Starting phenix.real_space_refine on Thu Mar 5 23:27:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w4o_21535/03_2026/6w4o_21535.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w4o_21535/03_2026/6w4o_21535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6w4o_21535/03_2026/6w4o_21535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w4o_21535/03_2026/6w4o_21535.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w4o_21535/03_2026/6w4o_21535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w4o_21535/03_2026/6w4o_21535.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14475 atoms to isotropic. 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 71 5.16 5 C 9185 2.51 5 N 2568 2.21 5 O 2651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14475 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1040 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1023 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1022 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain breaks: 1 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 994 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "E" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 994 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain breaks: 1 Chain: "F" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 988 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain breaks: 1 Chain: "G" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1041 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "I" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1023 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain breaks: 1 Chain: "J" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1022 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 994 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 994 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain breaks: 1 Chain: "M" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 988 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain breaks: 1 Chain: "O" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2352 Classifications: {'peptide': 293} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain breaks: 1 Time building chain proxies: 3.07, per 1000 atoms: 0.21 Number of scatterers: 14475 At special positions: 0 Unit cell: (121.03, 101.01, 137.41, 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 71 16.00 O 2651 8.00 N 2568 7.00 C 9185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 597.4 milliseconds 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 35.8% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 17 through 35 Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.566A pdb=" N PHE A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.904A pdb=" N ARG A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 78' Processing helix chain 'B' and resid 3 through 21 removed outlier: 3.975A pdb=" N ILE B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 29 Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'B' and resid 49 through 58 removed outlier: 4.230A pdb=" N PHE B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 25 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 44 through 47 Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.972A pdb=" N PHE C 59 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR C 60 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 23 Processing helix chain 'D' and resid 25 through 32 Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 52 through 62 removed outlier: 4.271A pdb=" N PHE D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 59 " --> pdb=" O HIS D 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 21 removed outlier: 3.640A pdb=" N VAL E 11 " --> pdb=" O GLU E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 30 Processing helix chain 'E' and resid 39 through 43 Processing helix chain 'E' and resid 50 through 58 removed outlier: 4.359A pdb=" N PHE E 55 " --> pdb=" O ASP E 51 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR E 56 " --> pdb=" O PHE E 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 20 removed outlier: 3.809A pdb=" N ILE F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 29 Processing helix chain 'F' and resid 38 through 42 Processing helix chain 'F' and resid 49 through 54 removed outlier: 4.323A pdb=" N PHE F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 35 Processing helix chain 'G' and resid 37 through 44 Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 64 through 73 removed outlier: 3.565A pdb=" N PHE G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR G 70 " --> pdb=" O PHE G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.907A pdb=" N ARG G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN G 78 " --> pdb=" O LEU G 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 73 through 78' Processing helix chain 'I' and resid 3 through 21 removed outlier: 3.976A pdb=" N ILE I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 29 Processing helix chain 'I' and resid 38 through 42 Processing helix chain 'I' and resid 49 through 58 removed outlier: 4.230A pdb=" N PHE I 54 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR I 55 " --> pdb=" O PHE I 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 25 Processing helix chain 'J' and resid 27 through 34 Processing helix chain 'J' and resid 44 through 47 Processing helix chain 'J' and resid 54 through 63 removed outlier: 3.971A pdb=" N PHE J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR J 60 " --> pdb=" O PHE J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 23 Processing helix chain 'K' and resid 25 through 32 Processing helix chain 'K' and resid 41 through 45 Processing helix chain 'K' and resid 52 through 62 removed outlier: 4.269A pdb=" N PHE K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR K 58 " --> pdb=" O PHE K 54 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE K 59 " --> pdb=" O HIS K 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 removed outlier: 3.639A pdb=" N VAL L 11 " --> pdb=" O GLU L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 30 Processing helix chain 'L' and resid 39 through 43 Processing helix chain 'L' and resid 50 through 58 removed outlier: 4.360A pdb=" N PHE L 55 " --> pdb=" O ASP L 51 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR L 56 " --> pdb=" O PHE L 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 20 removed outlier: 3.809A pdb=" N ILE M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 29 Processing helix chain 'M' and resid 38 through 42 Processing helix chain 'M' and resid 49 through 54 removed outlier: 4.323A pdb=" N PHE M 54 " --> pdb=" O ASP M 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 6 Processing helix chain 'O' and resid 41 through 59 removed outlier: 3.543A pdb=" N HIS O 46 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS O 48 " --> pdb=" O ARG O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 96 removed outlier: 4.094A pdb=" N VAL O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA O 95 " --> pdb=" O GLU O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 121 removed outlier: 3.756A pdb=" N GLN O 110 " --> pdb=" O HIS O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 172 removed outlier: 3.598A pdb=" N LEU O 172 " --> pdb=" O PRO O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 178 Processing helix chain 'O' and resid 184 through 201 removed outlier: 3.688A pdb=" N LEU O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA O 190 " --> pdb=" O VAL O 186 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE O 197 " --> pdb=" O VAL O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 209 through 220 Processing helix chain 'O' and resid 233 through 244 Processing helix chain 'O' and resid 253 through 260 removed outlier: 3.603A pdb=" N LYS O 259 " --> pdb=" O ALA O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 263 through 270 Processing helix chain 'O' and resid 275 through 293 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.303A pdb=" N HIS A 138 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N GLY A 48 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 11.984A pdb=" N HIS A 140 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 11.513A pdb=" N THR A 50 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 11.990A pdb=" N SER A 142 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 10.913A pdb=" N PHE A 52 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL A 126 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE A 139 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 124 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A 141 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU A 122 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N SER A 98 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU A 93 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS A 100 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A 91 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA A 102 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 removed outlier: 7.255A pdb=" N HIS B 120 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 10.893A pdb=" N GLY B 33 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 11.925A pdb=" N HIS B 122 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N THR B 35 " --> pdb=" O HIS B 122 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N SER B 124 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N PHE B 37 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL B 108 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE B 121 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 106 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 123 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU B 104 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY B 125 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN B 102 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER B 80 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU B 75 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 82 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 73 " --> pdb=" O CYS B 82 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 84 " --> pdb=" O PRO B 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 52 removed outlier: 7.430A pdb=" N HIS C 126 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N GLY C 38 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 11.823A pdb=" N HIS C 128 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 11.184A pdb=" N THR C 40 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N SER C 130 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N PHE C 42 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE C 124 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS C 116 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS C 126 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE C 92 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASN C 76 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE C 94 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE C 74 