT: A 186 SER cc_start: 0.8348 (t) cc_final: 0.7995 (m) REVERT: A 205 LYS cc_start: 0.7351 (ttmm) cc_final: 0.6431 (tmtt) REVERT: A 275 THR cc_start: 0.8050 (p) cc_final: 0.7785 (t) REVERT: B 21 LYS cc_start: 0.8445 (mttt) cc_final: 0.8015 (mtpt) REVERT: B 136 ILE cc_start: 0.7473 (tp) cc_final: 0.7182 (pt) REVERT: B 258 LEU cc_start: 0.7993 (pp) cc_final: 0.7761 (pp) REVERT: C 136 ILE cc_start: 0.7578 (tp) cc_final: 0.7351 (pt) REVERT: C 186 SER cc_start: 0.8266 (t) cc_final: 0.7986 (m) REVERT: C 205 LYS cc_start: 0.7478 (ttmm) cc_final: 0.6598 (tttm) REVERT: C 225 SER cc_start: 0.8691 (p) cc_final: 0.8392 (t) REVERT: C 258 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7814 (pp) REVERT: C 289 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7576 (mt-10) REVERT: C 290 GLU cc_start: 0.7866 (pt0) cc_final: 0.7469 (pt0) REVERT: D 136 ILE cc_start: 0.7577 (tp) cc_final: 0.7213 (pp) REVERT: D 205 LYS cc_start: 0.7377 (ttmm) cc_final: 0.6545 (tttm) REVERT: D 257 GLN cc_start: 0.8372 (mt0) cc_final: 0.8139 (mt0) REVERT: D 289 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7655 (mt-10) REVERT: E 30 LYS cc_start: 0.8387 (tttp) cc_final: 0.8009 (ttmm) REVERT: E 56 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7909 (mmm-85) REVERT: E 136 ILE cc_start: 0.7441 (tp) cc_final: 0.7175 (pt) REVERT: E 186 SER cc_start: 0.8218 (t) cc_final: 0.7888 (m) REVERT: E 205 LYS cc_start: 0.7415 (ttmm) cc_final: 0.6510 (tmtt) REVERT: E 253 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.6851 (mtp180) REVERT: E 257 GLN cc_start: 0.8457 (mt0) cc_final: 0.8173 (mt0) REVERT: E 289 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7656 (mt-10) REVERT: E 290 GLU cc_start: 0.7863 (pt0) cc_final: 0.7564 (pt0) REVERT: F 21 LYS cc_start: 0.8553 (mttt) cc_final: 0.8140 (mtpt) REVERT: F 56 ARG cc_start: 0.8334 (mtp85) cc_final: 0.8028 (mtt90) REVERT: F 64 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7485 (mp10) REVERT: F 136 ILE cc_start: 0.7628 (tp) cc_final: 0.7286 (pp) REVERT: F 141 SER cc_start: 0.8397 (m) cc_final: 0.8005 (t) REVERT: F 205 LYS cc_start: 0.7473 (ttmm) cc_final: 0.6488 (tmtt) REVERT: F 225 SER cc_start: 0.8772 (p) cc_final: 0.8536 (t) REVERT: F 257 GLN cc_start: 0.8504 (mt0) cc_final: 0.8167 (mt0) REVERT: F 277 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7846 (mtp180) REVERT: F 288 LYS cc_start: 0.8254 (mppt) cc_final: 0.7905 (mttm) REVERT: F 290 GLU cc_start: 0.7803 (pt0) cc_final: 0.7418 (pt0) outliers start: 74 outliers final: 40 residues processed: 375 average time/residue: 0.6546 time to fit residues: 271.8148 Evaluate side-chains 347 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 304 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 101 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 49 ASN G 64 GLN G 178 ASN G 194 GLN A 64 GLN B 172 ASN B 178 ASN B 194 GLN B 241 GLN C 32 ASN C 64 GLN C 241 GLN D 64 GLN D 194 GLN E 49 ASN E 64 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118697 restraints weight = 93275.645| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.92 r_work: 0.3091 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17108 Z= 0.258 Angle : 0.707 12.047 23128 Z= 0.369 Chirality : 0.050 0.154 2443 Planarity : 0.005 0.046 2961 Dihedral : 13.846 179.459 2464 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.77 % Allowed : 21.04 % Favored : 73.19 % 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 aren not related in a simple way. whole: -0.60 (0.18), residues: 2058 helix: -0.89 (0.93), residues: 42 sheet: 0.64 (0.16), residues: 1043 loop : -1.59 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 184 TYR 0.024 0.003 TYR C 191 PHE 0.013 0.002 PHE B 42 TRP 0.010 0.002 TRP G 274 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00619 (17108) covalent geometry : angle 0.70744 (23128) hydrogen bonds : bond 0.03604 ( 524) hydrogen bonds : angle 6.62479 ( 1464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 312 time to evaluate : 0.708 Fit side-chains REVERT: G 13 ASP cc_start: 0.7621 (m-30) cc_final: 0.7403 (m-30) REVERT: G 136 ILE cc_start: 0.7641 (mm) cc_final: 0.7235 (pt) REVERT: G 198 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7901 (ttmt) REVERT: G 200 ARG cc_start: 0.7681 (mtp85) cc_final: 0.6819 (mtp85) REVERT: G 205 LYS cc_start: 0.7588 (ttmm) cc_final: 0.6592 (tttm) REVERT: G 257 GLN cc_start: 0.8429 (mt0) cc_final: 0.8215 (mt0) REVERT: G 289 