Starting phenix.real_space_refine on Thu Mar 5 11:01:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tnz_56096/03_2026/9tnz_56096.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tnz_56096/03_2026/9tnz_56096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tnz_56096/03_2026/9tnz_56096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tnz_56096/03_2026/9tnz_56096.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tnz_56096/03_2026/9tnz_56096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tnz_56096/03_2026/9tnz_56096.map" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 13910 2.51 5 N 3562 2.21 5 O 3952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21502 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 827 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 94} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, X, Y, Z, AA Time building chain proxies: 1.97, per 1000 atoms: 0.09 Number of scatterers: 21502 At special positions: 0 Unit cell: (91.56, 91.56, 289.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3952 8.00 N 3562 7.00 C 13910 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: 1.56 Conformation dependent library (CDL) restraints added in 1.0 seconds 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5044 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 0 sheets defined 89.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.535A pdb=" N SER A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 143 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 60 through 68 removed outlier: 3.535A pdb=" N SER B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 136 through 147 removed outlier: 4.309A pdb=" N ILE B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 143 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 98 Processing helix chain 'C' and resid 101 through 114 Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 118 through 126 removed outlier: 3.992A pdb=" N LEU C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 134 Processing helix chain 'C' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C 143 " --> pdb=" O HIS C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 101 through 114 Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 134 Processing helix chain 'D' and resid 136 through 147 removed outlier: 4.309A pdb=" N ILE D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY D 143 " --> pdb=" O HIS D 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 98 Processing helix chain 'E' and resid 101 through 114 Processing helix chain 'E' and resid 115 through 117 No H-bonds generated for 'chain 'E' and resid 115 through 117' Processing helix chain 'E' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU E 122 " --> pdb=" O ASN E 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 134 Processing helix chain 'E' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY E 143 " --> pdb=" O HIS E 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 60 through 68 removed outlier: 3.535A pdb=" N SER F 65 " --> pdb=" O LYS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG F 79 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 98 Processing helix chain 'F' and resid 101 through 114 Processing helix chain 'F' and resid 115 through 117 No H-bonds generated for 'chain 'F' and resid 115 through 117' Processing helix chain 'F' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU F 122 " --> pdb=" O ASN F 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 134 Processing helix chain 'F' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY F 143 " --> pdb=" O HIS F 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 60 Processing helix chain 'G' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER G 65 " --> pdb=" O LYS G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP G 80 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 98 Processing helix chain 'G' and resid 101 through 114 Processing helix chain 'G' and resid 115 through 117 No H-bonds generated for 'chain 'G' and resid 115 through 117' Processing helix chain 'G' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU G 122 " --> pdb=" O ASN G 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU G 123 " --> pdb=" O LEU G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 134 Processing helix chain 'G' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY G 143 " --> pdb=" O HIS G 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 60 Processing helix chain 'H' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 81 removed outlier: 3.822A pdb=" N ARG H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'H' and resid 101 through 114 Processing helix chain 'H' and resid 115 through 117 No H-bonds generated for 'chain 'H' and resid 115 through 117' Processing helix chain 'H' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU H 122 " --> pdb=" O ASN H 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU H 123 " --> pdb=" O LEU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 134 Processing helix chain 'H' and resid 136 through 147 removed outlier: 4.309A pdb=" N ILE H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY H 143 " --> pdb=" O HIS H 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 60 Processing helix chain 'I' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP I 80 " --> pdb=" O GLU I 76 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG I 81 " --> pdb=" O GLY I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 98 Processing helix chain 'I' and resid 101 through 114 Processing helix chain 'I' and resid 115 through 117 No H-bonds generated for 'chain 'I' and resid 115 through 117' Processing helix chain 'I' and resid 118 through 126 removed outlier: 3.994A pdb=" N LEU I 122 " --> pdb=" O ASN I 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU I 123 " --> pdb=" O LEU I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 134 Processing helix chain 'I' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE I 140 " --> pdb=" O