Starting phenix.real_space_refine on Fri Jun 5 02:09:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ebc_47877/06_2026/9ebc_47877.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ebc_47877/06_2026/9ebc_47877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ebc_47877/06_2026/9ebc_47877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ebc_47877/06_2026/9ebc_47877.map" model { file = "/net/cci-nas-00/data/ceres_data/9ebc_47877/06_2026/9ebc_47877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ebc_47877/06_2026/9ebc_47877.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10584 2.51 5 N 2847 2.21 5 O 3213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16740 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2508 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1227 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 1, 'TRANS': 147} Chain: "G" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 992 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "H" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 853 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Restraints were copied for chains: C, E, D, F, I, K, J, L Time building chain proxies: 3.03, per 1000 atoms: 0.18 Number of scatterers: 16740 At special positions: 0 Unit cell: (140.765, 133.546, 152.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3213 8.00 N 2847 7.00 C 10584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 112 " distance=2.04 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 90 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 302 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 115 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 115 " distance=2.03 Simple disulfide: pdb=" SG CYS J 42 " - pdb=" SG CYS J 112 " distance=2.04 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 112 " distance=2.04 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: 1.39 Conformation dependent library (CDL) restraints added in 686.7 milliseconds 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 57 sheets defined 17.3% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.529A pdb=" N TRP A 122 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 191 Processing helix chain 'B' and resid 40 through 59 removed outlier: 4.480A pdb=" N VAL B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 109 Processing helix chain 'B' and resid 112 through 120 removed outlier: 4.062A pdb=" N LEU B 118 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.873A pdb=" N ARG B 153 " --> pdb=" O MET B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.805A pdb=" N GLN B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.557A pdb=" N CYS G 51 " --> pdb=" O PHE G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 110 removed outlier: 4.094A pdb=" N THR G 110 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.528A pdb=" N TRP C 122 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 191 Processing helix chain 'D' and resid 40 through 59 removed outlier: 4.480A pdb=" N VAL D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 109 Processing helix chain 'D' and resid 112 through 120 removed outlier: 4.062A pdb=" N LEU D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.872A pdb=" N ARG D 153 " --> pdb=" O MET D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.806A pdb=" N GLN D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 51 removed outlier: 3.558A pdb=" N CYS I 51 " --> pdb=" O PHE I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 110 removed outlier: 4.094A pdb=" N THR I 110 " --> pdb=" O ALA I 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 62 Processing helix chain 'E' and resid 97 through 106 Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.528A pdb=" N TRP E 122 " --> pdb=" O LYS E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 191 Processing helix chain 'F' and resid 40 through 59 removed outlier: 4.481A pdb=" N VAL F 52 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN F 53 " --> pdb=" O THR F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 109 Processing helix chain 'F' and resid 112 through 120 removed outlier: 4.061A pdb=" N LEU F 118 " --> pdb=" O ASN F 114 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.873A pdb=" N ARG F 153 " --> pdb=" O MET F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 162 removed outlier: 3.806A pdb=" N GLN F 161 " --> pdb=" O ASP F 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 51 removed outlier: 3.558A pdb=" N CYS K 51 " --> pdb=" O PHE K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 110 removed outlier: 4.094A pdb=" N THR K 110 " --> pdb=" O ALA K 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.824A pdb=" N GLY A 6 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY B 23 " --> pdb=" O GLY A 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 removed outlier: 4.318A pdb=" N GLU A 14 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.025A pdb=" N HIS A 28 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 44 removed outlier: 7.825A pdb=" N LEU A 41 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR A 276 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASP A 43 " --> pdb=" O THR A 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.931A pdb=" N LEU A 50 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 79 " --> pdb=" O MET A 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.732A pdb=" N SER A 94 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N TRP A 230 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU A 175 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 252 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 257 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N HIS A 110 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.732A pdb=" N SER A 94 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N TRP A 230 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU A 175 " --> pdb=" O PRO A 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AB1, first strand: chain 'A' and resid 132 through 136 removed outlier: 3.506A pdb=" N SER A 142 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 160 through 165 Processing sheet with id=AB3, first strand: chain 'A' and resid 278 through 279 removed outlier: 3.549A pdb=" N ILE A 299 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.849A pdb=" N ASN B 28 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB6, first strand: chain 'G' and resid 22 through 26 removed outlier: 3.548A pdb=" N SER G 44 " --> pdb=" O GLN G 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=AB8, first strand: chain 'G' and resid 77 through 79 removed outlier: 4.793A pdb=" N TRP G 66 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ARG G 57 " --> pdb=" O TRP G 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 29 through 31 removed outlier: 7.017A pdb=" N LEU H 30 " --> pdb=" O GLU H 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL H 128 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY H 108 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TRP H 59 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU H 71 " --> pdb=" O TRP H 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 38 through 43 Processing sheet with id=AC2, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.824A pdb=" N GLY C 6 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY D 23 " --> pdb=" O GLY C 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 14 through 