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN C 96 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR C 72 " --> pdb=" O GLN C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 49 through 50 removed outlier: 7.212A pdb=" N HIS D 120 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N GLY D 36 " --> pdb=" O HIS D 120 " (cutoff:3.500A) removed outlier: 11.593A pdb=" N HIS D 122 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 11.302A pdb=" N THR D 38 " --> pdb=" O HIS D 122 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N SER D 124 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 10.887A pdb=" N PHE D 40 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL D 108 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE D 121 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR D 106 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG D 123 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU D 104 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY D 125 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLN D 102 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER D 80 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU D 75 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS D 82 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE D 73 " --> pdb=" O CYS D 82 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA D 84 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 47 through 48 removed outlier: 9.061A pdb=" N GLN E 115 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N GLY E 34 " --> pdb=" O GLN E 115 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL E 117 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR E 36 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE E 116 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS E 108 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS E 118 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER E 78 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU E 73 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS E 80 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE E 71 " --> pdb=" O CYS E 80 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA E 82 " --> pdb=" O PRO E 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 46 through 47 removed outlier: 9.023A pdb=" N GLN F 114 " --> pdb=" O ASP F 31 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N GLY F 33 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL F 116 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL F 105 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE F 118 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR F 103 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG F 120 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU F 101 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLY F 122 " --> pdb=" O GLN F 99 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLN F 99 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N SER F 77 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU F 72 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS F 79 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE F 70 " --> pdb=" O CYS F 79 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA F 81 " --> pdb=" O PRO F 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 61 through 62 removed outlier: 7.303A pdb=" N HIS G 138 " --> pdb=" O ASP G 46 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N GLY G 48 " --> pdb=" O HIS G 138 " (cutoff:3.500A) removed outlier: 11.983A pdb=" N HIS G 140 " --> pdb=" O GLY G 48 " (cutoff:3.500A) removed outlier: 11.513A pdb=" N THR G 50 " --> pdb=" O HIS G 140 " (cutoff:3.500A) removed outlier: 11.990A pdb=" N SER G 142 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 10.913A pdb=" N PHE G 52 " --> pdb=" O SER G 142 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL G 126 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE G 139 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR G 124 " --> pdb=" O PHE G 139 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG G 141 " --> pdb=" O GLU G 122 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU G 122 " --> pdb=" O ARG G 141 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N SER G 98 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU G 93 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS G 100 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE G 91 " --> pdb=" O CYS G 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA G 102 " --> pdb=" O PRO G 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 46 through 47 removed outlier: 7.256A pdb=" N HIS I 120 " --> pdb=" O ASP I 31 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N GLY I 33 " --> pdb=" O HIS I 120 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N HIS I 122 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N THR I 35 " --> pdb=" O HIS I 122 " (cutoff:3.500A) removed outlier: 11.782A pdb=" N SER I 124 " --> pdb=" O THR I 35 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N PHE I 37 " --> pdb=" O SER I 124 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL I 108 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE I 121 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR I 106 " --> pdb=" O PHE I 121 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG I 123 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU I 104 " --> pdb=" O ARG I 123 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY I 125 " --> pdb=" O GLN I 102 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLN I 102 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER I 80 " --> pdb=" O LEU I 75 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU I 75 " --> pdb=" O SER I 80 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS I 82 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE I 73 " --> pdb=" O CYS I 82 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA I 84 " --> pdb=" O PRO I 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 50 through 52 removed outlier: 7.432A pdb=" N HIS J 126 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N GLY J 38 " --> pdb=" O HIS J 126 " (cutoff:3.500A) removed outlier: 11.821A pdb=" N HIS J 128 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N THR J 40 " --> pdb=" O HIS J 128 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N SER J 130 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 11.017A pdb=" N PHE J 42 " --> pdb=" O SER J 130 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE J 124 " --> pdb=" O HIS J 116 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N HIS J 116 " --> pdb=" O ILE J 124 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS J 126 " --> pdb=" O VAL J 114 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE J 92 " --> pdb=" O ASN J 76 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASN J 76 " --> pdb=" O ILE J 92 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE J 94 " --> pdb=" O ILE J 74 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE J 74 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN J 96 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N THR J 72 " --> pdb=" O GLN J 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 49 through 50 removed outlier: 7.212A pdb=" N HIS K 120 " --> pdb=" O ASP K 34 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N GLY K 36 " --> pdb=" O HIS K 120 " (cutoff:3.500A) removed outlier: 11.593A pdb=" N HIS K 122 " --> pdb=" O GLY K 36 " (cutoff:3.500A) removed outlier: 11.302A pdb=" N THR K 38 " --> pdb=" O HIS K 122 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N SER K 124 " --> pdb=" O THR K 38 " (cutoff:3.500A) removed outlier: 10.888A pdb=" N PHE K 40 " --> pdb=" O SER K 124 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL K 108 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE K 121 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR K 106 " --> pdb=" O PHE K 121 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG K 123 " --> pdb=" O GLU K 104 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU K 104 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLY K 125 " --> pdb=" O GLN K 102 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLN K 102 " --> pdb=" O GLY K 125 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER K 80 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU K 75 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS K 82 " --> pdb=" O ILE K 73 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE K 73 " --> pdb=" O CYS K 82 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA K 84 " --> pdb=" O PRO K 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 47 through 48 removed outlier: 9.060A pdb=" N GLN L 115 " --> pdb=" O ASP L 32 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N GLY L 34 " --> pdb=" O GLN L 115 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL L 117 " --> pdb=" O GLY L 34 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR L 36 " --> pdb=" O VAL L 117 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE L 116 " --> pdb=" O HIS L 108 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS L 108 " --> pdb=" O ILE L 116 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS L 118 " --> pdb=" O VAL L 106 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER L 78 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU L 73 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS L 80 " --> pdb=" O ILE L 71 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE L 71 " --> pdb=" O CYS L 80 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA L 82 " --> pdb=" O PRO L 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 46 through 47 removed outlier: 9.022A pdb=" N GLN M 114 " --> pdb=" O ASP M 31 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N GLY M 33 " --> pdb=" O GLN M 114 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL M 116 " --> pdb=" O GLY M 33 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL M 105 " --> pdb=" O VAL M 116 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE M 118 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR M 103 " --> pdb=" O PHE M 118 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG M 120 " --> pdb=" O GLU M 101 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU M 101 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLY M 122 " --> pdb=" O GLN M 99 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN M 99 " --> pdb=" O GLY M 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE M 94 " --> pdb=" O ASP M 90 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER M 77 " --> pdb=" O LEU M 72 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU M 72 " --> pdb=" O SER M 77 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS M 79 " --> pdb=" O ILE M 70 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE M 70 " --> pdb=" O CYS M 79 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA M 81 " --> pdb=" O PRO M 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 7 through 12 removed outlier: 5.693A pdb=" N LEU O 9 " --> pdb=" O VAL O 23 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL O 23 " --> pdb=" O LEU O 9 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU O 11 " --> pdb=" O ARG O 21 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA O 32 " --> pdb=" O PHE O 81 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP O 69 " --> pdb=" O ILE O 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 133 through 135 692 hydrogen bonds defined for protein. 