ASP I 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY I 143 " --> pdb=" O HIS I 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 60 Processing helix chain 'J' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 81 removed outlier: 3.822A pdb=" N ARG J 79 " --> pdb=" O LEU J 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP J 80 " --> pdb=" O GLU J 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG J 81 " --> pdb=" O GLY J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 98 Processing helix chain 'J' and resid 101 through 114 Processing helix chain 'J' and resid 115 through 117 No H-bonds generated for 'chain 'J' and resid 115 through 117' Processing helix chain 'J' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU J 122 " --> pdb=" O ASN J 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU J 123 " --> pdb=" O LEU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 134 Processing helix chain 'J' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE J 140 " --> pdb=" O ASP J 136 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY J 143 " --> pdb=" O HIS J 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 60 Processing helix chain 'K' and resid 60 through 68 removed outlier: 3.535A pdb=" N SER K 65 " --> pdb=" O LYS K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG K 81 " --> pdb=" O GLY K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 98 Processing helix chain 'K' and resid 101 through 114 Processing helix chain 'K' and resid 115 through 117 No H-bonds generated for 'chain 'K' and resid 115 through 117' Processing helix chain 'K' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU K 123 " --> pdb=" O LEU K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 134 Processing helix chain 'K' and resid 136 through 147 removed outlier: 4.309A pdb=" N ILE K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY K 143 " --> pdb=" O HIS K 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 60 Processing helix chain 'L' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER L 65 " --> pdb=" O LYS L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG L 79 " --> pdb=" O LEU L 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG L 81 " --> pdb=" O GLY L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 98 Processing helix chain 'L' and resid 101 through 114 Processing helix chain 'L' and resid 115 through 117 No H-bonds generated for 'chain 'L' and resid 115 through 117' Processing helix chain 'L' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU L 122 " --> pdb=" O ASN L 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 134 Processing helix chain 'L' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE L 140 " --> pdb=" O ASP L 136 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY L 143 " --> pdb=" O HIS L 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 60 Processing helix chain 'M' and resid 60 through 68 removed outlier: 3.535A pdb=" N SER M 65 " --> pdb=" O LYS M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG M 79 " --> pdb=" O LEU M 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP M 80 " --> pdb=" O GLU M 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG M 81 " --> pdb=" O GLY M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 98 Processing helix chain 'M' and resid 101 through 114 Processing helix chain 'M' and resid 115 through 117 No H-bonds generated for 'chain 'M' and resid 115 through 117' Processing helix chain 'M' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU M 122 " --> pdb=" O ASN M 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 134 Processing helix chain 'M' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE M 140 " --> pdb=" O ASP M 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY M 143 " --> pdb=" O HIS M 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 60 Processing helix chain 'N' and resid 60 through 68 removed outlier: 3.535A pdb=" N SER N 65 " --> pdb=" O LYS N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP N 80 " --> pdb=" O GLU N 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG N 81 " --> pdb=" O GLY N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 98 Processing helix chain 'N' and resid 101 through 114 Processing helix chain 'N' and resid 115 through 117 No H-bonds generated for 'chain 'N' and resid 115 through 117' Processing helix chain 'N' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU N 122 " --> pdb=" O ASN N 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU N 123 " --> pdb=" O LEU N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 134 Processing helix chain 'N' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE N 140 " --> pdb=" O ASP N 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY N 143 " --> pdb=" O HIS N 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 60 Processing helix chain 'O' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER O 65 " --> pdb=" O LYS O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG O 79 " --> pdb=" O LEU O 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP O 80 " --> pdb=" O GLU O 76 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG O 81 " --> pdb=" O GLY O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 98 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'O' and resid 115 through 117 No H-bonds generated for 'chain 'O' and resid 115 through 117' Processing helix chain 'O' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU O 122 " --> pdb=" O ASN O 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU O 123 " --> pdb=" O LEU O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 134 Processing helix chain 'O' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE O 140 " --> pdb=" O ASP O 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY O 143 " --> pdb=" O HIS O 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 60 Processing helix chain 'P' and resid 60 through 68 removed outlier: 3.535A pdb=" N SER P 65 " --> pdb=" O LYS