16 removed outlier: 4.318A pdb=" N GLU C 14 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.026A pdb=" N HIS C 28 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AC6, first strand: chain 'C' and resid 41 through 44 removed outlier: 7.825A pdb=" N LEU C 41 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR C 276 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASP C 43 " --> pdb=" O THR C 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.931A pdb=" N LEU C 50 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 79 " --> pdb=" O MET C 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.732A pdb=" N SER C 94 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N TRP C 230 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU C 175 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR C 252 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 257 " --> pdb=" O HIS C 110 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N HIS C 110 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.732A pdb=" N SER C 94 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N TRP C 230 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU C 175 " --> pdb=" O PRO C 250 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 125 through 126 Processing sheet with id=AD2, first strand: chain 'C' and resid 132 through 136 removed outlier: 3.506A pdb=" N SER C 142 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 160 through 165 Processing sheet with id=AD4, first strand: chain 'C' and resid 278 through 279 removed outlier: 3.548A pdb=" N ILE C 299 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 27 through 28 removed outlier: 3.850A pdb=" N ASN D 28 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AD7, first strand: chain 'I' and resid 22 through 26 removed outlier: 3.548A pdb=" N SER I 44 " --> pdb=" O GLN I 22 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 30 through 31 Processing sheet with id=AD9, first strand: chain 'I' and resid 77 through 79 removed outlier: 4.793A pdb=" N TRP I 66 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ARG I 57 " --> pdb=" O TRP I 66 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 29 through 31 removed outlier: 7.018A pdb=" N LEU J 30 " --> pdb=" O GLU J 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 128 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY J 108 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TRP J 59 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU J 71 " --> pdb=" O TRP J 59 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 38 through 43 Processing sheet with id=AE3, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.824A pdb=" N GLY E 6 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY F 23 " --> pdb=" O GLY E 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 14 through 16 removed outlier: 4.318A pdb=" N GLU E 14 " --> pdb=" O VAL E 26 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 28 through 31 removed outlier: 6.025A pdb=" N HIS E 28 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AE7, first strand: chain 'E' and resid 41 through 44 removed outlier: 7.824A pdb=" N LEU E 41 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR E 276 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASP E 43 " --> pdb=" O THR E 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'E' and resid 50 through 51 removed outlier: 6.932A pdb=" N LEU E 50 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE E 79 " --> pdb=" O MET E 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 93 through 95 removed outlier: 6.732A pdb=" N SER E 94 " --> pdb=" O PHE E 228 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N TRP E 230 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU E 175 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR E 252 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 257 " --> pdb=" O HIS E 110 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N HIS E 110 " --> pdb=" O VAL E 257 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 93 through 95 removed outlier: 6.732A pdb=" N SER E 94 " --> pdb=" O PHE E 228 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N TRP E 230 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU E 175 " --> pdb=" O PRO E 250 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 125 through 126 Processing sheet with id=AF3, first strand: chain 'E' and resid 132 through 136 removed outlier: 3.506A pdb=" N SER E 142 " --> pdb=" O SER E 132 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 160 through 165 Processing sheet with id=AF5, first strand: chain 'E' and resid 278 through 279 removed outlier: 3.549A pdb=" N ILE E 299 " --> pdb=" O GLN E 279 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 27 through 28 removed outlier: 3.849A pdb=" N ASN F 28 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 130 through 132 Processing sheet with id=AF8, first strand: chain 'K' and resid 22 through 26 removed outlier: 3.549A pdb=" N SER K 44 " --> pdb=" O GLN K 22 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 30 through 31 Processing sheet with id=AG1, first strand: chain 'K' and resid 77 through 79 removed outlier: 4.793A pdb=" N TRP K 66 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ARG K 57 " --> pdb=" O TRP K 66 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 29 through 31 removed outlier: 7.016A pdb=" N LEU L 30 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL L 128 " --> pdb=" O GLY L 108 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY L 108 " --> pdb=" O VAL L 128 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU L 71 " --> pdb=" O TRP L 59 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 38 through 43 558 hydrogen bonds defined for protein. 1458 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: 3.04 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.49: 9966 1.49 - 1.77: 7035 1.77 - 2.05: 141 2.05 - 2.33: 0 2.33 - 2.61: 3 Bond restraints: 17145 Sorted by residual: bond pdb=" C ARG F 127 " pdb=" N ASP F 128 " ideal model delta sigma weight residual 1.332 2.612 -1.280 1.40e-02 5.10e+03 8.36e+03 bond pdb=" C ARG B 127 " pdb=" N ASP B 128 " ideal model delta sigma weight residual 1.332 2.612 -1.280 1.40e-02 5.10e+03 8.35e+03 bond pdb=" C ARG D 127 " pdb=" N ASP D 128 " ideal model delta sigma weight residual 1.332 2.612 -1.279 1.40e-02 5.10e+03 8.35e+03 bond pdb=" N ASN E 189 " pdb=" CA ASN E 189 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.26e-02 6.30e+03 6.23e+00 bond pdb=" N ASN A 189 " pdb=" CA ASN A 189 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.26e-02 6.30e+03 5.84e+00 ... (remaining 17140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.34: 23211 12.34 - 24.67: 30 24.67 - 37.01: 3 37.01 - 49.35: 0 49.35 - 61.68: 3 Bond angle restraints: 23247 Sorted by residual: angle pdb=" O ARG F 127 " pdb=" C ARG F 127 " pdb=" N ASP F 128 " ideal model delta sigma weight residual 122.46 60.78 61.68 1.19e+00 7.06e-01 2.69e+03 angle pdb=" O ARG B 127 " pdb=" C ARG B 127 " pdb=" N ASP B 128 " ideal model delta sigma weight residual 122.46 60.78 61.68 1.19e+00 7.06e-01 2.69e+03 angle pdb=" O ARG D 127 " pdb=" C ARG D 127 " pdb=" N ASP D 128 " ideal model delta sigma weight residual 122.46 60.80 61.66 1.19e+00 7.06e-01 2.68e+03 angle pdb=" N ARG B 123 " pdb=" CA ARG B 123 " pdb=" C ARG B 123 " ideal model delta sigma weight residual 110.23 76.55 33.68 1.45e+00 4.76e-01 5.40e+02 angle pdb=" N ARG F 123 " pdb=" CA