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7671 (mt-10) REVERT: A 136 ILE cc_start: 0.7733 (mm) cc_final: 0.7360 (pt) REVERT: A 186 SER cc_start: 0.8362 (t) cc_final: 0.8070 (m) REVERT: A 205 LYS cc_start: 0.7505 (ttmm) cc_final: 0.6601 (tmtt) REVERT: A 273 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8267 (tptm) REVERT: A 277 ARG cc_start: 0.8328 (mtm180) cc_final: 0.7990 (mtp180) REVERT: A 289 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 290 GLU cc_start: 0.7625 (pt0) cc_final: 0.7276 (pt0) REVERT: B 21 LYS cc_start: 0.8407 (mttt) cc_final: 0.8009 (mtpt) REVERT: B 136 ILE cc_start: 0.7557 (tp) cc_final: 0.7295 (pt) REVERT: B 205 LYS cc_start: 0.7702 (ttmm) cc_final: 0.6811 (tttm) REVERT: B 289 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7879 (mt-10) REVERT: C 75 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7178 (ttpp) REVERT: C 136 ILE cc_start: 0.7721 (tp) cc_final: 0.7510 (pt) REVERT: C 186 SER cc_start: 0.8114 (t) cc_final: 0.7907 (m) REVERT: C 205 LYS cc_start: 0.7612 (ttmm) cc_final: 0.6641 (tttm) REVERT: C 225 SER cc_start: 0.8734 (p) cc_final: 0.8438 (t) REVERT: C 237 LYS cc_start: 0.7573 (ptpp) cc_final: 0.7091 (mppt) REVERT: C 289 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7787 (mt-10) REVERT: C 290 GLU cc_start: 0.7970 (pt0) cc_final: 0.7588 (pt0) REVERT: D 75 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7278 (ttpp) REVERT: D 136 ILE cc_start: 0.7635 (tp) cc_final: 0.7309 (pp) REVERT: D 205 LYS cc_start: 0.7611 (ttmm) cc_final: 0.6713 (tttm) REVERT: D 289 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7801 (mt-10) REVERT: E 30 LYS cc_start: 0.8452 (tttp) cc_final: 0.8110 (ttpt) REVERT: E 56 ARG cc_start: 0.8380 (mtp85) cc_final: 0.8105 (mmm-85) REVERT: E 70 GLU cc_start: 0.6322 (pm20) cc_final: 0.5962 (mt-10) REVERT: E 136 ILE cc_start: 0.7464 (tp) cc_final: 0.7238 (pt) REVERT: E 186 SER cc_start: 0.8321 (t) cc_final: 0.8005 (m) REVERT: E 205 LYS cc_start: 0.7567 (ttmm) cc_final: 0.6595 (tmtt) REVERT: E 253 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7195 (mtp180) REVERT: E 289 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7689 (mt-10) REVERT: E 290 GLU cc_start: 0.8017 (pt0) cc_final: 0.7700 (pt0) REVERT: F 70 GLU cc_start: 0.6374 (pm20) cc_final: 0.6034 (mt-10) REVERT: F 100 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: F 205 LYS cc_start: 0.7655 (ttmm) cc_final: 0.6655 (tmtt) REVERT: F 225 SER cc_start: 0.8865 (p) cc_final: 0.8544 (t) REVERT: F 257 GLN cc_start: 0.8516 (mt0) cc_final: 0.8266 (mt0) REVERT: F 271 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8275 (mtpt) REVERT: F 288 LYS cc_start: 0.8375 (mppt) cc_final: 0.8045 (mttm) REVERT: F 290 GLU cc_start: 0.7929 (pt0) cc_final: 0.7572 (pt0) outliers start: 105 outliers final: 63 residues processed: 384 average time/residue: 0.6439 time to fit residues: 272.7517 Evaluate side-chains 373 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 303 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 271 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 90 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 164 optimal weight: 0.2980 chunk 162 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 139 ASN A 64 GLN B 241 GLN C 32 ASN C 64 GLN D 32 ASN E 64 GLN E 259 HIS F 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119501 restraints weight = 88286.942| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.75 r_work: 0.3118 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17108 Z= 0.175 Angle : 0.618 10.929 23128 Z= 0.325 Chirality : 0.047 0.142 2443 Planarity : 0.004 0.034 2961 Dihedral : 13.638 178.610 2464 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.84 % Allowed : 22.75 % Favored : 72.42 % 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 aren not related in a simple way. whole: -0.63 (0.18), residues: 2058 helix: -1.18 (0.87), residues: 42 sheet: 0.64 (0.16), residues: 1043 loop : -1.63 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 281 TYR 0.019 0.002 TYR C 191 PHE 0.012 0.002 PHE B 196 TRP 0.011 0.001 TRP E 260 HIS 0.012 0.002 HIS D 259 Details of bonding type rmsd covalent geometry : bond 0.00415 (17108) covalent geometry : angle 0.61795 (23128) hydrogen bonds : bond 0.03190 ( 524) hydrogen bonds : angle 6.28227 ( 1464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 304 time to evaluate : 0.624 Fit side-chains REVERT: G 13 ASP cc_start: 0.7665 (m-30) cc_final: 0.7463 (m-30) REVERT: G 70 GLU cc_start: 0.6848 (pm20) cc_final: 0.6436 (mt-10) REVERT: G 136 ILE cc_start: 0.7550 (mm) cc_final: 0.7186 (pt) REVERT: G 198 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7900 (ttmt) REVERT: G 205 LYS cc_start: 0.7528 (ttmm) cc_final: 0.6564 (tttm) REVERT: G 257 GLN cc_start: 0.8395 (mt0) cc_final: 0.8142 (mt0) REVERT: G 289 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7573 (mt-10) REVERT: A 136 ILE cc_start: 0.7676 (mm) cc_final: 0.7334 (pt) REVERT: A 186 SER cc_start: 0.8335 (t) cc_final: 0.8017 (m) REVERT: A 205 LYS cc_start: 0.7454 (ttmm) cc_final: 0.6582 (tmtt) REVERT: A 290 GLU cc_start: 0.7642 (pt0) cc_final: 0.7293 (pt0) REVERT: B 21 LYS cc_start: 0.8362 (mttt) cc_final: 0.7974 (mtpt) REVERT: B 136 ILE cc_start: 0.7468 (tp) cc_final: 0.7259 (pt) REVERT: B 205 LYS cc_start: 0.7639 (ttmm) cc_final: 0.6798 (tttm) REVERT: B 289 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7845 (mt-10) REVERT: C 75 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7276 (ttpp) REVERT: C 186 SER cc_start: 0.8140 (t) cc_final: 0.7875 (m) REVERT: C 200 ARG cc_start: 0.7678 (mtp85) cc_final: 0.7132 (mtp85) REVERT: C 205 LYS cc_start: 0.7608 (ttmm) cc_final: 0.6703 (tttm) REVERT: C 225 SER cc_start: 0.8675 (p) cc_final: 0.8396 (t) REVERT: C 289 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7748 (mt-10) REVERT: C 290 GLU cc_start: 0.7935 (pt0) cc_final: 0.7559 (pt0) REVERT: D 60 THR cc_start: 0.8303 (m) cc_final: 0.7797 (m) REVERT: D 75 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7256 (ttpp) REVERT: D 136 ILE cc_start: 0.7526 (tp) cc_final: 0.7245 (pp) REVERT: D 205 LYS cc_start: 0.7525 (ttmm) cc_final: 0.6654 (tttm) REVERT: D 289 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7801 (mt-10) REVERT: E 30 LYS cc_start: 0.8404 (tttp) cc_final: 0.8020 (ttmm) REVERT: E 56 ARG cc_start: 0.8356 (mtp85) cc_final: 0.8094 (mmm-85) REVERT: E 70 GLU cc_start: 0.6246 (pm20) cc_final: 0.5973 (pt0) REVERT: E 186 SER cc_start: 0.8286 (t) cc_final: 0.8002 (m) REVERT: E 205 LYS cc_start: 0.7485 (ttmm) cc_final: 0.6520 (tmtt) REVERT: E 227 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: E 289 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7600 (mt-10) REVERT: E 290 GLU cc_start: 0.7966 (pt0) cc_final: 0.7651 (pt0) REVERT: F 4 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: F 70 GLU cc_start: 0.6374 (pm20) cc_final: 0.5957 (mt-10) REVERT: F 100 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: F 194 GLN cc_start: 0.8260 (mt0) cc_final: 0.8055 (mt0) REVERT: F 205 LYS cc_start: 0.7718 (ttmm) cc_final: 0.6686 (tmtt) REVERT: F 257 GLN cc_start: 0.8530 (mt0) cc_final: 0.8286 (mt0) REVERT: F 271 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8258 (mtpt) REVERT: F 290 GLU cc_start: 0.7921 (pt0) cc_final: 0.7583 (pt0) outliers start: 88 outliers final: 56 residues processed: 371 average time/residue: 0.5810 time to fit residues: 238.5980 Evaluate side-chains 352 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 289 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 4 ASP Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 271 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 0.1980 chunk 135 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 49 ASN A 32 ASN A 49 ASN A 194 GLN B 241 GLN C 32 ASN D 241 GLN E 64 GLN E 194 GLN F 49 ASN F 64 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118147 restraints weight = 93953.439| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.83 r_work: 0.3084 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17108 Z= 0.233 Angle : 0.678 11.408 23128 Z= 0.356 Chirality : 0.049 0.151 2443 Planarity : 0.005 0.036 2961 Dihedral : 13.721 178.103 2464 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 5.49 % Allowed : 22.25 % Favored : 72.25 % 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 aren not related in a simple way. whole: -0.71 (0.18), residues: 2058 helix: -1.06 (0.92), residues: 42 sheet: 0.63 (0.16), residues: 1043 loop : -1.74 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 184 TYR 0.021 0.002 TYR E 191 PHE 0.012 0.002 PHE B 42 TRP 0.010 0.001 TRP C 274 HIS 0.009 0.002 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00556 (17108) covalent geometry : angle 0.67790 (23128) hydrogen bonds : bond 0.03416 ( 524) hydrogen bonds : angle 6.43262 ( 1464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 298 