P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG P 79 " --> pdb=" O LEU P 75 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP P 80 " --> pdb=" O GLU P 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG P 81 " --> pdb=" O GLY P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 98 Processing helix chain 'P' and resid 101 through 114 Processing helix chain 'P' and resid 115 through 117 No H-bonds generated for 'chain 'P' and resid 115 through 117' Processing helix chain 'P' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU P 122 " --> pdb=" O ASN P 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU P 123 " --> pdb=" O LEU P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 134 Processing helix chain 'P' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE P 140 " --> pdb=" O ASP P 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY P 143 " --> pdb=" O HIS P 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 60 Processing helix chain 'Q' and resid 60 through 68 removed outlier: 3.535A pdb=" N SER Q 65 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG Q 79 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP Q 80 " --> pdb=" O GLU Q 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG Q 81 " --> pdb=" O GLY Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 98 Processing helix chain 'Q' and resid 101 through 114 Processing helix chain 'Q' and resid 115 through 117 No H-bonds generated for 'chain 'Q' and resid 115 through 117' Processing helix chain 'Q' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU Q 122 " --> pdb=" O ASN Q 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU Q 123 " --> pdb=" O LEU Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 134 Processing helix chain 'Q' and resid 136 through 147 removed outlier: 4.309A pdb=" N ILE Q 140 " --> pdb=" O ASP Q 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY Q 143 " --> pdb=" O HIS Q 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 60 Processing helix chain 'R' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER R 65 " --> pdb=" O LYS R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 81 removed outlier: 3.822A pdb=" N ARG R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP R 80 " --> pdb=" O GLU R 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 98 Processing helix chain 'R' and resid 101 through 114 Processing helix chain 'R' and resid 115 through 117 No H-bonds generated for 'chain 'R' and resid 115 through 117' Processing helix chain 'R' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU R 122 " --> pdb=" O ASN R 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU R 123 " --> pdb=" O LEU R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 134 Processing helix chain 'R' and resid 136 through 147 removed outlier: 4.307A pdb=" N ILE R 140 " --> pdb=" O ASP R 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY R 143 " --> pdb=" O HIS R 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 50 through 60 Processing helix chain 'S' and resid 60 through 68 removed outlier: 3.535A pdb=" N SER S 65 " --> pdb=" O LYS S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG S 79 " --> pdb=" O LEU S 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP S 80 " --> pdb=" O GLU S 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG S 81 " --> pdb=" O GLY S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 98 Processing helix chain 'S' and resid 101 through 114 Processing helix chain 'S' and resid 115 through 117 No H-bonds generated for 'chain 'S' and resid 115 through 117' Processing helix chain 'S' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU S 122 " --> pdb=" O ASN S 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU S 123 " --> pdb=" O LEU S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 134 Processing helix chain 'S' and resid 136 through 147 removed outlier: 4.309A pdb=" N ILE S 140 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY S 143 " --> pdb=" O HIS S 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 60 Processing helix chain 'T' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER T 65 " --> pdb=" O LYS T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG T 79 " --> pdb=" O LEU T 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP T 80 " --> pdb=" O GLU T 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG T 81 " --> pdb=" O GLY T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 98 Processing helix chain 'T' and resid 101 through 114 Processing helix chain 'T' and resid 115 through 117 No H-bonds generated for 'chain 'T' and resid 115 through 117' Processing helix chain 'T' and resid 118 through 126 removed outlier: 3.994A pdb=" N LEU T 122 " --> pdb=" O ASN T 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU T 123 " --> pdb=" O LEU T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 134 Processing helix chain 'T' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE T 140 " --> pdb=" O ASP T 136 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY T 143 " --> pdb=" O HIS T 139 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 60 Processing helix chain 'V' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER V 65 " --> pdb=" O LYS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG V 79 " --> pdb=" O LEU V 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG V 81 " --> pdb=" O GLY V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 98 Processing helix chain 'V' and resid 101 through 114 Processing helix chain 'V' and resid 115 through 117 No H-bonds generated for 'chain 'V' and resid 115 through 117' Processing helix chain 'V' and resid 118 through 126 removed outlier: 3.994A pdb=" N LEU V 122 " --> pdb=" O ASN V 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU V 123 " --> pdb=" O LEU V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 134 Processing helix chain 'V' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE V 140 " --> pdb=" O ASP V 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY V 143 " --> pdb=" O HIS V 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 60 Processing helix chain 'W' and resid 60 through 68 removed outlier: 3.535A pdb=" N SER W 65 " --> pdb=" O LYS W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG W 79 " --> pdb=" O LEU W 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP W 80 " --> pdb=" O GLU W 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG W 81 " --> pdb=" O GLY W 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 98 Processing helix chain 'W' and resid 101 through 114 Processing helix chain 'W' and resid 115 through 117 No H-bonds generated for 'chain 'W' and resid 115 through 117' Processing helix chain 'W' and resid 118 through 126 removed outlier: 3.994A pdb=" N LEU W 122 " --> pdb=" O ASN W 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU W 123 " --> pdb=" O LEU W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 134 Processing helix chain 'W' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE W 140 " --> pdb=" O ASP W 136 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY W 143 " --> pdb=" O HIS W 139 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 60 Processing helix chain 'X' and resid 60 through 68 removed outlier: 3.535A pdb=" N SER X 65 " --> pdb=" O LYS X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG X 79 " --> pdb=" O LEU X 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP X 80 " --> pdb=" O GLU X 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG X 81 " --> pdb=" O GLY X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 98 Processing helix chain 'X' and resid 101 through 114 Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU X 122 " --> pdb=" O ASN X 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU X 123 " --> pdb=" O LEU X 119 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 134 Processing helix chain 'X' and resid 136 through 147 removed outlier: 4.309A pdb=" N ILE X 140 " --> pdb=" O ASP X 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY X 143 " --> pdb=" O HIS X 139 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 60 Processing helix chain 'Y' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER Y 65 " --> pdb=" O LYS Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG Y 79 " --> pdb=" O LEU Y 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP Y 80 " --> pdb=" O GLU Y 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG Y 81 " --> pdb=" O GLY Y 77 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 98 Processing helix chain 'Y' and resid 101 through 114 Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 118 through 126 removed outlier: 3.992A pdb=" N LEU Y 122 " --> pdb=" O ASN Y 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU Y 123 " --> pdb=" O LEU Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 127 through 134 Processing helix chain 'Y' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILE Y 140 " --> pdb=" O ASP Y 136 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY Y 143 " --> pdb=" O HIS Y 139 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 60 Processing helix chain 'Z' and resid 60 through 68 removed outlier: 3.534A pdb=" N SER Z 65 " --> pdb=" O LYS Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 73 through 81 removed outlier: 3.821A pdb=" N ARG Z 79 " --> pdb=" O LEU Z 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP Z 80 " --> pdb=" O GLU Z 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG Z 81 " --> pdb=" O GLY Z 77 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 98 Processing helix chain 'Z' and resid 101 through 114 Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEU Z 122 " --> pdb=" O ASN Z 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU Z 123 " --> pdb=" O LEU Z 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 134 Processing helix chain 'Z' and resid 136 through 147 removed outlier: 4.309A pdb=" N ILE Z 140 " --> pdb=" O ASP Z 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY Z 143 " --> pdb=" O HIS Z 139 " (cutoff:3.500A) Processing helix chain 'AA' and resid 50 through 60 Processing helix chain 'AA' and resid 60 through 68 removed outlier: 3.535A pdb=" N SERAA 65 " --> pdb=" O LYSAA 61 " (cutoff:3.500A) Processing helix chain 'AA' and resid 73 through 81 removed outlier: 3.822A pdb=" N ARGAA 79 " --> pdb=" O LEUAA 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASPAA 80 " --> pdb=" O GLUAA 76 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARGAA 81 " --> pdb=" O GLYAA 77 " (cutoff:3.500A) Processing helix chain 'AA' and resid 85 through 98 Processing helix chain 'AA' and resid 101 through 114 Processing helix chain 'AA' and resid 115 through 117 No H-bonds generated for 'chain 'AA' and resid 115 through 117' Processing helix chain 'AA' and resid 118 through 126 removed outlier: 3.993A pdb=" N LEUAA 122 " --> pdb=" O ASNAA 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLUAA 123 " --> pdb=" O LEUAA 119 " (cutoff:3.500A) Processing helix chain 'AA' and resid 127 through 134 Processing helix chain 'AA' and resid 136 through 147 removed outlier: 4.308A pdb=" N ILEAA 140 " --> pdb=" O ASPAA 136 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLYAA 143 " --> pdb=" O HISAA 139 " (cutoff:3.500A) 1197 hydrogen bonds defined for protein. 