ARG F 123 " pdb=" C ARG F 123 " ideal model delta sigma weight residual 110.23 76.55 33.68 1.45e+00 4.76e-01 5.40e+02 ... (remaining 23242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 8542 17.62 - 35.25: 1157 35.25 - 52.87: 369 52.87 - 70.49: 87 70.49 - 88.12: 24 Dihedral angle restraints: 10179 sinusoidal: 4062 harmonic: 6117 Sorted by residual: dihedral pdb=" C ARG D 123 " pdb=" N ARG D 123 " pdb=" CA ARG D 123 " pdb=" CB ARG D 123 " ideal model delta harmonic sigma weight residual -122.60 -95.75 -26.85 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" C ARG B 123 " pdb=" N ARG B 123 " pdb=" CA ARG B 123 " pdb=" CB ARG B 123 " ideal model delta harmonic sigma weight residual -122.60 -95.75 -26.85 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" C ARG F 123 " pdb=" N ARG F 123 " pdb=" CA ARG F 123 " pdb=" CB ARG F 123 " ideal model delta harmonic sigma weight residual -122.60 -95.77 -26.83 0 2.50e+00 1.60e-01 1.15e+02 ... (remaining 10176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.229: 2478 0.229 - 0.457: 6 0.457 - 0.686: 3 0.686 - 0.914: 3 0.914 - 1.143: 3 Chirality restraints: 2493 Sorted by residual: chirality pdb=" CA LEU F 124 " pdb=" N LEU F 124 " pdb=" C LEU F 124 " pdb=" CB LEU F 124 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.14 2.00e-01 2.50e+01 3.27e+01 chirality pdb=" CA LEU D 124 " pdb=" N LEU D 124 " pdb=" C LEU D 124 " pdb=" CB LEU D 124 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.14 2.00e-01 2.50e+01 3.27e+01 chirality pdb=" CA LEU B 124 " pdb=" N LEU B 124 " pdb=" C LEU B 124 " pdb=" CB LEU B 124 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.14 2.00e-01 2.50e+01 3.26e+01 ... (remaining 2490 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 127 " -0.159 2.00e-02 2.50e+03 2.38e-01 5.68e+02 pdb=" C ARG D 127 " 0.368 2.00e-02 2.50e+03 pdb=" O ARG D 127 " -0.254 2.00e-02 2.50e+03 pdb=" N ASP D 128 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 127 " 0.159 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C ARG F 127 " -0.367 2.00e-02 2.50e+03 pdb=" O ARG F 127 " 0.254 2.00e-02 2.50e+03 pdb=" N ASP F 128 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 127 " 0.159 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C ARG B 127 " -0.367 2.00e-02 2.50e+03 pdb=" O ARG B 127 " 0.254 2.00e-02 2.50e+03 pdb=" N ASP B 128 " -0.046 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 0.66 - 1.51: 9 1.51 - 2.36: 138 2.36 - 3.20: 15735 3.20 - 4.05: 45242 4.05 - 4.90: 83642 Warning: very small nonbonded interaction distances. Nonbonded interactions: 144766 Sorted by model distance: nonbonded pdb=" O TYR I 133 " pdb=" OH TYR J 58 " model vdw 0.661 3.040 nonbonded pdb=" O TYR G 133 " pdb=" OH TYR H 58 " model vdw 0.662 3.040 nonbonded pdb=" O TYR K 133 " pdb=" OH TYR L 58 " model vdw 0.662 3.040 nonbonded pdb=" C TYR G 133 " pdb=" OH TYR H 58 " model vdw 1.423 3.270 nonbonded pdb=" C TYR I 133 " pdb=" OH TYR J 58 " model vdw 1.423 3.270 ... (remaining 144761 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 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 : 0.018 1.280 17163 Z= 1.230 Angle : 1.340 61.684 23283 Z= 0.912 Chirality : 0.072 1.143 2493 Planarity : 0.017 0.442 3000 Dihedral : 18.277 88.117 6231 Min Nonbonded Distance : 0.661 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.87 % Allowed : 35.83 % Favored : 61.30 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 2085 helix: -1.06 (0.27), residues: 318 sheet: -0.22 (0.24), residues: 480 loop : -1.25 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 208 TYR 0.052 0.002 TYR I 126 PHE 0.018 0.002 PHE I 122 TRP 0.013 0.002 TRP K 123 HIS 0.011 0.002 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.01753 / 1.23 (17145) covalent geometry : angle 1.34024 / 0.91 (23247) SS BOND : bond 0.00272 / 0.17 ( 18) SS BOND : angle 1.36987 / 0.90 ( 36) hydrogen bonds : bond 0.20323 / 13.42 ( 528) hydrogen bonds : angle 9.01638 / 6.38 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 282 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7496 (tt0) cc_final: 0.7081 (tt0) REVERT: A 66 MET cc_start: 0.7173 (mmm) cc_final: 0.6728 (mpt) REVERT: A 75 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7395 (tt0) REVERT: A 277 LYS cc_start: 0.7101 (tppt) cc_final: 0.6154 (ttpp) REVERT: B 22 TYR cc_start: 0.7839 (m-80) cc_final: 0.7480 (m-80) REVERT: B 37 ASP cc_start: 0.5314 (t0) cc_final: 0.4824 (m-30) REVERT: B 85 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: G 30 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6090 (tm) REVERT: H 66 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.6432 (pt0) REVERT: C 30 GLN cc_start: 0.7407 (tt0) cc_final: 0.6966 (tp40) REVERT: C 66 MET cc_start: 0.7241 (mmm) cc_final: 0.6677 (mpt) REVERT: C 277 LYS cc_start: 0.7078 (tppt) cc_final: 0.6117 (ttpp) REVERT: D 22 TYR cc_start: 0.7917 (m-80) cc_final: 0.7563 (m-80) REVERT: D 37 ASP cc_start: 0.5425 (t0) cc_final: 0.4602 (m-30) REVERT: D 58 LYS cc_start: 0.7584 (ttpt) cc_final: 0.7337 (tppp) REVERT: D 85 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: I 140 LYS cc_start: 0.8125 (mmpt) cc_final: 0.7876 (mmmt) REVERT: E 30 GLN cc_start: 0.7397 (tt0) cc_final: 0.6919 (tt0) REVERT: E 66 MET cc_start: 0.7275 (mmm) cc_final: 0.6765 (mpt) REVERT: E 277 LYS cc_start: 0.7063 (tppt) cc_final: 0.6118 (ttpp) REVERT: F 37 ASP cc_start: 0.5234 (t0) cc_final: 0.4422 (m-30) REVERT: F 85 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: F 109 ASP cc_start: 0.6167 (m-30) cc_final: 0.5959 (m-30) REVERT: K 95 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7602 (ttpm) REVERT: K 112 VAL cc_start: 0.7219 (m) cc_final: 0.6955 (p) REVERT: K 140 LYS cc_start: 0.8038 (mmpt) cc_final: 0.7815 (mmmt) REVERT: L 66 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6417 (pt0) outliers start: 53 outliers final: 25 residues processed: 322 average time/residue: 0.4782 time to fit residues: 174.9120 Evaluate side-chains 268 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 66 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 123 TRP Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 71 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.0980 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 183 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS B 129 ASN H 25 GLN H 66 GLN C 96 ASN C 183 ASN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS D 129 ASN J 25 GLN J 66 GLN J 117 HIS E 87 ASN E 183 ASN ** E 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS F 129 ASN L 25 GLN L 66 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.202156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.157632 restraints weight = 22155.001| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.83 r_work: 0.3734 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17163 Z= 0.166 Angle : 0.680 15.711 23283 Z= 0.340 Chirality : 0.045 0.198 2493 Planarity : 0.005 0.043 3000 Dihedral : 7.466 85.499 2351 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 8.35 % Allowed : 31.27 % Favored : 60.