1929 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: 2.10 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4812 1.34 - 1.46: 3266 1.46 - 1.58: 6647 1.58 - 1.70: 2 1.70 - 1.82: 111 Bond restraints: 14838 Sorted by residual: bond pdb=" CA VAL O 269 " pdb=" C VAL O 269 " ideal model delta sigma weight residual 1.517 1.581 -0.064 1.49e-02 4.50e+03 1.84e+01 bond pdb=" N ALA O 270 " pdb=" CA ALA O 270 " ideal model delta sigma weight residual 1.452 1.505 -0.053 1.25e-02 6.40e+03 1.77e+01 bond pdb=" CD GLN O 215 " pdb=" OE1 GLN O 215 " ideal model delta sigma weight residual 1.231 1.287 -0.056 1.90e-02 2.77e+03 8.83e+00 bond pdb=" CG GLN O 215 " pdb=" CD GLN O 215 " ideal model delta sigma weight residual 1.516 1.581 -0.065 2.50e-02 1.60e+03 6.74e+00 bond pdb=" CD GLN O 215 " pdb=" NE2 GLN O 215 " ideal model delta sigma weight residual 1.328 1.376 -0.048 2.10e-02 2.27e+03 5.12e+00 ... (remaining 14833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 19761 2.70 - 5.41: 268 5.41 - 8.11: 27 8.11 - 10.82: 5 10.82 - 13.52: 3 Bond angle restraints: 20064 Sorted by residual: angle pdb=" N VAL O 269 " pdb=" CA VAL O 269 " pdb=" C VAL O 269 " ideal model delta sigma weight residual 112.90 126.42 -13.52 9.60e-01 1.09e+00 1.98e+02 angle pdb=" N TRP O 262 " pdb=" CA TRP O 262 " pdb=" C TRP O 262 " ideal model delta sigma weight residual 113.01 101.60 11.41 1.20e+00 6.94e-01 9.05e+01 angle pdb=" N ALA O 43 " pdb=" CA ALA O 43 " pdb=" C ALA O 43 " ideal model delta sigma weight residual 111.14 120.74 -9.60 1.08e+00 8.57e-01 7.91e+01 angle pdb=" N ALA O 270 " pdb=" CA ALA O 270 " pdb=" C ALA O 270 " ideal model delta sigma weight residual 110.36 122.23 -11.87 1.55e+00 4.16e-01 5.87e+01 angle pdb=" N SER O 267 " pdb=" CA SER O 267 " pdb=" C SER O 267 " ideal model delta sigma weight residual 111.28 103.26 8.02 1.09e+00 8.42e-01 5.41e+01 ... (remaining 20059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 8199 16.80 - 33.61: 472 33.61 - 50.41: 67 50.41 - 67.21: 23 67.21 - 84.01: 4 Dihedral angle restraints: 8765 sinusoidal: 3617 harmonic: 5148 Sorted by residual: dihedral pdb=" CA GLY O 150 " pdb=" C GLY O 150 " pdb=" N LEU O 151 " pdb=" CA LEU O 151 " ideal model delta harmonic sigma weight residual 180.00 135.15 44.85 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA PHE O 149 " pdb=" C PHE O 149 " pdb=" N GLY O 150 " pdb=" CA GLY O 150 " ideal model delta harmonic sigma weight residual 0.00 40.86 -40.86 0 5.00e+00 4.00e-02 6.68e+01 dihedral pdb=" C VAL O 269 " pdb=" N VAL O 269 " pdb=" CA VAL O 269 " pdb=" CB VAL O 269 " ideal model delta harmonic sigma weight residual -122.00 -140.50 18.50 0 2.50e+00 1.60e-01 5.48e+01 ... (remaining 8762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 2099 0.142 - 0.284: 32 0.284 - 0.425: 3 0.425 - 0.567: 0 0.567 - 0.709: 1 Chirality restraints: 2135 Sorted by residual: chirality pdb=" CA VAL O 269 " pdb=" N VAL O 269 " pdb=" C VAL O 269 " pdb=" CB VAL O 269 " both_signs ideal model delta sigma weight residual False 2.44 1.73 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA ALA O 43 " pdb=" N ALA O 43 " pdb=" C ALA O 43 " pdb=" CB ALA O 43 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA ALA O 270 " pdb=" N ALA O 270 " pdb=" C ALA O 270 " pdb=" CB ALA O 270 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 2132 not shown) Planarity restraints: 2599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE O 149 " -0.025 2.00e-02 2.50e+03 1.66e-02 4.85e+00 pdb=" CG PHE O 149 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE O 149 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE O 149 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE O 149 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE O 149 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE O 149 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN O 127 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C ASN O 127 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN O 127 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU O 128 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 165 " -0.019 2.00e-02 2.50e+03 1.37e-02 3.30e+00 pdb=" CG PHE O 165 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE O 165 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE O 165 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE O 165 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE O 165 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE O 165 " -0.003 2.00e-02 2.50e+03 ... (remaining 2596 not shown) Histogram of nonbonded interaction distances: 0.83 - 1.65: 8 1.65 - 2.46: 111 2.46 - 3.27: 14819 3.27 - 4.09: 37164 4.09 - 4.90: 67761 Warning: very small nonbonded interaction distances. Nonbonded interactions: 119863 Sorted by model distance: nonbonded pdb=" CE LYS K 31 " pdb=" CH2 TRP O 162 " model vdw 0.834 3.740 nonbonded pdb=" OE2 GLU K 27 " pdb=" N GLY O 164 " model vdw 1.118 3.120 nonbonded pdb=" CE LYS K 31 " pdb=" CZ2 TRP O 162 " model vdw 1.318 3.740 nonbonded pdb=" NZ LYS K 31 " pdb=" CH2 TRP O 162 " model vdw 1.336 3.420 nonbonded pdb=" O SER J 67 " pdb=" CD LYS O 39 " model vdw 1.352 3.440 ... (remaining 119858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 73 or resid 81 through 144)) selection = (chain 'B' and ((resid 2 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 3 through 58 or resid 63 through 126)) selection = (chain 'C' and ((resid 7 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 8 through 63 or resid 69 through 132)) selection = (chain 'D' and ((resid 5 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 6 through 61 or resid 63 through 126)) selection = (chain 'E' and ((resid 3 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 4 through 59 or resid 61 through 124)) selection = (chain 'F' and ((resid 2 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 3 through 58 or resid 60 through 123)) selection = (chain 'G' and ((resid 17 and (name CA or name C or name O or name CB or name CG \ 1 or name CG2)) or resid 18 through 73 or resid 81 through 144)) selection = (chain 'I' and ((resid 2 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 3 through 58 or resid 63 through 126)) selection = (chain 'J' and ((resid 7 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 8 through 63 or resid 69 through 132)) selection = (chain 'K' and ((resid 5 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 6 through 61 or resid 63 through 126)) selection = (chain 'L' and ((resid 3 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 4 through 59 or resid 61 through 124)) selection = (chain 'M' and ((resid 2 and (name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 3 through 58 or resid 60 through 123)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.910 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 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 : 0.004 0.065 14838 Z= 0.233 Angle : 0.776 13.525 20064 Z= 0.502 Chirality : 0.053 0.709 2135 Planarity : 0.003 0.028 2599 Dihedral : 10.845 84.015 5441 Min Nonbonded Distance : 0.834 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.04 % Favored : 96.73 % Rotamer: Outliers : 0.91 % Allowed : 5.45 % Favored : 93.64 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.53 (0.18), residues: 1741 helix: -2.63 (0.16), residues: 530 sheet: 0.50 (0.20), residues: 582 loop : -0.78 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 58 TYR 0.018 0.002 TYR O 171 PHE 0.030 0.002 PHE O 149 TRP 0.012 0.001 TRP O 262 HIS 0.005 0.001 HIS O 117 Details of bonding type rmsd covalent geometry : bond 0.00393 (14838) covalent geometry : angle 0.77554 (20064) hydrogen bonds : bond 0.16357 ( 692) hydrogen bonds : angle 8.01153 ( 1929) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 650 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 29 LEU cc_start: 0.8800 (tp) cc_final: 0.8585 (tp) REVERT: A 122 GLU cc_start: 0.6662 (mp0) cc_final: 0.6269 (mp0) REVERT: A 136 ILE cc_start: 0.7948 (mm) cc_final: 0.7264 (mm) REVERT: B 34 MET cc_start: 0.8172 (ttp) cc_final: 0.7956 (ppp) REVERT: B 49 LEU cc_start: 0.7597 (mp) cc_final: 0.6398 (mt) REVERT: B 92 LEU cc_start: 0.9079 (mt) cc_final: 0.8553 (mt) REVERT: C 19 LEU cc_start: 0.9071 (tp) cc_final: 0.8815 (tp) REVERT: C 76 ASN cc_start: 0.8149 (m-40) cc_final: 0.7914 (m110) REVERT: C 92 ILE cc_start: 0.8910 (mt) cc_final: 0.8081 (mp) REVERT: D 11 ILE cc_start: 0.9291 (mt) cc_final: 0.9024 (pt) REVERT: D 70 ASN cc_start: 0.8032 (m-40) cc_final: 0.7828 (m110) REVERT: D 92 LEU cc_start: 0.9161 (mt) cc_final: 0.8882 (pt) REVERT: E 74 MET cc_start: 0.6413 (mtm) cc_final: 0.5788 (mpp) REVERT: E 80 CYS cc_start: 0.7424 (t) cc_final: 0.7007 (m) REVERT: E 102 GLU cc_start: 0.6529 (mp0) cc_final: 0.5910 (mp0) REVERT: F 37 PHE cc_start: 0.8259 (m-80) cc_final: 0.7633 (m-10) REVERT: F 49 LEU cc_start: 0.7109 (mp) cc_final: 0.4844 (mt) REVERT: F 121 SER cc_start: 0.9066 (m) cc_final: 0.8746 (p) REVERT: G 22 ILE cc_start: 0.8876 (mm) cc_final: 0.8646 (mm) REVERT: G 29 LEU cc_start: 0.9021 (tp) cc_final: 0.8793 (tp) REVERT: G 44 MET cc_start: 0.8029 (mtm) cc_final: 0.7605 (ttm) REVERT: G 67 HIS cc_start: 0.7844 (m90) cc_final: 0.6796 (m170) REVERT: G 87 LEU cc_start: 0.8623 (mt) cc_final: 0.8190 (tp) REVERT: G 118 THR cc_start: 0.8307 (m) cc_final: 0.7971 (p) REVERT: G 122 GLU cc_start: 0.7613 (mp0) cc_final: 0.7268 (mp0) REVERT: I 14 LEU cc_start: 0.9116 (tp) cc_final: 0.8681 (tp) REVERT: I 97 ILE cc_start: 0.8419 (mt) cc_final: 0.8219 (mp) REVERT: I 121 PHE cc_start: 0.6619 (p90) cc_final: 0.6151 (p90) REVERT: J 19 LEU cc_start: 0.9560 (tp) cc_final: 0.9193 (tt) REVERT: J 20 ILE cc_start: 0.9641 (mm) cc_final: 0.9391 (tt) REVERT: J 75 LEU cc_start: 0.8666 (mt) cc_final: 0.8342 (tp) REVERT: J 76 ASN cc_start: 0.8184 (m-40) cc_final: 0.7531 (m-40) REVERT: K 17 LEU cc_start: 0.9264 (tp) cc_final: 0.9016 (tp) REVERT: K 32 MET cc_start: 0.9055 (mtm) cc_final: 0.8855 (mtp) REVERT: K 40 PHE cc_start: 0.8659 (m-80) cc_final: 0.8034 (m-10) REVERT: K 69 LEU cc_start: 0.8502 (mp) cc_final: 0.8133 (mm) REVERT: K 86 ILE cc_start: 0.8875 (mm) cc_final: 0.8620 (mm) REVERT: K 91 TYR cc_start: 0.8347 (p90) cc_final: 0.7630 (p90) REVERT: K 92 LEU cc_start: 0.8308 (mt) cc_final: 0.7945 (mt) REVERT: K 118 ILE cc_start: 0.8641 (mt) cc_final: 0.8259 (tp) REVERT: K 122 HIS cc_start: 0.8215 (t-90) cc_final: 0.5603 (t-90) REVERT: L 11 VAL cc_start: 0.9206 (p) cc_final: 0.8980 (m) REVERT: L 21 ASN cc_start: 0.9068 (m-40) cc_final: 0.8473 (p0) REVERT: M 14 LEU cc_start: 0.9421 (tp) cc_final: 0.9145 (tt) REVERT: M 37 PHE cc_start: 0.8597 (m-80) cc_final: 0.8152 (m-10) outliers start: 14 outliers final: 6 residues processed: 660 average time/residue: 0.1529 time to fit residues: 135.7642 Evaluate side-chains 299 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 293 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.0020 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.7490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 135 GLN B 110 HIS ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN D 65 HIS ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 HIS E 120 HIS F 119 HIS G 73 ASN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 GLN M 44 ASN O 47 GLN O 63 ASN O 119 HIS ** O 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.049017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.039327 restraints weight = 126938.