time to evaluate : 0.679 Fit side-chains REVERT: G 70 GLU cc_start: 0.6856 (pm20) cc_final: 0.6421 (mt-10) REVERT: G 113 MET cc_start: 0.8875 (ttm) cc_final: 0.8571 (mtp) REVERT: G 136 ILE cc_start: 0.7536 (mm) cc_final: 0.7130 (pt) REVERT: G 198 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7916 (ttmt) REVERT: G 205 LYS cc_start: 0.7542 (ttmm) cc_final: 0.6600 (tttm) REVERT: G 257 GLN cc_start: 0.8444 (mt0) cc_final: 0.8228 (mt0) REVERT: G 289 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7760 (mt-10) REVERT: A 70 GLU cc_start: 0.6400 (pm20) cc_final: 0.6004 (pt0) REVERT: A 136 ILE cc_start: 0.7734 (mm) cc_final: 0.7361 (pt) REVERT: A 186 SER cc_start: 0.8237 (t) cc_final: 0.7983 (m) REVERT: A 205 LYS cc_start: 0.7527 (ttmm) cc_final: 0.6666 (tmtt) REVERT: A 258 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8034 (pp) REVERT: A 289 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7765 (mt-10) REVERT: A 290 GLU cc_start: 0.7756 (pt0) cc_final: 0.7426 (pt0) REVERT: B 70 GLU cc_start: 0.6543 (pm20) cc_final: 0.6201 (mt-10) REVERT: B 136 ILE cc_start: 0.7542 (tp) cc_final: 0.7332 (pt) REVERT: B 205 LYS cc_start: 0.7674 (ttmm) cc_final: 0.6860 (tttm) REVERT: B 289 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7924 (mt-10) REVERT: C 70 GLU cc_start: 0.6389 (pm20) cc_final: 0.6034 (mt-10) REVERT: C 75 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7443 (ttpp) REVERT: C 186 SER cc_start: 0.8110 (t) cc_final: 0.7909 (m) REVERT: C 205 LYS cc_start: 0.7618 (ttmm) cc_final: 0.6673 (tttm) REVERT: C 225 SER cc_start: 0.8677 (p) cc_final: 0.8397 (t) REVERT: C 289 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7891 (mt-10) REVERT: C 290 GLU cc_start: 0.8010 (pt0) cc_final: 0.7650 (pt0) REVERT: D 70 GLU cc_start: 0.6636 (pm20) cc_final: 0.6304 (pt0) REVERT: D 136 ILE cc_start: 0.7578 (tp) cc_final: 0.7301 (pp) REVERT: D 205 LYS cc_start: 0.7641 (ttmm) cc_final: 0.6718 (tttm) REVERT: D 289 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7834 (mt-10) REVERT: E 30 LYS cc_start: 0.8509 (tttp) cc_final: 0.8185 (ttpt) REVERT: E 32 ASN cc_start: 0.8498 (m110) cc_final: 0.8217 (m-40) REVERT: E 70 GLU cc_start: 0.6406 (pm20) cc_final: 0.6014 (pt0) REVERT: E 186 SER cc_start: 0.8194 (t) cc_final: 0.7898 (m) REVERT: E 205 LYS cc_start: 0.7620 (ttmm) cc_final: 0.6652 (tmtt) REVERT: E 227 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6922 (m-30) REVERT: E 253 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7216 (mtp180) REVERT: E 289 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7814 (mt-10) REVERT: E 290 GLU cc_start: 0.8062 (pt0) cc_final: 0.7739 (pt0) REVERT: F 4 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: F 70 GLU cc_start: 0.6611 (pm20) cc_final: 0.6143 (mt-10) REVERT: F 100 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: F 205 LYS cc_start: 0.7778 (ttmm) cc_final: 0.6773 (tmtt) REVERT: F 225 SER cc_start: 0.8811 (p) cc_final: 0.8460 (t) REVERT: F 257 GLN cc_start: 0.8547 (mt0) cc_final: 0.8316 (mt0) REVERT: F 271 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8296 (mtpt) REVERT: F 289 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7981 (mt-10) REVERT: F 290 GLU cc_start: 0.8039 (pt0) cc_final: 0.7691 (pt0) outliers start: 100 outliers final: 65 residues processed: 372 average time/residue: 0.6356 time to fit residues: 261.0759 Evaluate side-chains 364 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 291 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 4 ASP Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 271 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 196 optimal weight: 0.6980 chunk 46 optimal weight: 0.0470 chunk 191 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 139 ASN A 32 ASN B 177 GLN B 241 GLN C 32 ASN D 49 ASN D 172 ASN D 241 GLN E 64 GLN E 172 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.150993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125245 restraints weight = 86259.518| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.69 r_work: 0.3184 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17108 Z= 0.088 Angle : 0.514 8.632 23128 Z= 0.275 Chirality : 0.044 0.147 2443 Planarity : 0.003 0.033 2961 Dihedral : 13.060 177.590 2464 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.91 % Allowed : 24.73 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.18), residues: 2058 helix: -1.65 (0.79), residues: 42 sheet: 0.55 (0.16), residues: 1043 loop : -1.43 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 281 TYR 0.014 0.001 TYR A 102 PHE 0.011 0.001 PHE B 196 TRP 0.015 0.001 TRP E 260 HIS 0.005 0.001 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00191 (17108) covalent geometry : angle 0.51355 (23128) hydrogen bonds : bond 0.02713 ( 524) hydrogen bonds : angle 5.78845 ( 1464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.524 Fit side-chains REVERT: G 70 GLU cc_start: 0.6600 (pm20) cc_final: 0.6359 (pt0) REVERT: G 136 ILE cc_start: 0.7542 (mm) cc_final: 0.7120 (pt) REVERT: G 237 LYS cc_start: 0.7586 (ptpt) cc_final: 0.6951 (mtmt) REVERT: G 289 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7387 (mt-10) REVERT: G 290 GLU cc_start: 0.8014 (pt0) cc_final: 0.7409 (pt0) REVERT: A 70 GLU cc_start: 0.6355 (pm20) cc_final: 0.6042 (pt0) REVERT: A 136 ILE cc_start: 0.7626 (mm) cc_final: 0.7286 (pt) REVERT: A 141 SER cc_start: 0.8375 (m) cc_final: 0.8042 (t) REVERT: A 186 SER cc_start: 0.8201 (t) cc_final: 0.7841 (m) REVERT: A 205 LYS cc_start: 0.7285 (ttmm) cc_final: 0.6417 (tmtt) REVERT: A 290 GLU cc_start: 0.7710 (pt0) cc_final: 0.7429 (pt0) REVERT: B 148 TYR cc_start: 0.8945 (p90) cc_final: 0.8674 (p90) REVERT: B 289 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7814 (mt-10) REVERT: B 290 GLU cc_start: 0.8063 (pt0) cc_final: 0.7671 (pm20) REVERT: C 70 GLU cc_start: 0.6425 (pm20) cc_final: 0.6149 (pt0) REVERT: C 75 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7263 (ttpp) REVERT: C 186 SER cc_start: 0.8106 (t) cc_final: 0.7822 (m) REVERT: C 200 ARG cc_start: 0.7713 (mtp85) cc_final: 0.7125 (mtp85) REVERT: C 205 LYS cc_start: 0.7555 (ttmm) cc_final: 0.6670 (tttm) REVERT: C 225 SER cc_start: 0.8539 (p) cc_final: 0.8288 (t) REVERT: C 288 LYS cc_start: 0.8266 (mttm) cc_final: 0.8031 (mttt) REVERT: C 289 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7706 (mt-10) REVERT: C 290 GLU cc_start: 0.7896 (pt0) cc_final: 0.7561 (pt0) REVERT: D 70 GLU cc_start: 0.6501 (pm20) cc_final: 0.6265 (pt0) REVERT: D 205 LYS cc_start: 0.7340 (ttmm) cc_final: 0.6508 (tttm) REVERT: D 289 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7571 (mt-10) REVERT: E 30 LYS cc_start: 0.8376 (tttp) cc_final: 0.8027 (ttmm) REVERT: E 70 GLU cc_start: 0.6238 (pm20) cc_final: 0.5905 (pt0) REVERT: E 186 SER cc_start: 0.8120 (t) cc_final: 0.7802 (m) REVERT: E 289 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7575 (mt-10) REVERT: E 290 GLU cc_start: 0.7971 (pt0) cc_final: 0.7687 (pt0) REVERT: F 4 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: F 56 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7968 (mtt90) REVERT: F 70 GLU cc_start: 0.6613 (pm20) cc_final: 0.6207 (pt0) REVERT: F 205 LYS cc_start: 0.7589 (ttmm) cc_final: 0.6562 (tmtt) REVERT: F 257 GLN cc_start: 0.8453 (mt0) cc_final: 0.8175 (mt0) REVERT: F 289 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7894 (mt-10) REVERT: F 290 GLU cc_start: 0.7913 (pt0) cc_final: 0.7592 (pt0) outliers start: 53 outliers final: 28 residues processed: 372 average time/residue: 0.5704 time to fit residues: 236.6377 Evaluate side-chains 328 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 298 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 4 ASP Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 124 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 172 ASN A 32 ASN A 178 ASN B 177 GLN B 241 GLN C 32 ASN C 64 GLN C 241 GLN D 32 ASN D 64 GLN D 172 ASN D 241 GLN E 64 GLN E 172 ASN E 241 GLN F 64 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120720 restraints weight = 104077.856| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 4.08 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17108 Z= 0.159 Angle : 0.586 10.144 23128 Z= 0.309 Chirality : 0.046 0.144 2443 Planarity : 0.004 0.038 2961 Dihedral : 13.068 178.387 2464 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.97 % Allowed : 25.38 % Favored : 71.65 % 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 aren not related in a simple way. whole: -0.61 (0.18), residues: 2058 helix: -1.16 (0.89), residues: 42 sheet: 0.65 (0.16), residues: 1043 loop : -1.62 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 281 TYR 0.017 0.002 TYR B 118 PHE 0.010 0.002 PHE B 42 TRP 0.010 0.001 TRP C 260 HIS 0.009 0.002 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00374 (17108) covalent geometry : angle 0.58552 (23128) hydrogen bonds : bond 0.02996 ( 524) hydrogen bonds : angle 6.02692 ( 1464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 309 time to evaluate : 0.656 Fit side-chains REVERT: G 70 GLU cc_start: 0.6380 (pm20) cc_final: 0.6105 (pt0) REVERT: G 136 ILE cc_start: 0.7559 (mm) cc_final: 0.7183 (pt) REVERT: G 289 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7104 (mt-10) REVERT: G 290 GLU cc_start: 0.7441 (pt0) cc_final: 0.6819 (pt0) REVERT: A 70 GLU cc_start: 0.6255 (pm20) cc_final: 0.5891 (pt0) REVERT: A 136 ILE cc_start: 0.7646 (mm) cc_final: 0.7337 (pt) REVERT: A 186 SER cc_start: 0.7973 (t) cc_final: 0.7721 (m) REVERT: A 205 LYS cc_start: 0.7255 (ttmm) cc_final: 0.6301 (tmtt) REVERT: A 290 GLU cc_start: 0.7171 (pt0) cc_final: 0.6883 (pt0) REVERT: B 205 LYS cc_start: 0.7597 (ttmm) cc_final: 0.6723 (tttm) REVERT: B 289 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7305 (mt-10) REVERT: B 290 GLU cc_start: 0.7625 (pt0) cc_final: 0.7271 (pm20) REVERT: C 70 GLU cc_start: 0.6212 (pm20) cc_final: 0.5877 (pt0) REVERT: C 75 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7118 (ttpp) REVERT: C 200 ARG cc_start: 0.7448 (mtp85) cc_final: 0.6849 (mtp85) REVERT: C 205 LYS cc_start: 0.7371 (ttmm) cc_final: 0.6422 (tttm) REVERT: C 225 SER cc_start: 0.8379 (p) cc_final: 0.8118 (t) REVERT: C 237 LYS cc_start: 0.7131 (ptpp) cc_final: 0.6613 (mppt) REVERT: C 289 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7406 (mt-10) REVERT: C 290 GLU cc_start: 0.7240 (pt0) cc_final: 0.7000 (pt0) REVERT: D 60 THR cc_start: 0.8303 (m) cc_final: 0.7751 (m) REVERT: D 70 GLU cc_start: 0.6168 (pm20) cc_final: 0.5892 (pt0) REVERT: D 205 LYS cc_start: 0.7341 (ttmm) cc_final: 0.6470 (tttm) REVERT: D 289 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7409 (mt-10) REVERT: D 290 GLU cc_start: 0.7194 (pt0) cc_final: 0.6647 (pt0) REVERT: E 12 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8067 (p) REVERT: E 30 LYS cc_start: 0.8040 (tttp) cc_final: 0.7724 (ttmm) REVERT: E 70 GLU cc_start: 0.6084 (pm20) cc_final: 0.5808 (pt0) REVERT: E 186 SER cc_start: 0.7929 (t) cc_final: 0.7613 (m) REVERT: E 205 LYS cc_start: 0.7378 (ttmm) cc_final: 0.6476 (tmtt) REVERT: E 289 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7394 (mt-10) REVERT: E 290 GLU cc_start: 0.7390 (pt0) cc_final: 0.7057 (pt0) REVERT: F 4 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7146 (m-30) REVERT: F 70 GLU cc_start: 0.6249 (pm20) cc_final: 0.5867 (pt0) REVERT: F 111 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7053 (mm-30) REVERT: F 205 LYS cc_start: 0.7524 (ttmm) cc_final: 0.6488 (tmtt) REVERT: F 257 GLN cc_start: 0.8154 (mt0) cc_final: 0.7885 (mt0) REVERT: F 289 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7315 (mt-10) REVERT: F 290 GLU cc_start: 0.7334 (pt0) cc_final: 0.7019 (pt0) outliers start: 54 outliers final: 39 residues processed: 343 average time/residue: 0.6443 time to fit residues: 244.0187 Evaluate side-chains 340 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 298 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 4 ASP Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 157 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 95 optimal weight: 0.0980 chunk 130 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 241 GLN C 32 ASN C 64 GLN D 32 ASN D 49 ASN D 64 GLN D 241 GLN E 64 GLN F 64 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.149358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123363 restraints weight = 88788.953| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.86 r_work: 0.3150 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17108 Z= 0.102 Angle : 0.528 8.811 23128 Z= 0.281 Chirality : 0.044 0.144 2443 Planarity : 0.004 0.034 2961 Dihedral : 12.705 174.590 2464 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.31 % Allowed : 26.26 % Favored : 71.43 % 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 aren not related in a simple way. whole: -0.52 (0.18), residues: 2058 helix: -1.42 (0.82), residues: 42 sheet: 0.56 (0.16), residues: 1099 loop : -1.45 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 281 TYR 0.011 0.001 TYR E 191 PHE 0.011 0.001 PHE F 196 TRP 0.012 0.001 TRP D 260 HIS 0.007 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00232 (17108) covalent geometry : angle 0.52819 (23128) hydrogen bonds : bond 0.02777 ( 524) hydrogen bonds : angle 5.77653 ( 1464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 