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.18), residues: 2091 helix: -0.80 (0.26), residues: 318 sheet: -0.24 (0.23), residues: 516 loop : -1.22 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.021 0.002 TYR I 126 PHE 0.012 0.001 PHE C 111 TRP 0.010 0.001 TRP J 59 HIS 0.010 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (17145) covalent geometry : angle 0.67869 / 0.34 (23247) SS BOND : bond 0.00365 / 0.22 ( 18) SS BOND : angle 1.12662 / 0.74 ( 36) hydrogen bonds : bond 0.04118 / 2.81 ( 528) hydrogen bonds : angle 6.61793 / 4.71 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 231 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7328 (tt0) cc_final: 0.6940 (tt0) REVERT: A 66 MET cc_start: 0.7138 (mmm) cc_final: 0.6637 (mpt) REVERT: B 37 ASP cc_start: 0.5596 (t0) cc_final: 0.4813 (m-30) REVERT: B 105 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5860 (mt-10) REVERT: G 58 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6283 (pt0) REVERT: C 30 GLN cc_start: 0.7145 (tt0) cc_final: 0.6810 (tp40) REVERT: C 66 MET cc_start: 0.7148 (mmm) cc_final: 0.6584 (mpt) REVERT: C 277 LYS cc_start: 0.7047 (tppt) cc_final: 0.6137 (ttpp) REVERT: D 22 TYR cc_start: 0.8120 (m-80) cc_final: 0.7653 (m-80) REVERT: D 37 ASP cc_start: 0.5594 (t0) cc_final: 0.4607 (m-30) REVERT: D 112 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7230 (t0) REVERT: I 22 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: I 30 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6701 (tm) REVERT: E 30 GLN cc_start: 0.7061 (tt0) cc_final: 0.6744 (tt0) REVERT: E 66 MET cc_start: 0.7282 (mmm) cc_final: 0.6726 (mpt) REVERT: E 226 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8322 (mtt) REVERT: E 277 LYS cc_start: 0.6901 (tppt) cc_final: 0.6085 (ttpp) REVERT: F 22 TYR cc_start: 0.7993 (m-80) cc_final: 0.7564 (m-80) REVERT: F 37 ASP cc_start: 0.5476 (t0) cc_final: 0.4413 (m-30) REVERT: F 105 GLU cc_start: 0.5862 (OUTLIER) cc_final: 0.5640 (mt-10) REVERT: L 117 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.6766 (m-70) outliers start: 154 outliers final: 62 residues processed: 356 average time/residue: 0.4144 time to fit residues: 171.0801 Evaluate side-chains 280 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 210 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 123 TRP Chi-restraints excluded: chain G residue 126 TYR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 126 TYR Chi-restraints excluded: chain L residue 117 HIS Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 198 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 110 HIS A 183 ASN A 193 ASN ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN B 26 HIS B 114 ASN G 96 ASN C 11 ASN C 110 HIS C 183 ASN C 193 ASN ** C 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN D 26 HIS E 11 ASN E 96 ASN E 110 HIS E 183 ASN E 193 ASN ** E 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 ASN F 26 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.196824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.147942 restraints weight = 22376.119| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.10 r_work: 0.3657 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 17163 Z= 0.265 Angle : 0.763 16.548 23283 Z= 0.382 Chirality : 0.046 0.193 2493 Planarity : 0.005 0.049 3000 Dihedral : 7.154 91.074 2323 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 10.62 % Allowed : 28.89 % Favored : 60.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.18), residues: 2091 helix: -1.07 (0.26), residues: 318 sheet: -0.00 (0.24), residues: 474 loop : -1.35 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 225 TYR 0.024 0.002 TYR K 126 PHE 0.016 0.002 PHE E 144 TRP 0.014 0.002 TRP G 66 HIS 0.026 0.002 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.27 (17145) covalent geometry : angle 0.75975 / 0.38 (23247) SS BOND : bond 0.00473 / 0.29 ( 18) SS BOND : angle 2.04615 / 1.15 ( 36) hydrogen bonds : bond 0.04572 / 3.10 ( 528) hydrogen bonds : angle 6.51701 / 4.63 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 227 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7335 (tt0) cc_final: 0.7028 (tp40) REVERT: A 66 MET cc_start: 0.7485 (mmm) cc_final: 0.6862 (mpt) REVERT: B 25 HIS cc_start: 0.5880 (p-80) cc_final: 0.5353 (p90) REVERT: B 37 ASP cc_start: 0.5823 (t0) cc_final: 0.5025 (m-30) REVERT: G 30 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6180 (tm) REVERT: G 58 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6375 (pt0) REVERT: G 67 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7790 (t) REVERT: H 127 LYS cc_start: 0.5853 (OUTLIER) cc_final: 0.5490 (tttp) REVERT: C 30 GLN cc_start: 0.7254 (tt0) cc_final: 0.6941 (tp40) REVERT: C 66 MET cc_start: 0.7588 (mmm) cc_final: 0.6920 (mpt) REVERT: C 75 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: D 25 HIS cc_start: 0.5807 (p-80) cc_final: 0.5245 (p90) REVERT: D 86 ASP cc_start: 0.7786 (m-30) cc_final: 0.7544 (m-30) REVERT: D 112 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7190 (t0) REVERT: I 22 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7051 (pm20) REVERT: I 131 TYR cc_start: 0.8022 (m-10) cc_final: 0.7711 (m-80) REVERT: J 127 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.5424 (tttp) REVERT: E 30 GLN cc_start: 0.7334 (tt0) cc_final: 0.7068 (tp40) REVERT: E 66 MET cc_start: 0.7729 (mmm) cc_final: 0.7172 (mpt) REVERT: E 75 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: E 226 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8523 (mtt) REVERT: F 25 HIS cc_start: 0.5912 (p-80) cc_final: 0.5293 (p90) REVERT: F 102 MET cc_start: 0.7699 (ttp) cc_final: 0.7497 (ttm) REVERT: L 127 LYS cc_start: 0.5588 (OUTLIER) cc_final: 0.5092 (tttp) outliers start: 196 outliers final: 99 residues processed: 388 average time/residue: 0.4264 time to fit residues: 190.5554 Evaluate side-chains 314 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 204 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 123 TRP Chi-restraints excluded: chain G residue 126 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 58 GLN Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 TRP Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 126 TYR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 154 optimal weight: 0.0870 chunk 99 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN B 26 HIS G 96 ASN ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 183 ASN ** C 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 HIS E 183 ASN F 26 HIS ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.196630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.146649 restraints weight = 22557.456| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.05 r_work: 0.3661 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17163 Z= 0.182 Angle : 0.693 15.069 23283 Z= 0.342 Chirality : 0.044 0.194 2493 Planarity : 0.004 0.050 3000 Dihedral : 6.920 91.385 2322 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 8.56 % Allowed : 29.97 % Favored : 61.