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.040349 restraints weight = 95141.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.041148 restraints weight = 76140.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.041788 restraints weight = 63968.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.042275 restraints weight = 55590.562| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14838 Z= 0.173 Angle : 0.743 12.938 20064 Z= 0.397 Chirality : 0.049 0.229 2135 Planarity : 0.005 0.062 2599 Dihedral : 4.909 31.336 1939 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.67 % Favored : 98.10 % Rotamer: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1741 helix: -1.12 (0.19), residues: 531 sheet: 0.93 (0.20), residues: 591 loop : -0.25 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 129 TYR 0.025 0.002 TYR O 214 PHE 0.018 0.002 PHE E 57 TRP 0.031 0.002 TRP O 162 HIS 0.024 0.002 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00395 (14838) covalent geometry : angle 0.74331 (20064) hydrogen bonds : bond 0.04808 ( 692) hydrogen bonds : angle 5.74467 ( 1929) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 405 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 52 PHE cc_start: 0.9054 (m-80) cc_final: 0.8405 (m-10) REVERT: A 122 GLU cc_start: 0.7619 (mp0) cc_final: 0.7317 (mp0) REVERT: B 26 TYR cc_start: 0.9135 (t80) cc_final: 0.8681 (t80) REVERT: B 34 MET cc_start: 0.8659 (ttp) cc_final: 0.8379 (ppp) REVERT: B 37 PHE cc_start: 0.8506 (m-80) cc_final: 0.8065 (m-10) REVERT: B 51 PHE cc_start: 0.7865 (t80) cc_final: 0.7661 (t80) REVERT: C 19 LEU cc_start: 0.9532 (tp) cc_final: 0.9274 (tp) REVERT: C 56 PHE cc_start: 0.8328 (t80) cc_final: 0.7774 (t80) REVERT: C 57 HIS cc_start: 0.8947 (m90) cc_final: 0.8599 (m90) REVERT: C 76 ASN cc_start: 0.8093 (m-40) cc_final: 0.7796 (t0) REVERT: C 93 ARG cc_start: 0.8931 (ttp80) cc_final: 0.8521 (ttp-110) REVERT: D 48 LEU cc_start: 0.8834 (tp) cc_final: 0.8413 (tp) REVERT: D 54 PHE cc_start: 0.8275 (t80) cc_final: 0.7978 (t80) REVERT: E 15 LEU cc_start: 0.8665 (tp) cc_final: 0.8325 (mm) REVERT: E 27 TYR cc_start: 0.8532 (t80) cc_final: 0.8151 (t80) REVERT: E 35 MET cc_start: 0.6061 (tpt) cc_final: 0.4942 (tpt) REVERT: E 51 ASP cc_start: 0.9389 (m-30) cc_final: 0.9119 (m-30) REVERT: E 53 HIS cc_start: 0.8798 (m90) cc_final: 0.8170 (m90) REVERT: F 34 MET cc_start: 0.6878 (tpt) cc_final: 0.5948 (tpt) REVERT: F 37 PHE cc_start: 0.8395 (m-80) cc_final: 0.7996 (m-10) REVERT: F 40 GLU cc_start: 0.9089 (mp0) cc_final: 0.8762 (mp0) REVERT: F 49 LEU cc_start: 0.7525 (mp) cc_final: 0.5440 (mt) REVERT: F 101 GLU cc_start: 0.8595 (mp0) cc_final: 0.8317 (mp0) REVERT: G 37 ASP cc_start: 0.8948 (t0) cc_final: 0.8640 (t0) REVERT: G 44 MET cc_start: 0.8763 (mtm) cc_final: 0.7936 (ttm) REVERT: G 52 PHE cc_start: 0.8014 (m-80) cc_final: 0.6688 (m-10) REVERT: G 53 GLU cc_start: 0.7722 (pm20) cc_final: 0.6931 (mp0) REVERT: G 59 ASN cc_start: 0.8465 (m110) cc_final: 0.8014 (m110) REVERT: G 64 LEU cc_start: 0.8621 (pp) cc_final: 0.8238 (pp) REVERT: G 66 PHE cc_start: 0.7514 (t80) cc_final: 0.6062 (t80) REVERT: G 67 HIS cc_start: 0.8655 (m90) cc_final: 0.8273 (m-70) REVERT: G 70 TYR cc_start: 0.9062 (m-80) cc_final: 0.8764 (m-80) REVERT: G 88 ASN cc_start: 0.9180 (m110) cc_final: 0.8966 (t0) REVERT: G 139 PHE cc_start: 0.8233 (p90) cc_final: 0.7145 (p90) REVERT: I 26 TYR cc_start: 0.8953 (t80) cc_final: 0.8748 (t80) REVERT: I 51 PHE cc_start: 0.8194 (t80) cc_final: 0.7165 (t80) REVERT: I 121 PHE cc_start: 0.8195 (p90) cc_final: 0.7947 (p90) REVERT: I 123 ARG cc_start: 0.7811 (mtp-110) cc_final: 0.7608 (mtp-110) REVERT: J 29 GLU cc_start: 0.9591 (tp30) cc_final: 0.9337 (tp30) REVERT: J 34 MET cc_start: 0.9436 (mmm) cc_final: 0.8917 (mmm) REVERT: J 39 MET cc_start: 0.7958 (ppp) cc_final: 0.7753 (ppp) REVERT: J 42 PHE cc_start: 0.8454 (m-10) cc_final: 0.7907 (m-10) REVERT: J 43 GLU cc_start: 0.7467 (pm20) cc_final: 0.7230 (pm20) REVERT: J 56 PHE cc_start: 0.7580 (t80) cc_final: 0.6926 (t80) REVERT: J 60 TYR cc_start: 0.9248 (m-80) cc_final: 0.8527 (m-80) REVERT: J 76 ASN cc_start: 0.8671 (m-40) cc_final: 0.8285 (m-40) REVERT: K 40 PHE cc_start: 0.8747 (m-80) cc_final: 0.7840 (m-10) REVERT: K 48 LEU cc_start: 0.9396 (tp) cc_final: 0.9060 (tp) REVERT: K 70 ASN cc_start: 0.8935 (m110) cc_final: 0.8705 (t0) REVERT: K 78 ASP cc_start: 0.8104 (t0) cc_final: 0.7656 (p0) REVERT: K 91 TYR cc_start: 0.9371 (p90) cc_final: 0.8873 (p90) REVERT: L 21 ASN cc_start: 0.9218 (m-40) cc_final: 0.8763 (p0) REVERT: L 35 MET cc_start: 0.7568 (tpt) cc_final: 0.7281 (tpt) REVERT: L 46 LEU cc_start: 0.9415 (tp) cc_final: 0.9039 (tt) REVERT: L 83 TYR cc_start: 0.8645 (p90) cc_final: 0.8042 (p90) REVERT: L 122 SER cc_start: 0.9275 (m) cc_final: 0.8909 (m) REVERT: M 13 GLN cc_start: 0.9678 (mt0) cc_final: 0.9367 (mt0) REVERT: M 37 PHE cc_start: 0.8440 (m-80) cc_final: 0.7664 (m-10) REVERT: M 45 LEU cc_start: 0.9529 (tp) cc_final: 0.9201 (pt) REVERT: M 67 ASN cc_start: 0.8649 (t0) cc_final: 0.7799 (p0) REVERT: M 118 PHE cc_start: 0.8290 (p90) cc_final: 0.8089 (p90) REVERT: O 90 PHE cc_start: 0.8535 (m-80) cc_final: 0.7999 (m-80) REVERT: O 210 GLN cc_start: 0.9218 (pm20) cc_final: 0.8699 (tp-100) REVERT: O 214 TYR cc_start: 0.9137 (m-80) cc_final: 0.8606 (m-80) REVERT: O 285 PHE cc_start: 0.9561 (t80) cc_final: 0.9196 (t80) outliers start: 2 outliers final: 0 residues processed: 405 average time/residue: 0.1487 time to fit residues: 81.8659 Evaluate side-chains 272 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 88 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS G 83 HIS G 138 HIS I 65 HIS ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 63 HIS L 120 HIS M 44 ASN M 67 ASN ** O 286 ASN ** 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 = 0.3286 r_free = 0.3286 target = 0.046695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.037333 restraints weight = 132274.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.038391 restraints weight = 96597.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.039153 restraints weight = 76113.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.039713 restraints weight = 64023.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.040151 restraints weight = 55742.703| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14838 Z= 0.154 Angle : 0.673 14.266 20064 Z= 0.361 Chirality : 0.046 0.263 2135 Planarity : 0.005 0.068 2599 Dihedral : 4.824 29.552 1939 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.30 % Favored : 97.53 % Rotamer: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1741 helix: -0.63 (0.20), residues: 535 sheet: 1.24 (0.20), residues: 593 loop : -0.13 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 104 TYR 0.015 0.001 TYR O 214 PHE 0.017 0.002 PHE F 37 TRP 0.009 0.001 TRP O 262 HIS 0.017 0.002 HIS O 119 Details of bonding type rmsd covalent geometry : bond 0.00344 (14838) covalent geometry : angle 0.67268 (20064) hydrogen bonds : bond 0.04236 ( 692) hydrogen bonds : angle 5.28597 ( 1929) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 41 TYR cc_start: 0.9314 (t80) cc_final: 0.8838 (t80) REVERT: A 52 PHE cc_start: 0.9184 (m-80) cc_final: 0.8430 (m-10) REVERT: A 66 PHE cc_start: 0.7570 (t80) cc_final: 0.6210 (t80) REVERT: A 70 TYR cc_start: 0.9059 (m-80) cc_final: 0.8624 (m-80) REVERT: A 74 LEU cc_start: 0.8371 (tt) cc_final: 0.8156 (tp) REVERT: A 88 ASN cc_start: 0.8473 (t0) cc_final: 0.8139 (t0) REVERT: B 26 TYR cc_start: 0.9298 (t80) cc_final: 0.8683 (t80) REVERT: B 34 MET cc_start: 0.8829 (ttp) cc_final: 0.8183 (ppp) REVERT: B 92 LEU cc_start: 0.9387 (mt) cc_final: 0.9134 (mt) REVERT: C 27 ASP cc_start: 0.9349 (t0) cc_final: 0.9014 (t0) REVERT: C 31 TYR cc_start: 0.9172 (t80) cc_final: 0.8942 (t80) REVERT: C 34 MET cc_start: 0.9210 (mmp) cc_final: 0.8872 (mmp) REVERT: C 49 ASN cc_start: 0.8736 (m110) cc_final: 0.8485 (m110) REVERT: C 56 PHE cc_start: 0.8727 (t80) cc_final: 0.8201 (t80) REVERT: C 57 HIS cc_start: 0.9416 (m90) cc_final: 0.8988 (m90) REVERT: C 93 ARG cc_start: 0.9048 (ttp80) cc_final: 0.8688 (ttp-110) REVERT: C 110 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7786 (mm-30) REVERT: D 37 MET cc_start: 0.8329 (tpt) cc_final: 0.7707 (tpt) REVERT: D 70 ASN cc_start: 0.8532 (t0) cc_final: 0.8321 (t0) REVERT: E 27 TYR cc_start: 0.8776 (t80) cc_final: 0.8349 (t80) REVERT: E 35 MET cc_start: 0.6615 (tpt) cc_final: 0.5148 (tpt) REVERT: E 51 ASP cc_start: 0.9638 (m-30) cc_final: 0.9428 (m-30) REVERT: F 26 TYR cc_start: 0.9063 (t80) cc_final: 0.8705 (t80) REVERT: F 34 MET cc_start: 0.7094 (tpt) cc_final: 0.6609 (tpt) REVERT: F 40 GLU cc_start: 0.9081 (mp0) cc_final: 0.8813 (mp0) REVERT: F 49 LEU cc_start: 0.7768 (mp) cc_final: 0.6197 (mt) REVERT: G 37 ASP cc_start: 0.9040 (t0) cc_final: 0.8658 (t0) REVERT: G 44 MET cc_start: 0.8774 (mtm) cc_final: 0.7899 (ptt) REVERT: G 52 PHE cc_start: 0.7739 (m-80) cc_final: 0.7198 (m-10) REVERT: G 53 GLU cc_start: 0.7948 (pm20) cc_final: 0.7126 (mp0) REVERT: G 64 LEU cc_start: 0.8911 (pp) cc_final: 0.8342 (pp) REVERT: G 66 PHE cc_start: 0.7652 (t80) cc_final: 0.6260 (t80) REVERT: G 67 HIS cc_start: 0.8979 (m90) cc_final: 0.8464 (m-70) REVERT: G 70 TYR cc_start: 0.9215 (m-80) cc_final: 0.8777 (m-80) REVERT: G 88 ASN cc_start: 0.9123 (m110) cc_final: 0.8912 (t0) REVERT: G 105 ARG cc_start: 0.9067 (ttp-110) cc_final: 0.8500 (ptm-80) REVERT: G 122 GLU cc_start: 0.8229 (mp0) cc_final: 0.8017 (mp0) REVERT: G 139 PHE cc_start: 0.8758 (p90) cc_final: 0.7548 (p90) REVERT: I 26 TYR cc_start: 0.9236 (t80) cc_final: 0.8841 (t80) REVERT: I 51 PHE cc_start: 0.8584 (t80) cc_final: 0.6826 (t80) REVERT: I 104 GLU cc_start: 0.8211 (mp0) cc_final: 0.7725 (mp0) REVERT: I 121 PHE cc_start: 0.8667 (p90) cc_final: 0.8380 (p90) REVERT: I 123 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.7894 (mtp-110) REVERT: J 29 GLU cc_start: 0.9639 (tp30) cc_final: 0.9417 (tm-30) REVERT: J 42 PHE cc_start: 0.8827 (m-10) cc_final: 0.8459 (m-10) REVERT: J 56 PHE cc_start: 0.7852 (t80) cc_final: 0.6985 (t80) REVERT: J 60 TYR cc_start: 0.9436 (m-80) cc_final: 0.8524 (m-80) REVERT: J 105 ARG cc_start: 0.9303 (mmm-85) cc_final: 0.8978 (mtp85) REVERT: K 38 THR cc_start: 0.8954 (p) cc_final: 0.8568 (p) REVERT: K 40 PHE cc_start: 0.7967 (m-80) cc_final: 0.7326 (m-10) REVERT: K 48 LEU cc_start: 0.9341 (tp) cc_final: 0.9046 (tp) REVERT: K 54 PHE cc_start: 0.9229 (t80) cc_final: 0.8948 (t80) REVERT: K 70 ASN cc_start: 0.9173 (m110) cc_final: 0.8817 (t0) REVERT: K 78 ASP cc_start: 0.8245 (t0) cc_final: 0.7979 (p0) REVERT: K 91 TYR cc_start: 0.9504 (p90) cc_final: 0.9081 (p90) REVERT: K 92 LEU cc_start: 0.9091 (mt) cc_final: 0.8765 (mt) REVERT: K 99 ARG cc_start: 0.9485 (mmp80) cc_final: 0.9145 (mmm160) REVERT: K 122 HIS cc_start: 0.7258 (t-170) cc_final: 0.5590 (t-170) REVERT: L 35 MET cc_start: 0.7890 (tpt) cc_final: 0.7448 (tpt) REVERT: L 83 TYR cc_start: 0.9040 (p90) cc_final: 0.8483 (p90) REVERT: M 13 GLN cc_start: 0.9706 (mt0) cc_final: 0.9436 (mt0) REVERT: M 37 PHE cc_start: 0.8195 (m-80) cc_final: 0.7941 (m-10) REVERT: M 44 ASN cc_start: 0.9446 (m-40) cc_final: 0.9044 (m110) REVERT: M 45 LEU cc_start: 0.9557 (tp) cc_final: 0.9172 (tp) REVERT: M 67 ASN cc_start: 0.8985 (t0) cc_final: 0.8274 (p0) REVERT: O 90 PHE cc_start: 0.8748 (m-80) cc_final: 0.8203 (m-80) REVERT: O 285 PHE cc_start: 0.9648 (t80) cc_final: 0.9328 (t80) outliers start: 1 outliers final: 1 residues processed: 358 average time/residue: 0.1444 time to fit residues: 71.2321 Evaluate side-chains 261 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 60 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 160 optimal weight: 0.0870 chunk 109 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 HIS F 67 ASN F 117 HIS F 119 HIS I 72 HIS ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 GLN L 120 HIS ** O 117 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 = 0.3228 r_free = 0.3228 target = 0.044633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.035888 restraints weight = 136274.