315 time to evaluate : 0.681 Fit side-chains REVERT: G 70 GLU cc_start: 0.6701 (pm20) cc_final: 0.6325 (pt0) REVERT: G 136 ILE cc_start: 0.7564 (mm) cc_final: 0.7162 (pt) REVERT: G 289 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7492 (mt-10) REVERT: G 290 GLU cc_start: 0.8032 (pt0) cc_final: 0.7417 (pt0) REVERT: A 70 GLU cc_start: 0.6508 (pm20) cc_final: 0.6153 (pt0) REVERT: A 136 ILE cc_start: 0.7629 (mm) cc_final: 0.7308 (pt) REVERT: A 141 SER cc_start: 0.8396 (m) cc_final: 0.8069 (t) REVERT: A 186 SER cc_start: 0.8248 (t) cc_final: 0.7911 (m) REVERT: A 205 LYS cc_start: 0.7360 (ttmm) cc_final: 0.6471 (tmtt) REVERT: A 290 GLU cc_start: 0.7756 (pt0) cc_final: 0.7442 (pt0) REVERT: B 289 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7910 (mt-10) REVERT: B 290 GLU cc_start: 0.8079 (pt0) cc_final: 0.7813 (pm20) REVERT: C 70 GLU cc_start: 0.6484 (pm20) cc_final: 0.6069 (pt0) REVERT: C 75 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7244 (ttpp) REVERT: C 200 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7153 (mtp85) REVERT: C 205 LYS cc_start: 0.7410 (ttmm) cc_final: 0.6508 (tttm) REVERT: C 225 SER cc_start: 0.8576 (p) cc_final: 0.8327 (t) REVERT: C 237 LYS cc_start: 0.7437 (ptpp) cc_final: 0.6948 (mppt) REVERT: C 289 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7844 (mt-10) REVERT: C 290 GLU cc_start: 0.7877 (pt0) cc_final: 0.7537 (pt0) REVERT: D 60 THR cc_start: 0.8281 (m) cc_final: 0.7752 (m) REVERT: D 70 GLU cc_start: 0.6507 (pm20) cc_final: 0.6115 (pt0) REVERT: D 205 LYS cc_start: 0.7383 (ttmm) cc_final: 0.6534 (tttm) REVERT: D 289 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7509 (mt-10) REVERT: E 30 LYS cc_start: 0.8376 (tttp) cc_final: 0.8002 (ttmm) REVERT: E 70 GLU cc_start: 0.6311 (pm20) cc_final: 0.5954 (pt0) REVERT: E 186 SER cc_start: 0.8142 (t) cc_final: 0.7854 (m) REVERT: E 205 LYS cc_start: 0.7412 (ttmm) cc_final: 0.6497 (tmtt) REVERT: E 289 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7680 (mt-10) REVERT: E 290 GLU cc_start: 0.8052 (pt0) cc_final: 0.7760 (pt0) REVERT: F 56 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7952 (mtt90) REVERT: F 70 GLU cc_start: 0.6622 (pm20) cc_final: 0.6158 (pt0) REVERT: F 141 SER cc_start: 0.8424 (m) cc_final: 0.7999 (t) REVERT: F 205 LYS cc_start: 0.7580 (ttmm) cc_final: 0.6534 (tmtt) REVERT: F 237 LYS cc_start: 0.7336 (ptpp) cc_final: 0.6563 (mmpt) REVERT: F 257 GLN cc_start: 0.8531 (mt0) cc_final: 0.8280 (mt0) REVERT: F 289 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7918 (mt-10) REVERT: F 290 GLU cc_start: 0.7943 (pt0) cc_final: 0.7620 (pt0) outliers start: 42 outliers final: 29 residues processed: 343 average time/residue: 0.5915 time to fit residues: 224.9870 Evaluate side-chains 337 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 307 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 152 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 182 optimal weight: 0.0970 chunk 108 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 241 GLN C 32 ASN C 64 GLN C 241 GLN D 49 ASN D 64 GLN D 241 GLN E 64 GLN F 64 GLN F 172 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.148688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122381 restraints weight = 81503.224| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.74 r_work: 0.3153 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17108 Z= 0.115 Angle : 0.541 8.986 23128 Z= 0.287 Chirality : 0.045 0.144 2443 Planarity : 0.004 0.037 2961 Dihedral : 12.549 173.527 2464 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.14 % Allowed : 26.37 % Favored : 71.48 % 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 aren not related in a simple way. whole: -0.54 (0.18), residues: 2058 helix: -1.33 (0.84), residues: 42 sheet: 0.61 (0.16), residues: 1071 loop : -1.50 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 281 TYR 0.017 0.002 TYR A 118 PHE 0.011 0.001 PHE F 196 TRP 0.011 0.001 TRP E 260 HIS 0.008 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00267 (17108) covalent geometry : angle 0.54084 (23128) hydrogen bonds : bond 0.02794 ( 524) hydrogen bonds : angle 5.79003 ( 1464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 311 time to evaluate : 0.488 Fit side-chains REVERT: G 70 GLU cc_start: 0.6512 (pm20) cc_final: 0.6155 (pt0) REVERT: G 113 MET cc_start: 0.8834 (ttm) cc_final: 0.8539 (mtp) REVERT: G 136 ILE cc_start: 0.7567 (mm) cc_final: 