3591 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: 2.71 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6968 1.34 - 1.46: 3028 1.46 - 1.57: 11818 1.57 - 1.69: 0 1.69 - 1.81: 130 Bond restraints: 21944 Sorted by residual: bond pdb=" CG PRO C 73 " pdb=" CD PRO C 73 " ideal model delta sigma weight residual 1.512 1.490 0.022 2.70e-02 1.37e+03 6.42e-01 bond pdb=" CG PRO V 73 " pdb=" CD PRO V 73 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 6.33e-01 bond pdb=" CG PRO Z 73 " pdb=" CD PRO Z 73 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 6.30e-01 bond pdb=" CG PRO Q 73 " pdb=" CD PRO Q 73 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 6.29e-01 bond pdb=" CG PROAA 73 " pdb=" CD PROAA 73 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 6.26e-01 ... (remaining 21939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 28657 0.83 - 1.67: 621 1.67 - 2.50: 206 2.50 - 3.34: 104 3.34 - 4.17: 26 Bond angle restraints: 29614 Sorted by residual: angle pdb=" N ASP N 82 " pdb=" CA ASP N 82 " pdb=" C ASP N 82 " ideal model delta sigma weight residual 111.74 108.55 3.19 1.35e+00 5.49e-01 5.59e+00 angle pdb=" N ASP Q 82 " pdb=" CA ASP Q 82 " pdb=" C ASP Q 82 " ideal model delta sigma weight residual 111.74 108.56 3.18 1.35e+00 5.49e-01 5.55e+00 angle pdb=" N ASP H 82 " pdb=" CA ASP H 82 " pdb=" C ASP H 82 " ideal model delta sigma weight residual 111.74 108.56 3.18 1.35e+00 5.49e-01 5.53e+00 angle pdb=" N ASP P 82 " pdb=" CA ASP P 82 " pdb=" C ASP P 82 " ideal model delta sigma weight residual 111.74 108.58 3.16 1.35e+00 5.49e-01 5.47e+00 angle pdb=" N ASP D 82 " pdb=" CA ASP D 82 " pdb=" C ASP D 82 " ideal model delta sigma weight residual 111.74 108.58 3.16 1.35e+00 5.49e-01 5.46e+00 ... (remaining 29609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.83: 11181 11.83 - 23.67: 1434 23.67 - 35.50: 567 35.50 - 47.33: 156 47.33 - 59.17: 52 Dihedral angle restraints: 13390 sinusoidal: 5694 harmonic: 7696 Sorted by residual: dihedral pdb=" CA ILE W 140 " pdb=" CB ILE W 140 " pdb=" CG1 ILE W 140 " pdb=" CD1 ILE W 140 " ideal model delta sinusoidal sigma weight residual 60.00 105.95 -45.95 3 1.50e+01 4.44e-03 8.26e+00 dihedral pdb=" CA ILE O 140 " pdb=" CB ILE O 140 " pdb=" CG1 ILE O 140 " pdb=" CD1 ILE O 140 " ideal model delta sinusoidal sigma weight residual 60.00 105.95 -45.95 3 1.50e+01 4.44e-03 8.26e+00 dihedral pdb=" CA ILE I 140 " pdb=" CB ILE I 140 " pdb=" CG1 ILE I 140 " pdb=" CD1 ILE I 140 " ideal model delta sinusoidal sigma weight residual 60.00 105.94 -45.94 3 1.50e+01 4.44e-03 8.25e+00 ... (remaining 13387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1973 0.025 - 0.050: 770 0.050 - 0.075: 379 0.075 - 0.099: 148 0.099 - 0.124: 32 Chirality restraints: 3302 Sorted by residual: chirality pdb=" CA VAL V 100 " pdb=" N VAL V 100 " pdb=" C VAL V 100 " pdb=" CB VAL V 100 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL C 100 " pdb=" N VAL C 100 " pdb=" C VAL C 100 " pdb=" CB VAL C 100 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA VAL T 100 " pdb=" N VAL T 100 " pdb=" C VAL T 100 " pdb=" CB VAL T 100 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 3299 not shown) Planarity restraints: 3822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 72 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO C 73 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 73 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 73 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE S 72 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO S 73 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO S 73 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO S 73 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 72 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 73 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " 0.017 5.00e-02 4.00e+02 ... (remaining 3819 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 8628 2.93 - 3.42: 22518 3.42 - 3.91: 33868 3.91 - 4.41: 38881 4.41 - 4.90: 61588 Nonbonded interactions: 165483 Sorted by model distance: nonbonded pdb=" O LYS X 70 " pdb=" OH TYR X 134 " model vdw 2.434 3.040 nonbonded pdb=" O LYS B 70 " pdb=" OH TYR B 134 " model vdw 2.435 3.040 nonbonded pdb=" O LYS T 70 " pdb=" OH TYR T 134 " model vdw 2.435 3.040 nonbonded pdb=" O LYS Y 70 " pdb=" OH TYR Y 134 " model vdw 2.435 3.040 nonbonded pdb=" O LYS L 70 " pdb=" OH TYR L 134 " model vdw 2.435 3.040 ... (remaining 165478 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'AA' } 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 15.220 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 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 : 0.002 0.022 21944 Z= 0.104 Angle : 0.389 4.170 29614 Z= 0.212 Chirality : 0.036 0.124 3302 Planarity : 0.004 0.034 3822 Dihedral : 12.860 59.169 8346 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.16), residues: 2522 helix: 0.89 (0.11), residues: 2054 sheet: None (None), residues: 0 loop : 1.58 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 81 TYR 0.003 0.001 TYR G 50 PHE 0.010 0.001 PHE N 74 HIS 0.001 0.000 HIS N 56 Details of bonding type rmsd covalent geometry : bond 0.00248 (21944) covalent geometry : angle 0.38895 (29614) hydrogen bonds : bond 0.28446 ( 1197) hydrogen bonds : angle 6.73908 ( 3591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 732 time to evaluate : 0.772 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: C 63 GLU cc_start: 0.7180 (mp0) cc_final: 0.6867 (mp0) REVERT: C 87 LYS cc_start: 0.8290 (tptt) cc_final: 0.8040 (tptm) REVERT: C 118 ASN cc_start: 0.7830 (m-40) cc_final: 0.7495 (m-40) REVERT: D 66 ASN cc_start: 0.8774 (t0) cc_final: 0.8525 (t0) REVERT: D 87 LYS cc_start: 0.8160 (tptt) cc_final: 0.7602 (tttt) REVERT: D 91 ASP cc_start: 0.8544 (m-30) cc_final: 0.8299 (m-30) REVERT: D 118 ASN cc_start: 0.7189 (m-40) cc_final: 0.6800 (m-40) REVERT: E 52 ILE cc_start: 0.8506 (mt) cc_final: 0.8298 (mt) REVERT: E 87 LYS cc_start: 0.8459 (tptt) cc_final: 0.8041 (tppt) REVERT: E 142 LYS cc_start: 0.8362 (mmtp) cc_final: 0.8030 (mmtt) REVERT: F 82 ASP cc_start: 0.8100 (t0) cc_final: 0.7768 (t0) REVERT: F 142 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7371 (mtmm) REVERT: G 87 LYS cc_start: 0.8727 (tptt) cc_final: 0.8447 (tppt) REVERT: G 127 SER cc_start: 0.8986 (t) cc_final: 0.8691 (t) REVERT: H 87 LYS cc_start: 0.8488 (tptt) cc_final: 0.7793 (tttt) REVERT: I 142 LYS cc_start: 0.8555 (mmtp) cc_final: 0.7780 (mmtt) REVERT: J 59 ARG cc_start: 0.8017 (mmt90) cc_final: 0.7508 (mtm110) REVERT: J 66 ASN cc_start: 0.8750 (t0) cc_final: 0.8541 (t0) REVERT: J 88 MET cc_start: 0.8495 (tpp) cc_final: 0.8239 (tpp) REVERT: J 141 TYR cc_start: 0.8483 (t80) cc_final: 0.8077 (t80) REVERT: J 142 