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.036841 restraints weight = 100954.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.037530 restraints weight = 80406.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.037990 restraints weight = 67540.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.038349 restraints weight = 59956.316| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14838 Z= 0.166 Angle : 0.679 15.700 20064 Z= 0.358 Chirality : 0.045 0.158 2135 Planarity : 0.005 0.051 2599 Dihedral : 4.873 27.224 1939 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.55 % Favored : 98.28 % Rotamer: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1741 helix: -0.35 (0.21), residues: 535 sheet: 1.32 (0.21), residues: 609 loop : 0.03 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 54 TYR 0.016 0.001 TYR K 29 PHE 0.024 0.002 PHE K 59 TRP 0.012 0.002 TRP C 115 HIS 0.018 0.002 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00365 (14838) covalent geometry : angle 0.67893 (20064) hydrogen bonds : bond 0.04054 ( 692) hydrogen bonds : angle 5.21192 ( 1929) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9467 (t80) cc_final: 0.8921 (t80) REVERT: A 52 PHE cc_start: 0.8575 (m-80) cc_final: 0.8135 (m-10) REVERT: A 66 PHE cc_start: 0.8035 (t80) cc_final: 0.7025 (t80) REVERT: A 70 TYR cc_start: 0.9228 (m-80) cc_final: 0.8954 (m-80) REVERT: A 88 ASN cc_start: 0.8571 (t0) cc_final: 0.8264 (t0) REVERT: B 26 TYR cc_start: 0.9449 (t80) cc_final: 0.8835 (t80) REVERT: B 34 MET cc_start: 0.8728 (ttp) cc_final: 0.8468 (ppp) REVERT: B 104 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7268 (mm-30) REVERT: B 121 PHE cc_start: 0.9098 (p90) cc_final: 0.8885 (p90) REVERT: C 19 LEU cc_start: 0.9673 (mm) cc_final: 0.9336 (mm) REVERT: C 27 ASP cc_start: 0.9264 (t0) cc_final: 0.8993 (t0) REVERT: C 31 TYR cc_start: 0.9354 (t80) cc_final: 0.9014 (t80) REVERT: C 49 ASN cc_start: 0.8732 (m110) cc_final: 0.8420 (m110) REVERT: C 56 PHE cc_start: 0.8931 (t80) cc_final: 0.7994 (t80) REVERT: C 57 HIS cc_start: 0.9603 (m90) cc_final: 0.9211 (m90) REVERT: C 60 TYR cc_start: 0.8876 (m-80) cc_final: 0.8609 (m-10) REVERT: C 93 ARG cc_start: 0.9264 (ttp80) cc_final: 0.8841 (ttp-110) REVERT: D 37 MET cc_start: 0.8406 (tpt) cc_final: 0.7622 (tpp) REVERT: D 47 ASN cc_start: 0.9275 (m110) cc_final: 0.8978 (m110) REVERT: D 69 LEU cc_start: 0.9323 (mm) cc_final: 0.9099 (mm) REVERT: D 70 ASN cc_start: 0.8662 (t0) cc_final: 0.8270 (t0) REVERT: D 123 ARG cc_start: 0.8790 (ttp-110) cc_final: 0.8456 (tmm-80) REVERT: E 27 TYR cc_start: 0.8863 (t80) cc_final: 0.8397 (t80) REVERT: E 35 MET cc_start: 0.6836 (tpt) cc_final: 0.5313 (tpt) REVERT: E 68 ASN cc_start: 0.8616 (t0) cc_final: 0.8098 (p0) REVERT: F 26 TYR cc_start: 0.9284 (t80) cc_final: 0.9012 (t80) REVERT: F 34 MET cc_start: 0.6952 (tpt) cc_final: 0.6352 (tpt) REVERT: F 40 GLU cc_start: 0.9041 (mp0) cc_final: 0.8787 (mp0) REVERT: F 49 LEU cc_start: 0.7932 (mp) cc_final: 0.5993 (mt) REVERT: G 28 GLN cc_start: 0.9451 (tp40) cc_final: 0.9012 (tp40) REVERT: G 37 ASP cc_start: 0.8961 (t0) cc_final: 0.8683 (t0) REVERT: G 41 TYR cc_start: 0.9141 (t80) cc_final: 0.8727 (t80) REVERT: G 44 MET cc_start: 0.8689 (mtm) cc_final: 0.8232 (ttt) REVERT: G 52 PHE cc_start: 0.7949 (m-80) cc_final: 0.7471 (m-10) REVERT: G 64 LEU cc_start: 0.9035 (pp) cc_final: 0.8591 (pt) REVERT: G 66 PHE cc_start: 0.7804 (t80) cc_final: 0.6301 (t80) REVERT: G 67 HIS cc_start: 0.9326 (m90) cc_final: 0.8674 (m-70) REVERT: G 70 TYR cc_start: 0.9348 (m-80) cc_final: 0.8772 (m-80) REVERT: G 88 ASN cc_start: 0.9192 (m110) cc_final: 0.8879 (t0) REVERT: G 105 ARG cc_start: 0.9245 (ttp-110) cc_final: 0.8791 (ttp-110) REVERT: G 139 PHE cc_start: 0.9021 (p90) cc_final: 0.8027 (p90) REVERT: I 26 TYR cc_start: 0.9436 (t80) cc_final: 0.8924 (t80) REVERT: I 34 MET cc_start: 0.8837 (tpt) cc_final: 0.8609 (tpt) REVERT: I 51 PHE cc_start: 0.8647 (t80) cc_final: 0.8067 (t80) REVERT: I 104 GLU cc_start: 0.8590 (mp0) cc_final: 0.8255 (mp0) REVERT: I 123 ARG cc_start: 0.8917 (mtp-110) cc_final: 0.8389 (mtp-110) REVERT: J 29 GLU cc_start: 0.9697 (tp30) cc_final: 0.9473 (tm-30) REVERT: J 39 MET cc_start: 0.8479 (ppp) cc_final: 0.8120 (ppp) REVERT: J 42 PHE cc_start: 0.8541 (m-10) cc_final: 0.8038 (m-10) REVERT: J 43 GLU cc_start: 0.7856 (pm20) cc_final: 0.7479 (pm20) REVERT: J 56 PHE cc_start: 0.8096 (t80) cc_final: 0.7115 (t80) REVERT: J 60 TYR cc_start: 0.9510 (m-80) cc_final: 0.8707 (m-80) REVERT: J 75 LEU cc_start: 0.8934 (pp) cc_final: 0.8440 (pp) REVERT: J 76 ASN cc_start: 0.8890 (m110) cc_final: 0.8337 (m110) REVERT: J 105 ARG cc_start: 0.9357 (mmm-85) cc_final: 0.9071 (mmm-85) REVERT: K 26 PHE cc_start: 0.8833 (t80) cc_final: 0.8551 (t80) REVERT: K 34 ASP cc_start: 0.9161 (t0) cc_final: 0.8877 (t0) REVERT: K 40 PHE cc_start: 0.7837 (m-80) cc_final: 0.7345 (m-10) REVERT: K 54 PHE cc_start: 0.9020 (t80) cc_final: 0.8613 (t80) REVERT: K 58 TYR cc_start: 0.8466 (m-10) cc_final: 0.8184 (m-10) REVERT: K 70 ASN cc_start: 0.9198 (m110) cc_final: 0.8794 (t0) REVERT: K 91 TYR cc_start: 0.9571 (p90) cc_final: 0.9324 (p90) REVERT: L 35 MET cc_start: 0.8130 (tpt) cc_final: 0.7729 (tpt) REVERT: L 38 PHE cc_start: 0.7435 (m-10) cc_final: 0.7153 (m-10) REVERT: L 67 LEU cc_start: 0.9123 (mm) cc_final: 0.8883 (mm) REVERT: L 68 ASN cc_start: 0.8537 (m-40) cc_final: 0.8134 (p0) REVERT: L 83 TYR cc_start: 0.9034 (p90) cc_final: 0.8523 (p90) REVERT: M 26 TYR cc_start: 0.9224 (t80) cc_final: 0.9013 (t80) REVERT: M 34 MET cc_start: 0.7298 (mmt) cc_final: 0.6948 (mmt) REVERT: M 44 ASN cc_start: 0.9472 (m-40) cc_final: 0.9076 (m110) REVERT: M 67 ASN cc_start: 0.9214 (t0) cc_final: 0.8443 (p0) REVERT: O 90 PHE cc_start: 0.8994 (m-80) cc_final: 0.8425 (m-80) REVERT: O 285 PHE cc_start: 0.9682 (t80) cc_final: 0.9377 (t80) outliers start: 1 outliers final: 1 residues processed: 338 average time/residue: 0.1395 time to fit residues: 65.6352 Evaluate side-chains 258 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 86 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 47 optimal weight: 0.0570 chunk 113 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 HIS F 67 ASN F 117 HIS ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 HIS L 14 GLN ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 119 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.043792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.035591 restraints weight = 141370.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.036433 restraints weight = 106606.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.037040 restraints weight = 85961.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037574 restraints weight = 73321.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.037905 restraints weight = 64281.179| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14838 Z= 0.159 Angle : 0.656 12.910 20064 Z= 0.351 Chirality : 0.045 0.161 2135 Planarity : 0.004 0.050 2599 Dihedral : 4.825 28.796 1939 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.84 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1741 helix: -0.23 (0.21), residues: 554 sheet: 1.51 (0.21), residues: 593 loop : -0.15 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 110 TYR 0.022 0.001 TYR O 214 PHE 0.034 0.002 PHE I 121 TRP 0.027 0.002 TRP O 262 HIS 0.015 0.002 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00349 (14838) covalent geometry : angle 0.65647 (20064) hydrogen bonds : bond 0.03958 ( 692) hydrogen bonds : angle 5.10706 ( 1929) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 41 TYR cc_start: 0.9471 (t80) cc_final: 0.9238 (t80) REVERT: A 52 PHE cc_start: 0.8907 (m-80) cc_final: 0.7941 (m-10) REVERT: A 66 PHE cc_start: 0.7939 (t80) cc_final: 0.6844 (t80) REVERT: A 70 TYR cc_start: 0.9058 (m-80) cc_final: 0.8808 (m-80) REVERT: A 74 LEU cc_start: 0.8751 (tp) cc_final: 0.8513 (tp) REVERT: A 88 ASN cc_start: 0.8575 (t0) cc_final: 0.8251 (t0) REVERT: B 26 TYR cc_start: 0.9392 (t80) cc_final: 0.8703 (t80) REVERT: B 34 MET cc_start: 0.8800 (ttp) cc_final: 0.8395 (ppp) REVERT: C 19 LEU cc_start: 0.9631 (mm) cc_final: 0.9280 (mm) REVERT: C 27 ASP cc_start: 0.9304 (t0) cc_final: 0.9024 (t0) REVERT: C 31 TYR cc_start: 0.9303 (t80) cc_final: 0.8944 (t80) REVERT: C 49 ASN cc_start: 0.8725 (m110) cc_final: 0.8449 (m110) REVERT: C 56 PHE cc_start: 0.8826 (t80) cc_final: 0.7854 (t80) REVERT: C 57 HIS cc_start: 0.9550 (m90) cc_final: 0.9192 (m90) REVERT: C 60 TYR cc_start: 0.8857 (m-80) cc_final: 0.8557 (m-10) REVERT: C 93 ARG cc_start: 0.9201 (ttp80) cc_final: 0.8811 (ttp-110) REVERT: C 128 HIS cc_start: 0.6399 (t70) cc_final: 0.6148 (t70) REVERT: D 48 LEU cc_start: 0.9046 (tp) cc_final: 0.8833 (tp) REVERT: D 54 PHE cc_start: 0.8815 (t80) cc_final: 0.7536 (t80) REVERT: D 69 LEU cc_start: 0.9355 (mm) cc_final: 0.9123 (mm) REVERT: D 70 ASN cc_start: 0.8810 (t0) cc_final: 0.8383 (t0) REVERT: E 15 LEU cc_start: 0.8794 (tt) cc_final: 0.8270 (mt) REVERT: E 68 ASN cc_start: 0.8754 (t0) cc_final: 0.8187 (p0) REVERT: E 76 ASP cc_start: 0.9245 (t0) cc_final: 0.9040 (p0) REVERT: F 26 TYR cc_start: 0.9300 (t80) cc_final: 0.8837 (t80) REVERT: F 27 THR cc_start: 0.9334 (p) cc_final: 0.9122 (p) REVERT: F 34 MET cc_start: 0.7132 (tpt) cc_final: 0.6448 (tpt) REVERT: F 37 PHE cc_start: 0.8499 (m-10) cc_final: 0.8040 (m-10) REVERT: F 40 GLU cc_start: 0.9046 (mp0) cc_final: 0.8802 (mp0) REVERT: F 49 LEU cc_start: 0.8045 (mp) cc_final: 0.6546 (mt) REVERT: F 118 PHE cc_start: 0.8707 (p90) cc_final: 0.8351 (p90) REVERT: G 28 GLN cc_start: 0.9421 (tp40) cc_final: 0.8966 (tp40) REVERT: G 37 ASP cc_start: 0.9063 (t0) cc_final: 0.8794 (t0) REVERT: G 41 TYR cc_start: 0.9121 (t80) cc_final: 0.8759 (t80) REVERT: G 44 MET cc_start: 0.8878 (mtm) cc_final: 0.8417 (ttt) REVERT: G 64 LEU cc_start: 0.9012 (pp) cc_final: 0.8452 (pp) REVERT: G 66 PHE cc_start: 0.8137 (t80) cc_final: 0.6328 (t80) REVERT: G 67 HIS cc_start: 0.9185 (m90) cc_final: 0.8588 (m-70) REVERT: G 70 TYR cc_start: 0.9310 (m-80) cc_final: 0.8720 (m-80) REVERT: G 88 ASN cc_start: 0.9240 (m110) cc_final: 0.8992 (t0) REVERT: G 105 ARG cc_start: 0.9191 (ttp-110) cc_final: 0.8689 (ptm-80) REVERT: G 139 PHE cc_start: 0.8990 (p90) cc_final: 0.8617 (p90) REVERT: I 26 TYR cc_start: 0.9346 (t80) cc_final: 0.8909 (t80) REVERT: I 34 MET cc_start: 0.8817 (tpt) cc_final: 0.8421 (tpp) REVERT: I 51 PHE cc_start: 0.8705 (t80) cc_final: 0.7247 (t80) REVERT: J 29 GLU cc_start: 0.9670 (tp30) cc_final: 0.9448 (tm-30) REVERT: J 39 MET cc_start: 0.8527 (ppp) cc_final: 0.8201 (ppp) REVERT: J 42 PHE cc_start: 0.8562 (m-10) cc_final: 0.8238 (m-10) REVERT: J 56 PHE cc_start: 0.8041 (t80) cc_final: 0.7254 (t80) REVERT: J 60 TYR cc_start: 0.9524 (m-80) cc_final: 0.8617 (m-80) REVERT: J 75 LEU cc_start: 0.8966 (pp) cc_final: 0.8335 (pp) REVERT: J 76 ASN cc_start: 0.9024 (m110) cc_final: 0.8441 (m110) REVERT: J 82 MET cc_start: 0.7316 (mpp) cc_final: 0.7104 (mpp) REVERT: K 34 ASP cc_start: 0.9294 (t0) cc_final: 0.8988 (t0) REVERT: K 40 PHE cc_start: 0.8091 (m-80) cc_final: 0.7756 (m-10) REVERT: K 54 PHE cc_start: 0.9097 (t80) cc_final: 0.8439 (t80) REVERT: K 58 TYR cc_start: 0.8376 (m-10) cc_final: 0.8066 (m-10) REVERT: K 70 ASN cc_start: 0.9196 (m110) cc_final: 0.8859 (t0) REVERT: K 78 ASP cc_start: 0.8548 (t0) cc_final: 0.8280 (t0) REVERT: K 91 TYR cc_start: 0.9552 (p90) cc_final: 0.9265 (p90) REVERT: L 35 MET cc_start: 0.8073 (tpt) cc_final: 0.7773 (tpt) REVERT: L 67 LEU cc_start: 0.9194 (mm) cc_final: 0.8937 (mm) REVERT: L 68 ASN cc_start: 0.8526 (m-40) cc_final: 0.8201 (p0) REVERT: L 83 TYR cc_start: 0.9053 (p90) cc_final: 0.8463 (p90) REVERT: M 26 TYR cc_start: 0.9138 (t80) cc_final: 0.8864 (t80) REVERT: M 44 ASN cc_start: 0.9505 (m-40) cc_final: 0.9087 (m110) REVERT: M 67 ASN cc_start: 0.9281 (t0) cc_final: 0.8470 (p0) REVERT: O 90 PHE cc_start: 0.8903 (m-80) cc_final: 0.8413 (m-80) REVERT: O 214 TYR cc_start: 0.9018 (m-80) cc_final: 0.8771 (m-80) REVERT: O 285 PHE cc_start: 0.9660 (t80) cc_final: 0.9331 (t80) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.1457 time to fit residues: 64.7092 Evaluate side-chains 250 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 140 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 61 optimal weight: 0.0070 chunk 34 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 117 HIS ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 GLN ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.042623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.034869 restraints weight = 142557.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.035619 restraints weight = 109849.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.036144 restraints weight = 90676.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.036586 restraints weight = 78553.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.036957 restraints weight = 69802.760| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.6935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14838 Z= 0.163 Angle : 0.663 12.197 20064 Z= 0.352 Chirality : 0.044 0.189 2135 Planarity : 0.005 0.092 2599 Dihedral : 4.889 28.254 1939 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.90 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.20), residues: 1741 helix: -0.17 (0.21), residues: 554 sheet: 1.59 (0.21), residues: 618 loop : -0.02 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 104 TYR 0.021 0.001 TYR F 55 PHE 0.014 0.002 PHE K 26 TRP 0.026 0.002 TRP O 262 HIS 0.016 0.002 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00359 (14838) covalent geometry : angle 0.66268 (20064) hydrogen bonds : bond 0.03885 ( 692) hydrogen bonds : angle 5.08314 ( 1929) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9439 (t80) cc_final: 0.9205 (t80) REVERT: A 52 PHE cc_start: 0.8468 (m-80) cc_final: 0.8060 (m-10) REVERT: A 66 PHE cc_start: 0.8055 (t80) cc_final: 0.6944 (t80) REVERT: A 70 TYR cc_start: 0.9056 (m-80) cc_final: 0.8852 (m-80) REVERT: A 88 ASN cc_start: 0.8633 (t0) cc_final: 0.8167 (t0) REVERT: A 122 GLU cc_start: 0.8177 (mp0) cc_final: 0.7492 (pm20) REVERT: B 26 TYR cc_start: 0.9360 (t80) cc_final: 0.8809 (t80) REVERT: B 34 MET cc_start: 0.8866 (ttp) cc_final: 0.8184 (ppp) REVERT: B 121 PHE cc_start: 0.9101 (p90) cc_final: 0.8386 (p90) REVERT: C 19 LEU cc_start: 0.9644 (mm) cc_final: 0.9284 (mm) REVERT: C 27 ASP cc_start: 0.9306 (t0) cc_final: 0.9036 (t0) REVERT: C 31 TYR cc_start: 0.9333 (t80) cc_final: 0.8964 (t80) REVERT: C 49 ASN cc_start: 0.8713 (m110) cc_final: 0.8452 (m110) REVERT: C 56 PHE cc_start: 0.8824 (t80) cc_final: 0.7832 (t80) REVERT: C 57 HIS cc_start: 0.9585 (m90) cc_final: 0.9228 (m90) REVERT: C 60 TYR cc_start: 0.8875 (m-80) cc_final: 0.8547 (m-10) REVERT: C 93 ARG cc_start: 0.9236 (ttp80) cc_final: 0.8840 (ttp-110) REVERT: D 37 MET cc_start: 0.8594 (tpp) cc_final: 0.7499 (tpp) REVERT: D 54 PHE cc_start: 0.8865 (t80) cc_final: 0.7344 (t80) REVERT: D 69 LEU cc_start: 0.9246 (mm) cc_final: 0.8990 (mm) REVERT: D 70 ASN cc_start: 0.8848 (t0) cc_final: 0.8428 (t0) REVERT: E 15 LEU cc_start: 0.8856 (tt) cc_final: 0.8351 (mt) REVERT: E 68 ASN cc_start: 0.8673 (t0) cc_final: 0.8225 (p0) REVERT: F 26 TYR cc_start: 0.9280 (t80) cc_final: 0.8819 (t80) REVERT: F 27 THR cc_start: 0.9352 (p) cc_final: 0.9128 (p) REVERT: F 34 MET cc_start: 0.7354 (tpt) cc_final: 0.6814 (tpt) REVERT: F 40 GLU cc_start: 0.9034 (mp0) cc_final: 0.8788 (mp0) REVERT: F 49 LEU cc_start: 0.8175 (mp) cc_final: 0.6566 (mt) REVERT: G 37 ASP cc_start: 0.9053 (t0) cc_final: 0.8814 (t0) REVERT: G 41 TYR cc_start: 0.9093 (t80) cc_final: 0.8736 (t80) REVERT: G 44 MET cc_start: 0.8908 (mtm) cc_final: 0.8337 (ttt) REVERT: G 60 LEU cc_start: 0.8750 (tt) cc_final: 0.8424 (tt) REVERT: G 64 LEU cc_start: 0.8982 (pp) cc_final: 0.8418 (pp) REVERT: G 66 PHE cc_start: 0.8152 (t80) cc_final: 0.6286 (t80) REVERT: G 67 HIS cc_start: 0.9184 (m90) cc_final: 0.8630 (m-70) REVERT: G 70 TYR cc_start: 0.9284 (m-80) cc_final: 0.8685 (m-80) REVERT: G 88 ASN cc_start: 0.9262 (m110) cc_final: 0.9024 (t0) REVERT: G 139 PHE cc_start: 0.9077 (p90) cc_final: 0.8581 (p90) REVERT: I 26 TYR cc_start: 0.9394 (t80) cc_final: 0.8952 (t80) REVERT: I 34 MET cc_start: 0.8706 (tpt) cc_final: 0.8298 (tpp) REVERT: I 51 PHE cc_start: 0.8668 (t80) cc_final: 0.7113 (t80) REVERT: I 104 GLU cc_start: 0.8515 (mp0) cc_final: 0.8235 (mp0) REVERT: I 107 ARG cc_start: 0.8612 (mpt180) cc_final: 0.8299 (mmt180) REVERT: J 42 PHE cc_start: 0.8565 (m-10) cc_final: 0.7854 (m-10) REVERT: J 56 PHE cc_start: 0.8106 (t80) cc_final: 0.7112 (t80) REVERT: J 57 HIS cc_start: 0.8917 (m90) cc_final: 0.8043 (m-70) REVERT: J 60 TYR cc_start: 0.9532 (m-80) cc_final: 0.8580 (m-80) REVERT: J 76 ASN cc_start: 0.9131 (m110) cc_final: 0.8802 (m-40) REVERT: J 105 ARG cc_start: 0.9340 (mmm-85) cc_final: 0.9114 (mmm-85) REVERT: K 40 PHE cc_start: 0.8214 (m-80) cc_final: 0.7842 (m-10) REVERT: K 41 GLU cc_start: 0.8774 (pm20) cc_final: 0.8546 (pm20) REVERT: K 54 PHE cc_start: 0.9037 (t80) cc_final: 0.8408 (t80) REVERT: K 58 TYR cc_start: 0.8358 (m-10) cc_final: 0.8042 (m-10) REVERT: K 70 ASN cc_start: 0.9258 (m110) cc_final: 0.8874 (t0) REVERT: K 78 ASP cc_start: 0.8481 (t0) cc_final: 0.8182 (t0) REVERT: K 91 TYR cc_start: 0.9552 (p90) cc_final: 0.9263 (p90) REVERT: L 35 MET cc_start: 0.8055 (tpt) cc_final: 0.7753 (tpt) REVERT: L 67 LEU cc_start: 0.9235 (mm) cc_final: 0.8906 (mm) REVERT: L 68 ASN cc_start: 0.8616 (m-40) cc_final: 0.8269 (p0) REVERT: L 83 TYR cc_start: 0.8997 (p90) cc_final: 0.8411 (p90) REVERT: M 13 GLN cc_start: 0.9772 (mt0) cc_final: 0.9532 (mp10) REVERT: M 26 TYR cc_start: 0.9125 (t80) cc_final: 0.8343 (t80) REVERT: M 34 MET cc_start: 0.7779 (mmt) cc_final: 0.7466 (mmt) REVERT: M 44 ASN cc_start: 0.9487 (m-40) cc_final: 0.9124 (m-40) REVERT: M 52 HIS cc_start: 0.9010 (m90) cc_final: 0.8808 (m90) REVERT: M 67 ASN cc_start: 0.9347 (t0) cc_final: 0.8608 (p0) REVERT: O 90 PHE cc_start: 0.8870 (m-80) cc_final: 0.8414 (m-80) REVERT: O 214 TYR cc_start: 0.9013 (m-80) cc_final: 0.8803 (m-80) REVERT: O 285 PHE cc_start: 0.9660 (t80) cc_final: 0.9328 (t80) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1417 time to fit residues: 61.3322 Evaluate side-chains 249 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 25 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 91 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 HIS F 13 GLN F 117 HIS G 28 GLN ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 GLN ** O 117 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 = 0.3178 r_free = 0.3178 target = 0.042999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.035166 restraints weight = 143083.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.035985 restraints weight = 109261.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.036593 restraints weight = 88670.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.037006 restraints weight = 75536.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.037395 restraints weight = 67250.906| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.7201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14838 Z= 0.144 Angle : 0.685 13.181 20064 Z= 0.363 Chirality : 0.046 0.232 2135 Planarity : 0.005 0.060 2599 Dihedral : 4.867 28.680 1939 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.95 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1741 helix: -0.17 (0.21), residues: 558 sheet: 1.72 (0.22), residues: 575 loop : -0.27 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 87 TYR 0.020 0.001 TYR O 214 PHE 0.018 0.002 PHE B 51 TRP 0.021 0.002 TRP O 262 HIS 0.023 0.001 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00328 (14838) covalent geometry : angle 0.68536 (20064) hydrogen bonds : bond 0.03826 ( 692) hydrogen bonds : angle 5.09882 ( 1929) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9460 (t80) cc_final: 0.9221 (t80) REVERT: A 52 PHE cc_start: 0.8327 (m-80) cc_final: 0.7841 (m-10) REVERT: A 66 PHE cc_start: 0.8133 (t80) cc_final: 0.7807 (t80) REVERT: A 70 TYR cc_start: 0.9045 (m-80) cc_final: 0.8664 (m-80) REVERT: A 88 ASN cc_start: 0.8689 (t0) cc_final: 0.8257 (t0) REVERT: B 26 TYR cc_start: 0.9292 (t80) cc_final: 0.8597 (t80) REVERT: B 34 MET cc_start: 0.8600 (ttp) cc_final: 0.8153 (ppp) REVERT: B 121 PHE cc_start: 0.8923 (p90) cc_final: 0.8590 (p90) REVERT: C 19 LEU cc_start: 0.9633 (mm) cc_final: 0.9285 (mm) REVERT: C 27 ASP cc_start: 0.9344 (t0) cc_final: 0.9071 (t0) REVERT: C 31 TYR cc_start: 0.9303 (t80) cc_final: 0.8963 (t80) REVERT: C 49 ASN cc_start: 0.8740 (m110) cc_final: 0.8486 (m110) REVERT: C 56 PHE cc_start: 0.8764 (t80) cc_final: 0.7777 (t80) REVERT: C 57 HIS cc_start: 0.9537 (m90) cc_final: 0.9225 (m90) REVERT: C 60 TYR cc_start: 0.8919 (m-80) cc_final: 0.8561 (m-10) REVERT: C 93 ARG cc_start: 0.9269 (ttp80) cc_final: 0.8872 (ttp-110) REVERT: D 37 MET cc_start: 0.8467 (tpp) cc_final: 0.7437 (tpp) REVERT: D 48 LEU cc_start: 0.9079 (tp) cc_final: 0.8870 (tp) REVERT: D 54 PHE cc_start: 0.8786 (t80) cc_final: 0.7107 (t80) REVERT: D 69 LEU cc_start: 0.9218 (mm) cc_final: 0.8947 (mm) REVERT: D 70 ASN cc_start: 0.8790 (t0) cc_final: 0.8413 (t0) REVERT: E 15 LEU cc_start: 0.8890 (tt) cc_final: 0.8534 (mm) REVERT: F 26 TYR cc_start: 0.9256 (t80) cc_final: 0.8854 (t80) REVERT: F 27 THR cc_start: 0.9352 (p) cc_final: 0.9125 (p) REVERT: F 34 MET cc_start: 0.7440 (tpt) cc_final: 0.6800 (tpt) REVERT: F 49 LEU cc_start: 0.8263 (mp) cc_final: 0.6774 (mt) REVERT: F 67 ASN cc_start: 0.8877 (t0) cc_final: 0.7748 (p0) REVERT: G 37 ASP cc_start: 0.9120 (t0) cc_final: 0.8883 (t0) REVERT: G 41 TYR cc_start: 0.9092 (t80) cc_final: 0.8719 (t80) REVERT: G 44 MET cc_start: 0.8994 (mtm) cc_final: 0.8388 (ttt) REVERT: G 60 LEU cc_start: 0.8853 (tt) cc_final: 0.8627 (tt) REVERT: G 64 LEU cc_start: 0.8944 (pp) cc_final: 0.8417 (pp) REVERT: G 66 PHE cc_start: 0.8174 (t80) cc_final: 0.6397 (t80) REVERT: G 67 HIS cc_start: 0.9181 (m90) cc_final: 0.8624 (m-70) REVERT: G 70 TYR cc_start: 0.9279 (m-80) cc_final: 0.8654 (m-80) REVERT: G 88 ASN cc_start: 0.9279 (m110) cc_final: 0.9065 (t0) REVERT: G 139 PHE cc_start: 0.9119 (p90) cc_final: 0.8517 (p90) REVERT: I 26 TYR cc_start: 0.9354 (t80) cc_final: 0.8919 (t80) REVERT: I 34 MET cc_start: 0.8561 (tpt) cc_final: 0.8148 (tpp) REVERT: I 44 ASN cc_start: 0.8936 (m110) cc_final: 0.8702 (m-40) REVERT: I 104 GLU cc_start: 0.8562 (mp0) cc_final: 0.8300 (mp0) REVERT: I 107 ARG cc_start: 0.8532 (mpt180) cc_final: 0.8260 (mpt180) REVERT: J 56 PHE cc_start: 0.8053 (t80) cc_final: 0.7021 (t80) REVERT: J 57 HIS cc_start: 0.8880 (m90) cc_final: 0.7831 (m-70) REVERT: J 60 TYR cc_start: 0.9513 (m-80) cc_final: 0.8628 (m-80) REVERT: J 61 PHE cc_start: 0.8668 (m-80) cc_final: 0.8458 (m-80) REVERT: J 76 ASN cc_start: 0.9138 (m110) cc_final: 0.8800 (m-40) REVERT: K 34 ASP cc_start: 0.9492 (t0) cc_final: 0.9125 (t0) REVERT: K 40 PHE cc_start: 0.8186 (m-80) cc_final: 0.7285 (m-10) REVERT: K 54 PHE cc_start: 0.9008 (t80) cc_final: 0.8721 (t80) REVERT: K 58 TYR cc_start: 0.8288 (m-10) cc_final: 0.7968 (m-10) REVERT: K 70 ASN cc_start: 0.9265 (m110) cc_final: 0.8938 (t0) REVERT: K 78 ASP cc_start: 0.8473 (t0) cc_final: 0.8225 (p0) REVERT: K 87 ARG cc_start: 0.8793 (ptp-110) cc_final: 0.8545 (ptp90) REVERT: K 91 TYR cc_start: 0.9547 (p90) cc_final: 0.9244 (p90) REVERT: K 121 PHE cc_start: 0.9129 (p90) cc_final: 0.8703 (p90) REVERT: L 35 MET cc_start: 0.8417 (tpt) cc_final: 0.8117 (tpt) REVERT: L 67 LEU cc_start: 0.9242 (mm) cc_final: 0.8960 (mm) REVERT: L 68 ASN cc_start: 0.8633 (m-40) cc_final: 0.8343 (p0) REVERT: L 83 TYR cc_start: 0.9044 (p90) cc_final: 0.8470 (p90) REVERT: M 13 GLN cc_start: 0.9766 (mt0) cc_final: 0.9528 (mp10) REVERT: M 14 LEU cc_start: 0.9618 (mm) cc_final: 0.9393 (mm) REVERT: M 26 TYR cc_start: 0.9122 (t80) cc_final: 0.8266 (t80) REVERT: M 34 MET cc_start: 0.7412 (mmt) cc_final: 0.7208 (mmt) REVERT: M 44 ASN cc_start: 0.9405 (m-40) cc_final: 0.9038 (m-40) REVERT: M 45 LEU cc_start: 0.9237 (tp) cc_final: 0.9015 (tp) REVERT: M 52 HIS cc_start: 0.8955 (m90) cc_final: 0.8620 (m90) REVERT: M 67 ASN cc_start: 0.9387 (t0) cc_final: 0.8663 (p0) REVERT: M 101 GLU cc_start: 0.8263 (mp0) cc_final: 0.8038 (mm-30) REVERT: O 90 PHE cc_start: 0.8874 (m-80) cc_final: 0.8420 (m-80) REVERT: O 214 TYR cc_start: 0.9024 (m-80) cc_final: 0.8778 (m-80) REVERT: O 285 PHE cc_start: 0.9661 (t80) cc_final: 0.9331 (t80) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1378 time to fit residues: 58.1015 Evaluate side-chains 247 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 100 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 HIS G 59 ASN ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 HIS K 74 HIS ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 GLN ** O 117 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 = 0.3064 r_free = 0.3064 target = 0.039262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032023 restraints weight = 155942.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.032691 restraints weight = 121774.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.033209 restraints weight = 100404.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.033563 restraints weight = 87373.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.033939 restraints weight = 78602.801| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.7829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14838 Z= 0.260 Angle : 0.767 11.555 20064 Z= 0.413 Chirality : 0.045 0.210 2135 Planarity : 0.005 0.056 2599 Dihedral : 5.214 28.515 1939 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.53 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1741 helix: -0.27 (0.21), residues: 552 sheet: 1.45 (0.21), residues: 619 loop : -0.26 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 105 TYR 0.019 0.002 TYR O 214 PHE 0.024 0.002 PHE B 51 TRP 0.031 0.003 TRP O 262 HIS 0.026 0.003 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00545 (14838) covalent geometry : angle 0.76705 (20064) hydrogen bonds : bond 0.04210 ( 692) hydrogen bonds : angle 5.36521 ( 1929) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7734 (mmp) cc_final: 0.6969 (mmm) REVERT: A 52 PHE cc_start: 0.8489 (m-80) cc_final: 0.7749 (m-10) REVERT: A 66 PHE cc_start: 0.8385 (t80) cc_final: 0.7399 (t80) REVERT: A 67 HIS cc_start: 0.9529 (m90) cc_final: 0.9267 (m90) REVERT: A 70 TYR cc_start: 0.9299 (m-80) cc_final: 0.9057 (m-80) REVERT: A 88 ASN cc_start: 0.8704 (t0) cc_final: 0.8216 (t0) REVERT: A 122 GLU cc_start: 0.8395 (mp0) cc_final: 0.7834 (pm20) REVERT: B 26 TYR cc_start: 0.9534 (t80) cc_final: 0.8815 (t80) REVERT: B 34 MET cc_start: 0.8966 (ttp) cc_final: 0.8156 (ppp) REVERT: B 121 PHE cc_start: 0.9314 (p90) cc_final: 0.8690 (p90) REVERT: C 19 LEU cc_start: 0.9603 (mm) cc_final: 0.9304 (mm) REVERT: C 31 TYR cc_start: 0.9453 (t80) cc_final: 0.9059 (t80) REVERT: C 49 ASN cc_start: 0.8732 (m110) cc_final: 0.8430 (m-40) REVERT: C 56 PHE cc_start: 0.8949 (t80) cc_final: 0.8073 (t80) REVERT: C 60 TYR cc_start: 0.9103 (m-80) cc_final: 0.8730 (m-10) REVERT: C 93 ARG cc_start: 0.9446 (ttp80) cc_final: 0.8974 (ttp-110) REVERT: D 32 MET cc_start: 0.9571 (mtm) cc_final: 0.9335 (mtp) REVERT: D 37 MET cc_start: 0.8834 (tpp) cc_final: 0.7847 (tpp) REVERT: D 55 HIS cc_start: 0.9037 (m90) cc_final: 0.8802 (m90) REVERT: D 69 LEU cc_start: 0.9245 (mm) cc_final: 0.8954 (mm) REVERT: D 70 ASN cc_start: 0.8858 (t0) cc_final: 0.8493 (t0) REVERT: E 15 LEU cc_start: 0.9062 (tt) cc_final: 0.8715 (mt) REVERT: E 105 ARG cc_start: 0.8804 (tpp-160) cc_final: 0.8170 (tpp-160) REVERT: E 106 VAL cc_start: 0.9295 (t) cc_final: 0.9074 (t) REVERT: F 26 TYR cc_start: 0.9440 (t80) cc_final: 0.8822 (t80) REVERT: F 34 MET cc_start: 0.7272 (tpt) cc_final: 0.6784 (tpt) REVERT: F 49 LEU cc_start: 0.8592 (mp) cc_final: 0.7188 (mt) REVERT: F 52 HIS cc_start: 0.9399 (m90) cc_final: 0.9146 (m90) REVERT: F 75 ASP cc_start: 0.9508 (p0) cc_final: 0.9221 (t70) REVERT: G 37 ASP cc_start: 0.9094 (t0) cc_final: 0.8845 (t0) REVERT: G 41 TYR cc_start: 0.9380 (t80) cc_final: 0.8839 (t80) REVERT: G 44 MET cc_start: 0.8970 (mtm) cc_final: 0.8432 (ttt) REVERT: G 60 LEU cc_start: 0.8746 (tt) cc_final: 0.8515 (tt) REVERT: G 64 LEU cc_start: 0.9028 (pp) cc_final: 0.8459 (pp) REVERT: G 66 PHE cc_start: 0.8611 (t80) cc_final: 0.6959 (t80) REVERT: G 67 HIS cc_start: 0.9435 (m90) cc_final: 0.9118 (m-70) REVERT: G 70 TYR cc_start: 0.9377 (m-80) cc_final: 0.8686 (m-80) REVERT: G 105 ARG cc_start: 0.9272 (ttp-110) cc_final: 0.8497 (ttp80) REVERT: G 122 GLU cc_start: 0.7972 (mp0) cc_final: 0.7578 (mp0) REVERT: G 139 PHE cc_start: 0.9406 (p90) cc_final: 0.9100 (p90) REVERT: I 26 TYR cc_start: 0.9510 (t80) cc_final: 0.9040 (t80) REVERT: I 44 ASN cc_start: 0.9025 (m110) cc_final: 0.8658 (m110) REVERT: J 61 PHE cc_start: 0.8875 (m-80) cc_final: 0.8638 (m-80) REVERT: J 76 ASN cc_start: 0.9202 (m110) cc_final: 0.8916 (m-40) REVERT: K 40 PHE cc_start: 0.7768 (m-80) cc_final: 0.7299 (m-10) REVERT: K 54 PHE cc_start: 0.8855 (t80) cc_final: 0.8390 (t80) REVERT: K 58 TYR cc_start: 0.8412 (m-10) cc_final: 0.8171 (m-10) REVERT: K 70 ASN cc_start: 0.9325 (m110) cc_final: 0.8981 (t0) REVERT: K 91 TYR cc_start: 0.9475 (p90) cc_final: 0.9264 (p90) REVERT: K 121 PHE cc_start: 0.9316 (p90) cc_final: 0.9077 (p90) REVERT: L 35 MET cc_start: 0.8826 (tpt) cc_final: 0.8460 (tpt) REVERT: L 67 LEU cc_start: 0.9412 (mm) cc_final: 0.9135 (mm) REVERT: L 68 ASN cc_start: 0.8863 (m-40) cc_final: 0.8316 (p0) REVERT: M 26 TYR cc_start: 0.9374 (t80) cc_final: 0.8482 (t80) REVERT: M 34 MET cc_start: 0.7593 (mmt) cc_final: 0.7143 (mmt) REVERT: M 44 ASN cc_start: 0.9331 (m-40) cc_final: 0.8884 (m-40) REVERT: M 52 HIS cc_start: 0.9462 (m90) cc_final: 0.8736 (m-70) REVERT: M 67 ASN cc_start: 0.9416 (t0) cc_final: 0.8729 (p0) REVERT: O 90 PHE cc_start: 0.9172 (m-80) cc_final: 0.8553 (m-80) REVERT: O 285 PHE cc_start: 0.9683 (t80) cc_final: 0.9408 (t80) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1440 time to fit residues: 53.9107 Evaluate side-chains 220 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 28 optimal weight: 7.9990 chunk 145 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.040290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.033056 restraints weight = 150541.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.033793 restraints weight = 114411.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.034338 restraints weight = 93057.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.034757 restraints weight = 79585.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.035079 restraints weight = 70391.431| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.7961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14838 Z= 0.155 Angle : 0.690 11.758 20064 Z= 0.370 Chirality : 0.045 0.166 2135 Planarity : 0.005 0.056 2599 Dihedral : 5.120 28.895 1939 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.30 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.20), residues: 1741 helix: -0.26 (0.21), residues: 564 sheet: 1.52 (0.22), residues: 584 loop : -0.17 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 113 TYR 0.027 0.001 TYR O 214 PHE 0.030 0.002 PHE I 51 TRP 0.020 0.002 TRP O 262 HIS 0.019 0.002 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00347 (14838) covalent geometry : angle 0.69035 (20064) hydrogen bonds : bond 0.03910 ( 692) hydrogen bonds : angle 5.23131 ( 1929) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7585 (mmp) cc_final: 0.6797 (mmm) REVERT: A 52 PHE cc_start: 0.8422 (m-80) cc_final: 0.7706 (m-10) REVERT: A 66 PHE cc_start: 0.8344 (t80) cc_final: 0.7294 (t80) REVERT: A 67 HIS cc_start: 0.9480 (m90) cc_final: 0.9245 (m90) REVERT: A 70 TYR cc_start: 0.9294 (m-80) cc_final: 0.8999 (m-80) REVERT: A 88 ASN cc_start: 0.8700 (t0) cc_final: 0.8220 (t0) REVERT: A 122 GLU cc_start: 0.8354 (mp0) cc_final: 0.7845 (pm20) REVERT: B 26 TYR cc_start: 0.9437 (t80) cc_final: 0.8712 (t80) REVERT: B 34 MET cc_start: 0.8950 (ttp) cc_final: 0.8407 (ppp) REVERT: B 70 ASN cc_start: 0.8935 (t0) cc_final: 0.8634 (t0) REVERT: B 121 PHE cc_start: 0.9271 (p90) cc_final: 0.8848 (p90) REVERT: C 19 LEU cc_start: 0.9615 (mm) cc_final: 0.9353 (mm) REVERT: C 31 TYR cc_start: 0.9453 (t80) cc_final: 