0.7159 (pt) REVERT: G 237 LYS cc_start: 0.7607 (ptpt) cc_final: 0.6960 (mtmt) REVERT: G 289 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7495 (mt-10) REVERT: G 290 GLU cc_start: 0.8020 (pt0) cc_final: 0.7381 (pt0) REVERT: A 70 GLU cc_start: 0.6537 (pm20) cc_final: 0.6172 (pt0) REVERT: A 136 ILE cc_start: 0.7621 (mm) cc_final: 0.7278 (pt) REVERT: A 141 SER cc_start: 0.8377 (m) cc_final: 0.8051 (t) REVERT: A 186 SER cc_start: 0.8258 (t) cc_final: 0.7984 (m) REVERT: A 205 LYS cc_start: 0.7378 (ttmm) cc_final: 0.6534 (tmtt) REVERT: A 290 GLU cc_start: 0.7721 (pt0) cc_final: 0.7406 (pt0) REVERT: B 289 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 290 GLU cc_start: 0.8115 (pt0) cc_final: 0.7851 (pm20) REVERT: C 70 GLU cc_start: 0.6507 (pm20) cc_final: 0.6051 (pt0) REVERT: C 75 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7269 (ttpp) REVERT: C 200 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7163 (mtp85) REVERT: C 205 LYS cc_start: 0.7390 (ttmm) cc_final: 0.6481 (tttm) REVERT: C 225 SER cc_start: 0.8577 (p) cc_final: 0.8325 (t) REVERT: C 237 LYS cc_start: 0.7456 (ptpp) cc_final: 0.6951 (mppt) REVERT: C 289 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7784 (mt-10) REVERT: C 290 GLU cc_start: 0.7893 (pt0) cc_final: 0.7563 (pt0) REVERT: D 60 THR cc_start: 0.8272 (m) cc_final: 0.7777 (m) REVERT: D 70 GLU cc_start: 0.6453 (pm20) cc_final: 0.6065 (pt0) REVERT: D 205 LYS cc_start: 0.7353 (ttmm) cc_final: 0.6513 (tttm) REVERT: D 289 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7542 (mt-10) REVERT: D 290 GLU cc_start: 0.7807 (pt0) cc_final: 0.7241 (pt0) REVERT: E 12 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8126 (p) REVERT: E 30 LYS cc_start: 0.8355 (tttp) cc_final: 0.7982 (ttmm) REVERT: E 70 GLU cc_start: 0.6296 (pm20) cc_final: 0.5925 (pt0) REVERT: E 186 SER cc_start: 0.8117 (t) cc_final: 0.7822 (m) REVERT: E 205 LYS cc_start: 0.7410 (ttmm) cc_final: 0.6489 (tmtt) REVERT: E 289 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7667 (mt-10) REVERT: E 290 GLU cc_start: 0.8041 (pt0) cc_final: 0.7747 (pt0) REVERT: F 56 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7954 (mtt90) REVERT: F 70 GLU cc_start: 0.6614 (pm20) cc_final: 0.6140 (pt0) REVERT: F 111 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7882 (mm-30) REVERT: F 141 SER cc_start: 0.8412 (m) cc_final: 0.7980 (t) REVERT: F 205 LYS cc_start: 0.7611 (ttmm) cc_final: 0.6578 (tmtt) REVERT: F 237 LYS cc_start: 0.7324 (ptpp) cc_final: 0.6556 (mmpt) REVERT: F 257 GLN cc_start: 0.8515 (mt0) cc_final: 0.8251 (mt0) REVERT: F 289 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7913 (mt-10) REVERT: F 290 GLU cc_start: 0.7908 (pt0) cc_final: 0.7598 (pt0) outliers start: 39 outliers final: 33 residues processed: 336 average time/residue: 0.6281 time to fit residues: 233.5557 Evaluate side-chains 340 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 305 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 129 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 165 optimal weight: 0.0870 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 177 GLN B 241 GLN C 32 ASN C 64 GLN D 32 ASN D 49 ASN D 64 GLN D 241 GLN E 64 GLN F 64 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.146219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120957 restraints weight = 89979.606| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.77 r_work: 0.3119 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 63 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17108 Z= 0.161 Angle : 0.596 9.769 23128 Z= 0.314 Chirality : 0.046 0.142 2443 Planarity : 0.004 0.040 2961 Dihedral : 12.587 174.796 2464 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.36 % Allowed : 26.48 % Favored : 71.15 % 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 aren not related in a simple way. whole: -0.58 (0.18), residues: 2058 helix: -1.20 (0.87), residues: 42 sheet: 0.64 (0.16), residues: 1064 loop : -1.60 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 281 TYR 0.016 0.002 TYR E 191 PHE 0.010 0.002 PHE E 196 TRP 0.009 0.001 TRP F 260 HIS 0.009 0.002 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00381 (17108) covalent geometry : angle 0.59631 (23128) hydrogen bonds : bond 0.03005 ( 524) hydrogen bonds : angle 6.01281 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6301.70 seconds wall clock time: 108 minutes 10.59 seconds (6490.59 seconds total)