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8113 (mmtt) REVERT: L 59 ARG cc_start: 0.7748 (mmt90) cc_final: 0.7448 (mtm110) REVERT: M 60 ASN cc_start: 0.7843 (m110) cc_final: 0.7153 (m-40) REVERT: N 118 ASN cc_start: 0.7940 (m-40) cc_final: 0.7689 (m-40) REVERT: N 142 LYS cc_start: 0.8296 (mmtp) cc_final: 0.8033 (mmtt) REVERT: O 133 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7771 (mm-30) REVERT: P 142 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8068 (mmtt) REVERT: Q 87 LYS cc_start: 0.8398 (tptt) cc_final: 0.8136 (tttt) REVERT: T 66 ASN cc_start: 0.8419 (t0) cc_final: 0.8108 (t0) REVERT: T 88 MET cc_start: 0.7895 (tpp) cc_final: 0.7531 (tpp) REVERT: V 69 LYS cc_start: 0.8558 (pttt) cc_final: 0.8346 (ptpp) REVERT: X 142 LYS cc_start: 0.8392 (mmtp) cc_final: 0.8031 (mmtp) REVERT: Y 69 LYS cc_start: 0.8121 (pttt) cc_final: 0.7742 (ptmm) REVERT: Y 142 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8385 (mmtt) outliers start: 0 outliers final: 0 residues processed: 732 average time/residue: 0.1661 time to fit residues: 181.3347 Evaluate side-chains 486 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS B 56 HIS B 66 ASN B 132 GLN B 139 HIS C 132 GLN C 139 HIS D 66 ASN D 139 HIS E 132 GLN E 139 HIS F 56 HIS F 66 ASN G 139 HIS I 66 ASN I 139 HIS ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 ASN M 66 ASN M 139 HIS N 60 ASN N 139 HIS O 66 ASN O 139 HIS P 132 GLN P 139 HIS Q 66 ASN Q 139 HIS R 66 ASN R 103 GLN T 66 ASN T 132 GLN V 56 HIS V 66 ASN W 132 GLN W 139 HIS X 66 ASN X 139 HIS Z 103 GLN Z 108 ASN AA 66 ASN AA 103 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.159549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127408 restraints weight = 36286.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125439 restraints weight = 30170.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.127107 restraints weight = 26839.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130994 restraints weight = 20213.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.130825 restraints weight = 14075.796| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21944 Z= 0.158 Angle : 0.508 6.045 29614 Z= 0.266 Chirality : 0.040 0.131 3302 Planarity : 0.005 0.040 3822 Dihedral : 3.573 13.065 2782 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.94 % Allowed : 10.20 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.16), residues: 2522 helix: 1.28 (0.11), residues: 2184 sheet: None (None), residues: 0 loop : 0.04 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 81 TYR 0.012 0.001 TYR M 107 PHE 0.013 0.001 PHE H 54 HIS 0.005 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00374 (21944) covalent geometry : angle 0.50767 (29614) hydrogen bonds : bond 0.04667 ( 1197) hydrogen bonds : angle 4.60204 ( 3591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 509 time to evaluate : 0.721 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: A 76 GLU cc_start: 0.7542 (mp0) cc_final: 0.7085 (mp0) REVERT: B 132 GLN cc_start: 0.8007 (tt0) cc_final: 0.7762 (tt0) REVERT: C 63 GLU cc_start: 0.7233 (mp0) cc_final: 0.6867 (mp0) REVERT: C 87 LYS cc_start: 0.7934 (tptt) cc_final: 0.7603 (tptm) REVERT: C 118 ASN cc_start: 0.7728 (m-40) cc_final: 0.7433 (m-40) REVERT: D 87 LYS cc_start: 0.7968 (tptt) cc_final: 0.7562 (tttt) REVERT: D 118 ASN cc_start: 0.7189 (m-40) cc_final: 0.6920 (m110) REVERT: D 131 MET cc_start: 0.8784 (mmm) cc_final: 0.8528 (mmm) REVERT: E 87 LYS cc_start: 0.8351 (tptt) cc_final: 0.8085 (tppt) REVERT: E 91 ASP cc_start: 0.8511 (m-30) cc_final: 0.8274 (m-30) REVERT: E 142 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7477 (mmtt) REVERT: F 142 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7786 (mtmm) REVERT: G 95 SER cc_start: 0.8968 (m) cc_final: 0.8485 (t) REVERT: H 87 LYS cc_start: 0.8385 (tptt) cc_final: 0.7808 (tttt) REVERT: H 95 SER cc_start: 0.8764 (m) cc_final: 0.8424 (t) REVERT: H 127 SER cc_start: 0.8851 (t) cc_final: 0.8640 (m) REVERT: I 95 SER cc_start: 0.8725 (m) cc_final: 0.8326 (t) REVERT: I 142 LYS cc_start: 0.8342 (mmtp) cc_final: 0.8136 (mmtt) REVERT: J 66 ASN cc_start: 0.8841 (t0) cc_final: 0.8601 (t0) REVERT: J 88 MET cc_start: 0.8363 (tpp) cc_final: 0.7976 (tpp) REVERT: J 95 SER cc_start: 0.8564 (m) cc_final: 0.8156 (t) REVERT: J 142 LYS cc_start: 0.8614 (mmtp) cc_final: 0.8389 (mmtt) REVERT: L 59 ARG cc_start: 0.6913 (mmt90) cc_final: 0.6323 (mtm180) REVERT: L 63 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6876 (mt-10) REVERT: L 88 MET cc_start: 0.7784 (tpp) cc_final: 0.7481 (tpt) REVERT: M 88 MET cc_start: 0.8056 (tpp) cc_final: 0.7598 (ttp) REVERT: N 91 ASP cc_start: 0.8234 (m-30) cc_final: 0.7815 (t70) REVERT: N 118 ASN cc_start: 0.7854 (m-40) cc_final: 0.7534 (m-40) REVERT: O 133 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7770 (mm-30) REVERT: P 76 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: P 142 LYS cc_start: 0.8219 (mmtp) cc_final: 0.7952 (mmtt) REVERT: Q 87 LYS cc_start: 0.8235 (tptt) cc_final: 0.7854 (tttp) REVERT: Q 88 MET cc_start: 0.7815 (tpp) cc_final: 0.7346 (tpp) REVERT: Q 91 ASP cc_start: 0.8609 (m-30) cc_final: 0.8381 (m-30) REVERT: Q 142 LYS cc_start: 0.8516 (mptt) cc_final: 0.8073 (mmtm) REVERT: R 88 MET cc_start: 0.6778 (ttp) cc_final: 0.6522 (tpt) REVERT: R 130 ASN cc_start: 0.6903 (m-40) cc_final: 0.6676 (m-40) REVERT: S 66 ASN cc_start: 0.7504 (t0) cc_final: 0.7156 (t0) REVERT: T 66 ASN cc_start: 0.8653 (t0) cc_final: 0.8308 (t0) REVERT: T 88 MET cc_start: 0.7868 (tpp) cc_final: 0.7368 (tpp) REVERT: T 127 SER cc_start: 0.8173 (t) cc_final: 0.7877 (m) REVERT: W 60 ASN cc_start: 0.8512 (m-40) cc_final: 0.8279 (m-40) REVERT: W 142 LYS cc_start: 0.8043 (mmtp) cc_final: 0.7734 (mmmt) REVERT: X 142 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7257 (mtmt) REVERT: Y 69 LYS cc_start: 0.8081 (pttt) cc_final: 0.7732 (ptmm) REVERT: Y 90 GLU cc_start: 0.8211 (tt0) cc_final: 0.7937 (mt-10) REVERT: Y 131 MET cc_start: 0.8372 (mmm) cc_final: 0.8153 (mmm) REVERT: Z 131 MET cc_start: 0.6357 (tpp) cc_final: 0.6151 (mpp) outliers start: 48 outliers final: 38 residues processed: 541 average time/residue: 0.1524 time to fit residues: 126.2021 Evaluate side-chains 487 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 448 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 76 GLU Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 90 GLU Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 138 ILE Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 177 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 133 optimal weight: 0.0050 chunk 130 optimal weight: 3.