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 2091 helix: -1.03 (0.26), residues: 318 sheet: -0.41 (0.23), residues: 522 loop : -1.23 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.019 0.002 TYR I 126 PHE 0.022 0.001 PHE A 111 TRP 0.009 0.001 TRP G 123 HIS 0.017 0.002 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (17145) covalent geometry : angle 0.69028 / 0.34 (23247) SS BOND : bond 0.00540 / 0.31 ( 18) SS BOND : angle 1.71193 / 1.01 ( 36) hydrogen bonds : bond 0.03992 / 2.73 ( 528) hydrogen bonds : angle 6.20082 / 4.41 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 224 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7333 (tt0) cc_final: 0.7001 (tp40) REVERT: A 66 MET cc_start: 0.7241 (mmm) cc_final: 0.6491 (mpt) REVERT: A 313 LEU cc_start: 0.7544 (tt) cc_final: 0.6928 (mp) REVERT: B 25 HIS cc_start: 0.5695 (p-80) cc_final: 0.5270 (p90) REVERT: B 97 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6599 (tp30) REVERT: G 30 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.5988 (tm) REVERT: G 58 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6343 (pt0) REVERT: G 120 TYR cc_start: 0.5258 (OUTLIER) cc_final: 0.4634 (t80) REVERT: H 58 TYR cc_start: 0.5614 (OUTLIER) cc_final: 0.2797 (p90) REVERT: H 127 LYS cc_start: 0.5801 (OUTLIER) cc_final: 0.5401 (tttp) REVERT: C 30 GLN cc_start: 0.7227 (tt0) cc_final: 0.6869 (tp40) REVERT: C 66 MET cc_start: 0.7390 (mmm) cc_final: 0.6876 (mpt) REVERT: C 227 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7320 (t0) REVERT: D 22 TYR cc_start: 0.7981 (m-80) cc_final: 0.7421 (m-80) REVERT: D 25 HIS cc_start: 0.5631 (p-80) cc_final: 0.5117 (p90) REVERT: D 37 ASP cc_start: 0.5780 (t0) cc_final: 0.4778 (m-30) REVERT: D 72 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7348 (t0) REVERT: D 112 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7028 (t0) REVERT: I 22 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: I 131 TYR cc_start: 0.7879 (m-10) cc_final: 0.7606 (m-10) REVERT: J 54 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6955 (ttmt) REVERT: J 58 TYR cc_start: 0.5695 (OUTLIER) cc_final: 0.2868 (p90) REVERT: J 127 LYS cc_start: 0.5619 (OUTLIER) cc_final: 0.5241 (tttp) REVERT: E 30 GLN cc_start: 0.7221 (tt0) cc_final: 0.6908 (tp40) REVERT: E 66 MET cc_start: 0.7491 (mmm) cc_final: 0.6919 (mpt) REVERT: E 226 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8598 (mtt) REVERT: E 313 LEU cc_start: 0.7841 (tt) cc_final: 0.7051 (mp) REVERT: K 102 MET cc_start: 0.7896 (mtm) cc_final: 0.7581 (mtm) REVERT: L 58 TYR cc_start: 0.5854 (OUTLIER) cc_final: 0.2921 (p90) REVERT: L 127 LYS cc_start: 0.5498 (OUTLIER) cc_final: 0.5052 (tttp) outliers start: 158 outliers final: 90 residues processed: 346 average time/residue: 0.4067 time to fit residues: 163.0954 Evaluate side-chains 314 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 208 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 TYR Chi-restraints excluded: chain G residue 123 TRP Chi-restraints excluded: chain G residue 126 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 TRP Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 58 TYR Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 126 TYR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 127 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 182 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 191 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 79 optimal weight: 0.0770 chunk 136 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 293 ASN B 26 HIS G 96 ASN ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS D 114 ASN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN E 183 ASN F 26 HIS ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.197255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.146909 restraints weight = 22518.842| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.07 r_work: 0.3672 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17163 Z= 0.169 Angle : 0.683 14.397 23283 Z= 0.338 Chirality : 0.044 0.193 2493 Planarity : 0.004 0.050 3000 Dihedral : 6.813 92.226 2321 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 8.83 % Allowed : 30.68 % Favored : 60.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 2091 helix: -0.95 (0.26), residues: 318 sheet: -0.45 (0.23), residues: 552 loop : -1.19 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.019 0.002 TYR K 126 PHE 0.017 0.001 PHE A 111 TRP 0.009 0.001 TRP G 66 HIS 0.017 0.002 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (17145) covalent geometry : angle 0.67742 / 0.34 (23247) SS BOND : bond 0.00465 / 0.27 ( 18) SS BOND : angle 2.35437 / 1.39 ( 36) hydrogen bonds : bond 0.03793 / 2.60 ( 528) hydrogen bonds : angle 6.00497 / 4.28 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 222 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7284 (tt0) cc_final: 0.6974 (tp40) REVERT: A 66 MET cc_start: 0.7177 (mmm) cc_final: 0.6333 (mpt) REVERT: A 313 LEU cc_start: 0.7556 (tt) cc_final: 0.6850 (mp) REVERT: B 25 HIS cc_start: 0.5651 (p-80) cc_final: 0.5211 (p90) REVERT: B 97 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6563 (tp30) REVERT: B 105 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5883 (mt-10) REVERT: G 30 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.5922 (tm) REVERT: G 58 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6282 (pt0) REVERT: G 120 TYR cc_start: 0.5248 (OUTLIER) cc_final: 0.4640 (t80) REVERT: H 58 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.2975 (p90) REVERT: H 127 LYS cc_start: 0.5905 (OUTLIER) cc_final: 0.5408 (tttp) REVERT: C 30 GLN cc_start: 0.7265 (tt0) cc_final: 0.6905 (tp40) REVERT: C 66 MET cc_start: 0.7329 (mmm) cc_final: 0.6732 (mpt) REVERT: C 226 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8579 (mtt) REVERT: C 227 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7343 (t0) REVERT: D 25 HIS cc_start: 0.5549 (p-80) cc_final: 0.5061 (p90) REVERT: D 72 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7280 (t0) REVERT: D 112 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7160 (t0) REVERT: I 22 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: I 131 TYR cc_start: 0.7812 (m-10) cc_final: 0.7571 (m-10) REVERT: I 135 MET cc_start: 0.6440 (mpm) cc_final: 0.6233 (mpm) REVERT: J 58 TYR cc_start: 0.5868 (OUTLIER) cc_final: 0.3022 (p90) REVERT: J 127 LYS cc_start: 0.5667 (OUTLIER) cc_final: 0.5150 (tttp) REVERT: E 30 GLN cc_start: 0.7157 (tt0) cc_final: 0.6859 (tp40) REVERT: E 66 MET cc_start: 0.7517 (mmm) cc_final: 0.6943 (mpt) REVERT: E 75 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: E 226 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8579 (mtt) REVERT: E 313 LEU cc_start: 0.7792 (tt) cc_final: 0.7030 (mp) REVERT: F 37 ASP cc_start: 0.5646 (t0) cc_final: 0.4429 (m-30) REVERT: K 38 ARG cc_start: 0.7627 (tpp80) cc_final: 0.7231 (tpp80) REVERT: K 102 MET cc_start: 0.8032 (mtm) cc_final: 0.7793 (mtm) REVERT: K 109 ASP cc_start: 0.7010 (t0) cc_final: 0.6680 (t0) REVERT: L 58 TYR cc_start: 0.6032 (OUTLIER) cc_final: 0.3151 (p90) REVERT: L 127 LYS cc_start: 0.5541 (OUTLIER) cc_final: 0.5229 (tttp) outliers start: 163 outliers final: 103 residues processed: 349 average time/residue: 0.4260 time to fit residues: 171.1091 Evaluate side-chains 321 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 200 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 TYR Chi-restraints excluded: chain G residue 123 TRP Chi-restraints excluded: chain G residue 126 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 TRP Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 58 TYR Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 120 TYR Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 126 TYR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 108 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 181 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 293 ASN B 26 HIS G 58 GLN ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN C 11 ASN C 146 ASN C 183 ASN ** C 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN D 26 HIS ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS F 114 ASN ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.198476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.148433 restraints weight = 22517.522| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.09 r_work: 0.3681 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17163 Z= 0.156 Angle : 0.662 12.538 23283 Z= 0.328 Chirality : 0.044 0.192 2493 Planarity : 0.004 0.052 3000 Dihedral : 6.734 92.662 2321 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 8.67 % Allowed : 31.17 % Favored : 60.