0.9081 (t80) REVERT: C 49 ASN cc_start: 0.8804 (m110) cc_final: 0.8513 (m110) REVERT: C 56 PHE cc_start: 0.8962 (t80) cc_final: 0.8070 (t80) REVERT: C 60 TYR cc_start: 0.9081 (m-80) cc_final: 0.8742 (m-10) REVERT: C 93 ARG cc_start: 0.9465 (ttp80) cc_final: 0.8963 (ttp-110) REVERT: C 105 ARG cc_start: 0.9803 (mmm-85) cc_final: 0.9459 (mmt90) REVERT: D 37 MET cc_start: 0.8732 (tpp) cc_final: 0.7688 (tpp) REVERT: D 54 PHE cc_start: 0.8838 (t80) cc_final: 0.7649 (t80) REVERT: D 69 LEU cc_start: 0.9198 (mm) cc_final: 0.8897 (mm) REVERT: D 70 ASN cc_start: 0.8804 (t0) cc_final: 0.8407 (t0) REVERT: E 14 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8607 (tm-30) REVERT: E 15 LEU cc_start: 0.9012 (tt) cc_final: 0.8548 (mt) REVERT: E 51 ASP cc_start: 0.9656 (m-30) cc_final: 0.9437 (p0) REVERT: F 26 TYR cc_start: 0.9381 (t80) cc_final: 0.8823 (t80) REVERT: F 34 MET cc_start: 0.7176 (tpt) cc_final: 0.6625 (tpt) REVERT: F 49 LEU cc_start: 0.8493 (mp) cc_final: 0.6939 (mt) REVERT: F 52 HIS cc_start: 0.9330 (m90) cc_final: 0.9061 (m90) REVERT: F 75 ASP cc_start: 0.9501 (p0) cc_final: 0.9208 (t70) REVERT: G 37 ASP cc_start: 0.9167 (t0) cc_final: 0.8955 (t0) REVERT: G 41 TYR cc_start: 0.9298 (t80) cc_final: 0.8760 (t80) REVERT: G 44 MET cc_start: 0.8909 (mtm) cc_final: 0.8349 (ttt) REVERT: G 60 LEU cc_start: 0.8726 (tt) cc_final: 0.8492 (tt) REVERT: G 64 LEU cc_start: 0.9081 (pp) cc_final: 0.8400 (pp) REVERT: G 66 PHE cc_start: 0.8272 (t80) cc_final: 0.6796 (t80) REVERT: G 70 TYR cc_start: 0.9376 (m-80) cc_final: 0.8670 (m-80) REVERT: G 88 ASN cc_start: 0.9065 (t0) cc_final: 0.8812 (t0) REVERT: G 139 PHE cc_start: 0.9337 (p90) cc_final: 0.8856 (p90) REVERT: I 26 TYR cc_start: 0.9532 (t80) cc_final: 0.9070 (t80) REVERT: I 44 ASN cc_start: 0.9017 (m110) cc_final: 0.8640 (m110) REVERT: I 87 ARG cc_start: 0.8665 (ttp-170) cc_final: 0.8436 (ttp80) REVERT: I 121 PHE cc_start: 0.9506 (p90) cc_final: 0.9032 (p90) REVERT: J 61 PHE cc_start: 0.8935 (m-80) cc_final: 0.8320 (m-80) REVERT: J 76 ASN cc_start: 0.9225 (m110) cc_final: 0.8963 (m-40) REVERT: K 26 PHE cc_start: 0.8685 (t80) cc_final: 0.8413 (t80) REVERT: K 40 PHE cc_start: 0.7761 (m-80) cc_final: 0.7370 (m-10) REVERT: K 48 LEU cc_start: 0.8464 (tp) cc_final: 0.8240 (tp) REVERT: K 54 PHE cc_start: 0.8794 (t80) cc_final: 0.8509 (t80) REVERT: K 58 TYR cc_start: 0.8372 (m-10) cc_final: 0.8104 (m-10) REVERT: K 70 ASN cc_start: 0.9332 (m110) cc_final: 0.8941 (t0) REVERT: K 78 ASP cc_start: 0.8656 (t0) cc_final: 0.8356 (t0) REVERT: K 91 TYR cc_start: 0.9535 (p90) cc_final: 0.9329 (p90) REVERT: K 121 PHE cc_start: 0.9212 (p90) cc_final: 0.8984 (p90) REVERT: L 35 MET cc_start: 0.8873 (tpt) cc_final: 0.8519 (tpt) REVERT: L 45 ASN cc_start: 0.8761 (m110) cc_final: 0.8509 (m110) REVERT: L 67 LEU cc_start: 0.9402 (mm) cc_final: 0.9167 (mm) REVERT: L 68 ASN cc_start: 0.8847 (m-40) cc_final: 0.8376 (p0) REVERT: L 83 TYR cc_start: 0.9078 (p90) cc_final: 0.8521 (p90) REVERT: M 26 TYR cc_start: 0.9319 (t80) cc_final: 0.8467 (t80) REVERT: M 34 MET cc_start: 0.7476 (mmt) cc_final: 0.6999 (mmt) REVERT: M 44 ASN cc_start: 0.9208 (m-40) cc_final: 0.8844 (m-40) REVERT: M 52 HIS cc_start: 0.9321 (m90) cc_final: 0.8586 (m-70) REVERT: M 67 ASN cc_start: 0.9408 (t0) cc_final: 0.8710 (p0) REVERT: O 90 PHE cc_start: 0.9148 (m-80) cc_final: 0.8611 (m-80) REVERT: O 285 PHE cc_start: 0.9698 (t80) cc_final: 0.9392 (t80) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.1370 time to fit residues: 52.8832 Evaluate side-chains 228 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 90 optimal weight: 0.2980 chunk 54 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 104 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 HIS J 116 HIS K 74 HIS K 117 GLN ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.041403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.034270 restraints weight = 147607.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.034934 restraints weight = 113662.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.035517 restraints weight = 93048.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.035902 restraints weight = 80196.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036286 restraints weight = 70189.897| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.8050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14838 Z= 0.135 Angle : 0.699 10.914 20064 Z= 0.373 Chirality : 0.047 0.189 2135 Planarity : 0.005 0.106 2599 Dihedral : 4.988 27.677 1939 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.35 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1741 helix: -0.22 (0.21), residues: 560 sheet: 1.55 (0.22), residues: 576 loop : -0.12 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG D 87 TYR 0.027 0.001 TYR O 214 PHE 0.023 0.002 PHE B 51 TRP 0.021 0.002 TRP J 65 HIS 0.019 0.001 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00300 (14838) covalent geometry : angle 0.69925 (20064) hydrogen bonds : bond 0.03776 ( 692) hydrogen bonds : angle 5.10222 ( 1929) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 41 TYR cc_start: 0.9577 (t80) cc_final: 0.9303 (t80) REVERT: A 49 MET cc_start: 0.7445 (mmp) cc_final: 0.6567 (mmm) REVERT: A 52 PHE cc_start: 0.8342 (m-80) cc_final: 0.7538 (m-10) REVERT: A 66 PHE cc_start: 0.8372 (t80) cc_final: 0.7313 (t80) REVERT: A 67 HIS cc_start: 0.9449 (m90) cc_final: 0.9192 (m90) REVERT: A 70 TYR cc_start: 0.9266 (m-80) cc_final: 0.8973 (m-80) REVERT: A 88 ASN cc_start: 0.8648 (t0) cc_final: 0.8161 (t0) REVERT: A 122 GLU cc_start: 0.8221 (mp0) cc_final: 0.7741 (pm20) REVERT: B 26 TYR cc_start: 0.9350 (t80) cc_final: 0.8629 (t80) REVERT: B 34 MET cc_start: 0.8887 (ttp) cc_final: 0.8119 (ppp) REVERT: B 121 PHE cc_start: 0.9302 (p90) cc_final: 0.8618 (p90) REVERT: C 19 LEU cc_start: 0.9597 (mm) cc_final: 0.9317 (mm) REVERT: C 31 TYR cc_start: 0.9468 (t80) cc_final: 0.9039 (t80) REVERT: C 39 MET cc_start: 0.7902 (ppp) cc_final: 0.7654 (ppp) REVERT: C 49 ASN cc_start: 0.8723 (m110) cc_final: 0.8371 (m110) REVERT: C 50 LEU cc_start: 0.8662 (pp) cc_final: 0.8329 (pp) REVERT: C 56 PHE cc_start: 0.9048 (t80) cc_final: 0.8516 (t80) REVERT: C 57 HIS cc_start: 0.9637 (m90) cc_final: 0.9313 (m90) REVERT: C 60 TYR cc_start: 0.9059 (m-80) cc_final: 0.8756 (m-10) REVERT: C 93 ARG cc_start: 0.9451 (ttp80) cc_final: 0.8962 (ttp-110) REVERT: C 105 ARG cc_start: 0.9820 (mmm-85) cc_final: 0.9514 (mmt90) REVERT: D 37 MET cc_start: 0.8602 (tpp) cc_final: 0.7474 (tpp) REVERT: D 69 LEU cc_start: 0.9173 (mm) cc_final: 0.8885 (mm) REVERT: D 70 ASN cc_start: 0.8737 (t0) cc_final: 0.8364 (t0) REVERT: E 15 LEU cc_start: 0.8984 (tt) cc_final: 0.8534 (mt) REVERT: F 26 TYR cc_start: 0.9390 (t80) cc_final: 0.8830 (t80) REVERT: F 27 THR cc_start: 0.9241 (p) cc_final: 0.8926 (p) REVERT: F 34 MET cc_start: 0.7291 (tpt) cc_final: 0.6673 (tpt) REVERT: F 49 LEU cc_start: 0.8440 (mp) cc_final: 0.6720 (mt) REVERT: F 52 HIS cc_start: 0.9294 (m90) cc_final: 0.9061 (m90) REVERT: F 75 ASP cc_start: 0.9517 (p0) cc_final: 0.9183 (t70) REVERT: G 37 ASP cc_start: 0.9175 (t0) cc_final: 0.8969 (t0) REVERT: G 41 TYR cc_start: 0.9377 (t80) cc_final: 0.8854 (t80) REVERT: G 44 MET cc_start: 0.8901 (mtm) cc_final: 0.8324 (ttt) REVERT: G 60 LEU cc_start: 0.8614 (tt) cc_final: 0.8411 (tt) REVERT: G 64 LEU cc_start: 0.9038 (pp) cc_final: 0.8379 (pp) REVERT: G 66 PHE cc_start: 0.8124 (t80) cc_final: 0.6749 (t80) REVERT: G 70 TYR cc_start: 0.9404 (m-80) cc_final: 0.8663 (m-80) REVERT: G 88 ASN cc_start: 0.9035 (t0) cc_final: 0.8783 (t0) REVERT: G 122 GLU cc_start: 0.7922 (mp0) cc_final: 0.7599 (mp0) REVERT: G 139 PHE cc_start: 0.9231 (p90) cc_final: 0.8816 (p90) REVERT: I 26 TYR cc_start: 0.9522 (t80) cc_final: 0.8989 (t80) REVERT: I 44 ASN cc_start: 0.9015 (m110) cc_final: 0.8632 (m110) REVERT: I 85 TYR cc_start: 0.8667 (p90) cc_final: 0.7990 (p90) REVERT: I 87 ARG cc_start: 0.8696 (ttp-170) cc_final: 0.8435 (ttp80) REVERT: J 14 LYS cc_start: 0.9532 (tttt) cc_final: 0.9293 (mttt) REVERT: J 29 GLU cc_start: 0.9647 (tp30) cc_final: 0.9433 (tp30) REVERT: J 42 PHE cc_start: 0.8241 (m-10) cc_final: 0.7899 (m-10) REVERT: J 56 PHE cc_start: 0.7682 (t80) cc_final: 0.7230 (t80) REVERT: J 61 PHE cc_start: 0.9266 (m-80) cc_final: 0.8939 (m-80) REVERT: J 76 ASN cc_start: 0.9182 (m110) cc_final: 0.8876 (t0) REVERT: K 40 PHE cc_start: 0.7655 (m-80) cc_final: 0.6987 (m-10) REVERT: K 48 LEU cc_start: 0.8276 (tp) cc_final: 0.8074 (tp) REVERT: K 54 PHE cc_start: 0.9039 (t80) cc_final: 0.8530 (t80) REVERT: K 58 TYR cc_start: 0.8291 (m-10) cc_final: 0.7980 (m-10) REVERT: K 70 ASN cc_start: 0.9296 (m110) cc_final: 0.8885 (t0) REVERT: K 78 ASP cc_start: 0.8622 (t0) cc_final: 0.8343 (t0) REVERT: K 122 HIS cc_start: 0.7652 (t-170) cc_final: 0.6888 (t-170) REVERT: L 35 MET cc_start: 0.8767 (tpt) cc_final: 0.8514 (tpt) REVERT: L 45 ASN cc_start: 0.8668 (m110) cc_final: 0.8454 (m110) REVERT: L 46 LEU cc_start: 0.9245 (pp) cc_final: 0.9020 (pp) REVERT: L 67 LEU cc_start: 0.9350 (mm) cc_final: 0.9099 (mm) REVERT: L 68 ASN cc_start: 0.8815 (m-40) cc_final: 0.8305 (p0) REVERT: L 83 TYR cc_start: 0.9112 (p90) cc_final: 0.8626 (p90) REVERT: M 26 TYR cc_start: 0.9259 (t80) cc_final: 0.8751 (t80) REVERT: M 34 MET cc_start: 0.7555 (mmt) cc_final: 0.7067 (mmt) REVERT: M 44 ASN cc_start: 0.9159 (m-40) cc_final: 0.8791 (m-40) REVERT: M 52 HIS cc_start: 0.9291 (m90) cc_final: 0.8552 (m-70) REVERT: M 67 ASN cc_start: 0.9419 (t0) cc_final: 0.8708 (p0) REVERT: O 90 PHE cc_start: 0.9093 (m-80) cc_final: 0.8479 (m-80) REVERT: O 285 PHE cc_start: 0.9683 (t80) cc_final: 0.9346 (t80) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1369 time to fit residues: 55.7131 Evaluate side-chains 239 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 1 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS L 14 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.039819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.032475 restraints weight = 152517.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.033191 restraints weight = 115761.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.033686 restraints weight = 94295.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.034038 restraints weight = 81895.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.034433 restraints weight = 72977.309| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.8285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14838 Z= 0.161 Angle : 0.689 10.005 20064 Z= 0.374 Chirality : 0.045 0.230 2135 Planarity : 0.005 0.112 2599 Dihedral : 5.067 26.994 1939 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.58 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1741 helix: -0.20 (0.21), residues: 560 sheet: 1.49 (0.22), residues: 608 loop : -0.08 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 87 TYR 0.025 0.001 TYR O 214 PHE 0.021 0.002 PHE B 51 TRP 0.018 0.002 TRP O 262 HIS 0.018 0.002 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00353 (14838) covalent geometry : angle 0.68903 (20064) hydrogen bonds : bond 0.03836 ( 692) hydrogen bonds : angle 5.15165 ( 1929) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2295.42 seconds wall clock time: 40 minutes 48.39 seconds (2448.39 seconds total)