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 66 ASN A 130 ASN A 139 HIS B 139 HIS C 139 HIS D 56 HIS D 60 ASN G 56 HIS H 56 HIS I 66 ASN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 ASN L 130 ASN L 132 GLN M 60 ASN M 139 HIS N 60 ASN N 130 ASN N 132 GLN N 139 HIS P 60 ASN ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 HIS R 66 ASN V 66 ASN V 108 ASN X 103 GLN Z 56 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.156169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.124723 restraints weight = 36279.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122936 restraints weight = 28545.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.123789 restraints weight = 33415.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.126023 restraints weight = 24983.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126397 restraints weight = 18751.371| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 21944 Z= 0.205 Angle : 0.557 6.598 29614 Z= 0.286 Chirality : 0.043 0.138 3302 Planarity : 0.005 0.036 3822 Dihedral : 3.805 15.305 2782 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.51 % Allowed : 12.39 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.16), residues: 2522 helix: 1.44 (0.11), residues: 2132 sheet: None (None), residues: 0 loop : -0.47 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 81 TYR 0.012 0.001 TYR Z 107 PHE 0.015 0.001 PHE H 54 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00504 (21944) covalent geometry : angle 0.55712 (29614) hydrogen bonds : bond 0.04362 ( 1197) hydrogen bonds : angle 4.41604 ( 3591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 477 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7783 (mp0) cc_final: 0.7298 (mp0) REVERT: A 108 ASN cc_start: 0.8594 (m-40) cc_final: 0.8300 (m110) REVERT: A 115 LYS cc_start: 0.9124 (mtmt) cc_final: 0.8887 (mtmt) REVERT: C 87 LYS cc_start: 0.8107 (tptt) cc_final: 0.7874 (tptm) REVERT: C 118 ASN cc_start: 0.7825 (m-40) cc_final: 0.7617 (m110) REVERT: C 141 TYR cc_start: 0.7957 (t80) cc_final: 0.7671 (t80) REVERT: C 142 LYS cc_start: 0.8278 (mttp) cc_final: 0.8071 (mttm) REVERT: D 87 LYS cc_start: 0.8031 (tptt) cc_final: 0.7692 (tttt) REVERT: E 91 ASP cc_start: 0.8572 (m-30) cc_final: 0.8316 (m-30) REVERT: E 142 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7600 (mmtt) REVERT: F 142 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7935 (mtmm) REVERT: G 95 SER cc_start: 0.9023 (m) cc_final: 0.8542 (t) REVERT: H 87 LYS cc_start: 0.8470 (tptt) cc_final: 0.7860 (tttt) REVERT: H 95 SER cc_start: 0.8813 (m) cc_final: 0.8505 (t) REVERT: I 95 SER cc_start: 0.8759 (m) cc_final: 0.8340 (t) REVERT: I 142 LYS cc_start: 0.8489 (mmtp) cc_final: 0.8232 (mmtt) REVERT: J 69 LYS cc_start: 0.8156 (pttt) cc_final: 0.7629 (pttp) REVERT: J 76 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7501 (mp0) REVERT: J 88 MET cc_start: 0.8286 (tpp) cc_final: 0.7952 (tpp) REVERT: J 95 SER cc_start: 0.8581 (m) cc_final: 0.8082 (t) REVERT: L 59 ARG cc_start: 0.7023 (mmt90) cc_final: 0.6483 (mtm110) REVERT: L 63 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6869 (mt-10) REVERT: L 88 MET cc_start: 0.7912 (tpp) cc_final: 0.7100 (ttp) REVERT: M 136 ASP cc_start: 0.8077 (t70) cc_final: 0.7268 (t0) REVERT: N 49 LEU cc_start: 0.5244 (OUTLIER) cc_final: 0.5042 (pp) REVERT: N 91 ASP cc_start: 0.8295 (m-30) cc_final: 0.7856 (t70) REVERT: N 108 ASN cc_start: 0.8627 (m-40) cc_final: 0.8416 (m-40) REVERT: N 112 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7408 (mm-30) REVERT: N 118 ASN cc_start: 0.7891 (m-40) cc_final: 0.7618 (m-40) REVERT: O 112 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7697 (mp0) REVERT: O 133 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7892 (mm-30) REVERT: P 142 LYS cc_start: 0.8202 (mmtp) cc_final: 0.7912 (mmtt) REVERT: Q 87 LYS cc_start: 0.8273 (tptt) cc_final: 0.7869 (tttt) REVERT: Q 91 ASP cc_start: 0.8579 (m-30) cc_final: 0.8347 (m-30) REVERT: Q 142 LYS cc_start: 0.8629 (mptt) cc_final: 0.8322 (mmtm) REVERT: R 130 ASN cc_start: 0.6850 (m-40) cc_final: 0.6602 (m-40) REVERT: S 66 ASN cc_start: 0.7561 (t0) cc_final: 0.7198 (t0) REVERT: T 66 ASN cc_start: 0.8668 (t0) cc_final: 0.8367 (t0) REVERT: T 88 MET cc_start: 0.7688 (tpp) cc_final: 0.7309 (tpp) REVERT: T 127 SER cc_start: 0.8106 (t) cc_final: 0.7803 (m) REVERT: W 90 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: W 142 LYS cc_start: 0.8070 (mmtp) cc_final: 0.7865 (mmmt) REVERT: X 142 LYS cc_start: 0.8397 (mmtp) cc_final: 0.7382 (mtmt) REVERT: Y 69 LYS cc_start: 0.8008 (pttt) cc_final: 0.7685 (ptmm) outliers start: 62 outliers final: 50 residues processed: 520 average time/residue: 0.1500 time to fit residues: 120.9360 Evaluate side-chains 493 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 441 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 125 LEU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 90 GLU Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 127 SER Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain Y residue 127 SER Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain Z residue 127 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 126 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 223 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS B 139 HIS ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN E 139 HIS H 86 ASN I 66 ASN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 ASN L 132 GLN M 60 ASN M 139 HIS M 146 ASN N 139 HIS ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN T 132 GLN V 66 ASN V 108 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.159045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.127444 restraints weight = 36330.