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.18), residues: 2091 helix: -0.85 (0.26), residues: 318 sheet: -0.39 (0.23), residues: 552 loop : -1.17 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.018 0.001 TYR K 126 PHE 0.016 0.001 PHE A 111 TRP 0.009 0.001 TRP G 66 HIS 0.020 0.002 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (17145) covalent geometry : angle 0.65818 / 0.33 (23247) SS BOND : bond 0.00489 / 0.28 ( 18) SS BOND : angle 1.97894 / 1.17 ( 36) hydrogen bonds : bond 0.03653 / 2.51 ( 528) hydrogen bonds : angle 5.85114 / 4.17 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 223 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7346 (tt0) cc_final: 0.6981 (tp40) REVERT: A 66 MET cc_start: 0.7125 (mmm) cc_final: 0.6323 (mpt) REVERT: A 313 LEU cc_start: 0.7556 (tt) cc_final: 0.6887 (mp) REVERT: B 25 HIS cc_start: 0.5704 (p-80) cc_final: 0.5345 (p90) REVERT: B 97 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6514 (tp30) REVERT: G 30 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.5824 (tm) REVERT: G 120 TYR cc_start: 0.5238 (OUTLIER) cc_final: 0.4658 (t80) REVERT: H 58 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.3244 (p90) REVERT: H 127 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5562 (tttp) REVERT: C 30 GLN cc_start: 0.7190 (tt0) cc_final: 0.6843 (tp40) REVERT: C 66 MET cc_start: 0.7240 (mmm) cc_final: 0.6649 (mpt) REVERT: C 227 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7307 (t0) REVERT: C 313 LEU cc_start: 0.7580 (tt) cc_final: 0.7088 (mp) REVERT: D 25 HIS cc_start: 0.5646 (p-80) cc_final: 0.5191 (p90) REVERT: D 72 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7247 (t0) REVERT: D 112 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7142 (t0) REVERT: I 22 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6873 (pm20) REVERT: I 131 TYR cc_start: 0.7780 (m-10) cc_final: 0.7555 (m-10) REVERT: J 58 TYR cc_start: 0.5984 (OUTLIER) cc_final: 0.3149 (p90) REVERT: J 127 LYS cc_start: 0.5719 (OUTLIER) cc_final: 0.5218 (tttp) REVERT: E 30 GLN cc_start: 0.7155 (tt0) cc_final: 0.6855 (tp40) REVERT: E 66 MET cc_start: 0.7482 (mmm) cc_final: 0.6935 (mpt) REVERT: E 75 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: E 226 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8576 (mtt) REVERT: K 38 ARG cc_start: 0.7652 (tpp80) cc_final: 0.7359 (tpp80) REVERT: K 102 MET cc_start: 0.7999 (mtm) cc_final: 0.7728 (mtm) REVERT: K 109 ASP cc_start: 0.6536 (t0) cc_final: 0.6159 (t0) REVERT: L 58 TYR cc_start: 0.6050 (OUTLIER) cc_final: 0.3122 (p90) REVERT: L 127 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.5314 (tttp) outliers start: 160 outliers final: 94 residues processed: 344 average time/residue: 0.4256 time to fit residues: 168.0210 Evaluate side-chains 313 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 204 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 TYR Chi-restraints excluded: chain G residue 123 TRP Chi-restraints excluded: chain G residue 126 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 123 TRP Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 58 TYR Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 120 TYR Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 126 TYR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 156 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 293 ASN B 26 HIS ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN E 165 ASN E 183 ASN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.198787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149376 restraints weight = 22433.278| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.06 r_work: 0.3689 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17163 Z= 0.156 Angle : 0.662 12.229 23283 Z= 0.327 Chirality : 0.044 0.190 2493 Planarity : 0.004 0.055 3000 Dihedral : 6.636 92.059 2317 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 8.35 % Allowed : 31.38 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.18), residues: 2091 helix: -0.81 (0.26), residues: 318 sheet: -0.38 (0.23), residues: 552 loop : -1.17 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.019 0.001 TYR G 126 PHE 0.016 0.001 PHE A 111 TRP 0.009 0.001 TRP K 138 HIS 0.016 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (17145) covalent geometry : angle 0.65850 / 0.33 (23247) SS BOND : bond 0.00464 / 0.27 ( 18) SS BOND : angle 1.80692 / 1.08 ( 36) hydrogen bonds : bond 0.03582 / 2.45 ( 528) hydrogen bonds : angle 5.79148 / 4.12 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 212 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7323 (tt0) cc_final: 0.6971 (tp40) REVERT: A 66 MET cc_start: 0.7148 (mmm) cc_final: 0.6312 (mpt) REVERT: A 107 ARG cc_start: 0.6926 (mpt180) cc_final: 0.6677 (mmt180) REVERT: A 191 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: B 25 HIS cc_start: 0.5685 (p-80) cc_final: 0.5343 (p90) REVERT: B 97 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6446 (tp30) REVERT: B 105 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5826 (mt-10) REVERT: G 30 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.5820 (tm) REVERT: G 122 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6466 (t80) REVERT: H 58 TYR cc_start: 0.6087 (OUTLIER) cc_final: 0.3213 (p90) REVERT: H 127 LYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5436 (tttp) REVERT: C 30 GLN cc_start: 0.7176 (tt0) cc_final: 0.6830 (tp40) REVERT: C 66 MET cc_start: 0.7124 (mmm) cc_final: 0.6619 (mpt) REVERT: C 226 MET cc_start: 0.8789 (mtt) cc_final: 0.8575 (mtt) REVERT: C 227 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7292 (t0) REVERT: D 25 HIS cc_start: 0.5667 (p-80) cc_final: 0.5200 (p90) REVERT: D 72 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7247 (t0) REVERT: D 112 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7108 (t0) REVERT: D 120 ASP cc_start: 0.5994 (m-30) cc_final: 0.5304 (OUTLIER) REVERT: I 22 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6925 (pm20) REVERT: I 30 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6864 (mm) REVERT: I 115 CYS cc_start: 0.7300 (OUTLIER) cc_final: 0.7035 (p) REVERT: I 131 TYR cc_start: 0.7775 (m-10) cc_final: 0.7561 (m-10) REVERT: J 58 TYR cc_start: 0.6027 (OUTLIER) cc_final: 0.3214 (p90) REVERT: J 127 LYS cc_start: 0.5768 (OUTLIER) cc_final: 0.5301 (tttp) REVERT: E 30 GLN cc_start: 0.7143 (tt0) cc_final: 0.6862 (tp40) REVERT: E 66 MET cc_start: 0.7479 (mmm) cc_final: 0.6906 (mpt) REVERT: E 126 GLU cc_start: 0.8452 (tp30) cc_final: 0.8246 (tp30) REVERT: E 226 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8607 (mtt) REVERT: K 38 ARG cc_start: 0.7678 (tpp80) cc_final: 0.7445 (tpp80) REVERT: K 102 MET cc_start: 0.8044 (mtm) cc_final: 0.7815 (mtm) REVERT: K 109 ASP cc_start: 0.6336 (t0) cc_final: 0.5897 (t0) REVERT: K 120 TYR cc_start: 0.5200 (OUTLIER) cc_final: 0.4606 (t80) REVERT: L 58 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.3323 (p90) REVERT: L 127 LYS cc_start: 0.5593 (OUTLIER) cc_final: 0.5304 (tttp) outliers start: 154 outliers final: 102 residues processed: 337 average time/residue: 0.4436 time to fit residues: 171.6062 Evaluate side-chains 321 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 201 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain G residue 123 TRP Chi-restraints excluded: chain G residue 126 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 115 CYS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 TRP Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 58 TYR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 120 TYR Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 126 TYR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 131 optimal weight: 0.0770 chunk 92 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN E 183 ASN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.198259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.148736 restraints weight = 22548.998| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.07 r_work: 0.3682 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17163 Z= 0.169 Angle : 0.672 12.341 23283 Z= 0.334 Chirality : 0.044 0.189 2493 Planarity : 0.004 0.055 3000 Dihedral : 6.653 91.429 2317 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 8.18 % Allowed : 31.54 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.18), residues: 2091 helix: -0.84 (0.26), residues: 318 sheet: -0.35 (0.23), residues: 552 loop : -1.21 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.022 0.002 TYR G 126 PHE 0.018 0.001 PHE L 122 TRP 0.011 0.001 TRP K 138 HIS 0.014 0.002 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (17145) covalent geometry : angle 0.66853 / 0.33 (23247) SS BOND : bond 0.00493 / 0.29 ( 18) SS BOND : angle 1.91575 / 1.13 ( 36) hydrogen bonds : bond 0.03625 / 2.48 ( 528) hydrogen bonds : angle 5.80224 / 4.14 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 210 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7285 (tt0) cc_final: 0.6938 (tp40) REVERT: A 66 MET cc_start: 0.7120 (mmm) cc_final: 0.6316 (mpt) REVERT: A 107 ARG cc_start: 0.6937 (mpt180) cc_final: 0.6683 (mmt180) REVERT: A 191 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: B 25 HIS cc_start: 0.5696 (p-80) cc_final: 0.5423 (p90) REVERT: B 97 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6486 (tp30) REVERT: B 105 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5828 (mt-10) REVERT: B 120 ASP cc_start: 0.5998 (m-30) cc_final: 0.5295 (OUTLIER) REVERT: G 30 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.5807 (tm) REVERT: G 120 TYR cc_start: 0.5185 (OUTLIER) cc_final: 0.4613 (t80) REVERT: H 58 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.3110 (p90) REVERT: C 30 GLN cc_start: 0.7185 (tt0) cc_final: 0.6844 (tp40) REVERT: C 66 MET cc_start: 0.7097 (mmm) cc_final: 0.6588 (mpt) REVERT: C 226 MET cc_start: 0.8830 (mtt) cc_final: 0.8621 (mtt) REVERT: C 227 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7206 (t0) REVERT: D 25 HIS cc_start: 0.5552 (p-80) cc_final: 0.5144 (p90) REVERT: D 120 ASP cc_start: 0.5967 (m-30) cc_final: 0.5342 (OUTLIER) REVERT: I 22 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: I 30 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6864 (mm) REVERT: I 58 GLN cc_start: 0.6768 (tt0) cc_final: 0.6563 (tt0) REVERT: I 115 CYS cc_start: 0.7287 (OUTLIER) cc_final: 0.7075 (p) REVERT: J 58 TYR cc_start: 0.6208 (OUTLIER) cc_final: 0.3303 (p90) REVERT: J 127 LYS cc_start: 0.5770 (OUTLIER) cc_final: 0.5244 (tttp) REVERT: E 30 GLN cc_start: 0.7291 (tt0) cc_final: 0.6929 (tp40) REVERT: E 66 MET cc_start: 0.7381 (mmm) cc_final: 0.6803 (mpt) REVERT: E 126 GLU cc_start: 0.8453 (tp30) cc_final: 0.8237 (tp30) REVERT: E 226 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8579 (mtt) REVERT: F 25 HIS cc_start: 0.5900 (p-80) cc_final: 0.5430 (p90) REVERT: K 38 ARG cc_start: 0.7661 (tpp80) cc_final: 0.7456 (tpp80) REVERT: K 58 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.6167 (tt0) REVERT: K 102 MET cc_start: 0.8014 (mtm) cc_final: 0.7761 (mtm) REVERT: K 109 ASP cc_start: 0.6278 (t0) cc_final: 0.5812 (t0) REVERT: K 120 TYR cc_start: 0.5194 (OUTLIER) cc_final: 0.4583 (t80) REVERT: L 58 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.3409 (p90) REVERT: L 127 LYS cc_start: 0.5534 (OUTLIER) cc_final: 0.5269 (tttp) outliers start: 151 outliers final: 105 residues processed: 331 average time/residue: 0.4689 time to fit residues: 176.8230 Evaluate side-chains 318 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 198 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 TYR Chi-restraints excluded: chain G residue 123 TRP Chi-restraints excluded: chain G residue 126 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain I residue 115 CYS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 TRP Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 58 TYR Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 111 PHE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 58 GLN Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 120 TYR Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 126 TYR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 51 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 119 optimal weight: 0.0170 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 293 ASN B 26 HIS ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN E 183 ASN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.198027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.147979 restraints weight = 22455.189| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.08 r_work: 0.3681 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17163 Z= 0.170 Angle : 0.685 12.137 23283 Z= 0.339 Chirality : 0.044 0.190 2493 Planarity : 0.004 0.055 3000 Dihedral : 6.657 91.009 2317 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 7.80 % Allowed : 31.98 % Favored : 60.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.18), residues: 2091 helix: -0.85 (0.26), residues: 318 sheet: -0.34 (0.23), residues: 552 loop : -1.22 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.022 0.002 TYR G 126 PHE 0.018 0.002 PHE L 122 TRP 0.011 0.001 TRP K 138 HIS 0.018 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (17145) covalent geometry : angle 0.68178 / 0.34 (23247) SS BOND : bond 0.00493 / 0.29 ( 18) SS BOND : angle 1.88051 / 1.12 ( 36) hydrogen bonds : bond 0.03622 / 2.48 ( 528) hydrogen bonds : angle 5.80602 / 4.14 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 203 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7286 (tt0) cc_final: 0.6933 (tp40) REVERT: A 66 MET cc_start: 0.7011 (mmm) cc_final: 0.6272 (mpt) REVERT: A 107 ARG cc_start: 0.6931 (mpt180) cc_final: 0.6673 (mmt180) REVERT: A 191 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.6908 (m-80) REVERT: B 25 HIS cc_start: 0.5746 (p-80) cc_final: 0.5500 (p90) REVERT: B 97 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6467 (tp30) REVERT: B 105 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5825 (mt-10) REVERT: B 120 ASP cc_start: 0.6085 (m-30) cc_final: 0.5400 (OUTLIER) REVERT: G 30 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.5788 (tm) REVERT: G 120 TYR cc_start: 0.5174 (OUTLIER) cc_final: 0.4600 (t80) REVERT: H 58 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.3185 (p90) REVERT: H 127 LYS cc_start: 0.5769 (OUTLIER) cc_final: 0.5264 (tttp) REVERT: C 30 GLN cc_start: 0.7167 (tt0) cc_final: 0.6836 (tp40) REVERT: C 66 MET cc_start: 0.7074 (mmm) cc_final: 0.6568 (mpt) REVERT: C 226 MET cc_start: 0.8844 (mtt) cc_final: 0.8639 (mtt) REVERT: C 227 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7197 (t0) REVERT: D 25 HIS cc_start: 0.5527 (p-80) cc_final: 0.5145 (p90) REVERT: D 120 ASP cc_start: 0.6022 (m-30) cc_final: 0.5405 (OUTLIER) REVERT: I 22 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: I 30 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6835 (mm) REVERT: J 23 MET cc_start: 0.6736 (mmm) cc_final: 0.6346 (mtt) REVERT: J 58 TYR cc_start: 0.6284 (OUTLIER) cc_final: 0.3397 (p90) REVERT: J 127 LYS cc_start: 0.5751 (OUTLIER) cc_final: 0.5242 (tttp) REVERT: E 30 GLN cc_start: 0.7282 (tt0) cc_final: 0.6924 (tp40) REVERT: E 66 MET cc_start: 0.7319 (mmm) cc_final: 0.6771 (mpt) REVERT: E 126 GLU cc_start: 0.8463 (tp30) cc_final: 0.8249 (tp30) REVERT: E 226 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8588 (mtt) REVERT: E 301 GLU cc_start: 0.7763 (tt0) cc_final: 0.7014 (tp30) REVERT: F 25 HIS cc_start: 0.5943 (p-80) cc_final: 0.5505 (p90) REVERT: F 120 ASP cc_start: 0.6092 (m-30) cc_final: 0.5487 (OUTLIER) REVERT: K 102 MET cc_start: 0.8024 (mtm) cc_final: 0.7776 (mtm) REVERT: K 109 ASP cc_start: 0.6105 (t0) cc_final: 0.5678 (t0) REVERT: K 120 TYR cc_start: 0.5195 (OUTLIER) cc_final: 0.4567 (t80) REVERT: L 58 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.3461 (p90) REVERT: L 63 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7811 (ptpp) REVERT: L 127 LYS cc_start: 0.5497 (OUTLIER) cc_final: 0.5186 (tttp) outliers start: 144 outliers final: 106 residues processed: 319 average time/residue: 0.4733 time to fit residues: 172.1618 Evaluate side-chains 316 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 196 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 TYR Chi-restraints excluded: chain G residue 123 TRP Chi-restraints excluded: chain G residue 126 TYR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 TRP Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 58 TYR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 120 TYR Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 126 TYR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 63 LYS Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 11 optimal weight: 0.6980 chunk 121 optimal weight: 0.0270 chunk 169 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 115 optimal weight: 0.0060 chunk 159 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 293 ASN B 26 HIS ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 183 ASN ** C 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.201146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.151987 restraints weight = 22484.614| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.06 r_work: 0.3723 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17163 Z= 0.131 Angle : 0.665 12.357 23283 Z= 0.327 Chirality : 0.044 0.195 2493 Planarity : 0.004 0.056 3000 Dihedral : 6.541 90.608 2317 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 6.40 % Allowed : 33.44 % Favored : 60.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.18), residues: 2091 helix: -0.75 (0.26), residues: 318 sheet: -0.42 (0.23), residues: 558 loop : -1.16 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 38 TYR 0.017 0.001 TYR G 126 PHE 0.019 0.001 PHE J 122 TRP 0.011 0.001 TRP K 138 HIS 0.022 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (17145) covalent geometry : angle 0.65942 / 0.32 (23247) SS BOND : bond 0.00425 / 0.25 ( 18) SS BOND : angle 2.26830 / 1.47 ( 36) hydrogen bonds : bond 0.03369 / 2.32 ( 528) hydrogen bonds : angle 5.63079 / 4.02 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 201 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7285 (tt0) cc_final: 0.6921 (tp40) REVERT: A 66 MET cc_start: 0.6813 (mmm) cc_final: 0.6084 (mpt) REVERT: B 25 HIS cc_start: 0.5845 (p-80) cc_final: 0.5610 (p90) REVERT: B 97 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6335 (tp30) REVERT: B 105 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5754 (mt-10) REVERT: B 120 ASP cc_start: 0.5876 (m-30) cc_final: 0.5335 (OUTLIER) REVERT: G 30 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.5795 (tm) REVERT: H 58 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.3156 (p90) REVERT: H 127 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5247 (tttp) REVERT: C 30 GLN cc_start: 0.7028 (tt0) cc_final: 0.6739 (tp40) REVERT: C 66 MET cc_start: 0.6917 (mmm) cc_final: 0.6513 (mpt) REVERT: C 107 ARG cc_start: 0.6909 (mpt90) cc_final: 0.6646 (mmt180) REVERT: C 226 MET cc_start: 0.8839 (mtt) cc_final: 0.8624 (mtt) REVERT: C 227 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7148 (t70) REVERT: D 25 HIS cc_start: 0.5602 (p-80) cc_final: 0.5203 (p90) REVERT: I 22 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: I 30 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6748 (mm) REVERT: J 58 TYR cc_start: 0.6141 (OUTLIER) cc_final: 0.3369 (p90) REVERT: J 113 MET cc_start: 0.0999 (ptt) cc_final: 0.0476 (ptt) REVERT: J 127 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5233 (tttp) REVERT: E 30 GLN cc_start: 0.7200 (tt0) cc_final: 0.6846 (tp40) REVERT: E 66 MET cc_start: 0.7088 (mmm) cc_final: 0.6560 (mpt) REVERT: E 126 GLU cc_start: 0.8475 (tp30) cc_final: 0.8255 (tp30) REVERT: E 226 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8575 (mtt) REVERT: F 120 ASP cc_start: 0.5912 (m-30) cc_final: 0.5456 (t0) REVERT: K 102 MET cc_start: 0.8075 (mtm) cc_final: 0.7749 (mtm) REVERT: K 109 ASP cc_start: 0.5913 (t0) cc_final: 0.5459 (t0) REVERT: K 120 TYR cc_start: 0.5028 (OUTLIER) cc_final: 0.4466 (t80) REVERT: K 122 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.6135 (t80) REVERT: L 58 TYR cc_start: 0.6125 (OUTLIER) cc_final: 0.3441 (p90) REVERT: L 127 LYS cc_start: 0.5554 (OUTLIER) cc_final: 0.5263 (tttp) outliers start: 118 outliers final: 79 residues processed: 297 average time/residue: 0.4823 time to fit residues: 162.8825 Evaluate side-chains 285 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 192 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 126 TYR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 58 TYR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 120 TYR Chi-restraints excluded: chain K residue 122 PHE Chi-restraints excluded: chain K residue 123 TRP Chi-restraints excluded: chain K residue 126 TYR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 127 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.0570 chunk 103 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 165 ASN C 183 ASN ** C 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.199003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.149128 restraints weight = 22557.876| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.09 r_work: 0.3707 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17163 Z= 0.147 Angle : 0.667 13.137 23283 Z= 0.330 Chirality : 0.044 0.194 2493 Planarity : 0.004 0.057 3000 Dihedral : 6.145 86.668 2314 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.47 % Allowed : 34.53 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 2091 helix: -0.67 (0.27), residues: 318 sheet: -0.44 (0.23), residues: 564 loop : -1.26 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 38 TYR 0.019 0.001 TYR G 126 PHE 0.020 0.001 PHE J 122 TRP 0.011 0.001 TRP G 66 HIS 0.011 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (17145) covalent geometry : angle 0.66447 / 0.33 (23247) SS BOND : bond 0.00481 / 0.28 ( 18) SS BOND : angle 1.68715 / 1.00 ( 36) hydrogen bonds : bond 0.03362 / 2.31 ( 528) hydrogen bonds : angle 5.61042 / 4.01 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7313.81 seconds wall clock time: 125 minutes 15.42 seconds (7515.42 seconds total)