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.125488 restraints weight = 28539.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.127007 restraints weight = 28182.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.130189 restraints weight = 21398.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130205 restraints weight = 15750.977| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21944 Z= 0.127 Angle : 0.457 6.985 29614 Z= 0.241 Chirality : 0.039 0.129 3302 Planarity : 0.004 0.038 3822 Dihedral : 3.559 13.912 2782 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.02 % Allowed : 13.93 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.17), residues: 2522 helix: 1.68 (0.11), residues: 2158 sheet: None (None), residues: 0 loop : -0.46 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 81 TYR 0.010 0.001 TYR T 107 PHE 0.009 0.001 PHE D 54 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00301 (21944) covalent geometry : angle 0.45737 (29614) hydrogen bonds : bond 0.03359 ( 1197) hydrogen bonds : angle 4.01649 ( 3591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 455 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7793 (mp0) cc_final: 0.7296 (mp0) REVERT: A 108 ASN cc_start: 0.8555 (m-40) cc_final: 0.8258 (m110) REVERT: A 115 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8856 (mtmt) REVERT: B 86 ASN cc_start: 0.7979 (t0) cc_final: 0.7756 (p0) REVERT: C 87 LYS cc_start: 0.8069 (tptt) cc_final: 0.7672 (tptm) REVERT: C 118 ASN cc_start: 0.7737 (m-40) cc_final: 0.7533 (m110) REVERT: D 87 LYS cc_start: 0.7945 (tptt) cc_final: 0.7614 (tttt) REVERT: E 142 LYS cc_start: 0.7831 (mmtp) cc_final: 0.7509 (mmtt) REVERT: F 142 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7797 (mtmm) REVERT: G 95 SER cc_start: 0.8952 (m) cc_final: 0.8467 (t) REVERT: H 87 LYS cc_start: 0.8240 (tptt) cc_final: 0.7703 (tttt) REVERT: H 95 SER cc_start: 0.8701 (m) cc_final: 0.8402 (t) REVERT: I 59 ARG cc_start: 0.8263 (ttm110) cc_final: 0.7607 (mtp-110) REVERT: I 95 SER cc_start: 0.8695 (m) cc_final: 0.8249 (t) REVERT: J 69 LYS cc_start: 0.7985 (pttt) cc_final: 0.7476 (pttp) REVERT: J 88 MET cc_start: 0.8168 (tpp) cc_final: 0.7881 (tpp) REVERT: J 95 SER cc_start: 0.8529 (m) cc_final: 0.8003 (t) REVERT: L 59 ARG cc_start: 0.7031 (mmt90) cc_final: 0.6535 (mtm110) REVERT: L 63 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6888 (mt-10) REVERT: L 88 MET cc_start: 0.7818 (tpp) cc_final: 0.7562 (tpt) REVERT: M 115 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8308 (mtmt) REVERT: M 136 ASP cc_start: 0.8031 (t70) cc_final: 0.7205 (t0) REVERT: N 91 ASP cc_start: 0.8221 (m-30) cc_final: 0.7835 (t70) REVERT: N 108 ASN cc_start: 0.8553 (m-40) cc_final: 0.8295 (m-40) REVERT: N 112 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7325 (mm-30) REVERT: O 112 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7667 (mp0) REVERT: O 115 LYS cc_start: 0.8602 (mttp) cc_final: 0.8253 (mtmt) REVERT: O 133 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7863 (mm-30) REVERT: P 76 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: P 142 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7868 (mmpt) REVERT: Q 87 LYS cc_start: 0.8208 (tptt) cc_final: 0.7917 (tttt) REVERT: Q 88 MET cc_start: 0.7729 (tpp) cc_final: 0.7520 (tpp) REVERT: R 130 ASN cc_start: 0.6668 (m-40) cc_final: 0.6419 (m-40) REVERT: S 66 ASN cc_start: 0.7503 (t0) cc_final: 0.7137 (t0) REVERT: T 66 ASN cc_start: 0.8569 (t0) cc_final: 0.8331 (t0) REVERT: T 88 MET cc_start: 0.7539 (tpp) cc_final: 0.7335 (tpp) REVERT: T 127 SER cc_start: 0.8249 (t) cc_final: 0.7935 (m) REVERT: V 112 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7095 (mm-30) REVERT: W 60 ASN cc_start: 0.8519 (m-40) cc_final: 0.8239 (m-40) REVERT: W 90 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: W 142 LYS cc_start: 0.8108 (mmtp) cc_final: 0.7844 (mmmt) REVERT: X 112 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6985 (mm-30) REVERT: X 142 LYS cc_start: 0.8354 (mmtp) cc_final: 0.7319 (mtmt) REVERT: Y 69 LYS cc_start: 0.7824 (pttt) cc_final: 0.7507 (ptmm) REVERT: Y 90 GLU cc_start: 0.8147 (tt0) cc_final: 0.7943 (mt-10) REVERT: Y 131 MET cc_start: 0.8100 (mmm) cc_final: 0.7609 (mpp) REVERT: Y 142 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7392 (mtmt) REVERT: Z 131 MET cc_start: 0.6348 (tpp) cc_final: 0.6048 (mpp) outliers start: 50 outliers final: 40 residues processed: 488 average time/residue: 0.1460 time to fit residues: 110.1719 Evaluate side-chains 472 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 430 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 76 GLU Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 108 ASN Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 90 GLU Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 85 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 159 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 139 HIS B 132 GLN B 139 HIS C 66 ASN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS I 66 ASN J 60 ASN L 66 ASN L 132 GLN M 60 ASN N 139 HIS O 139 HIS P 130 ASN ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 HIS V 108 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.158729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.126841 restraints weight = 36134.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.125805 restraints weight = 28660.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.127357 restraints weight = 27774.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.127919 restraints weight = 20920.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.128225 restraints weight = 19698.730| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21944 Z= 0.131 Angle : 0.468 13.228 29614 Z= 0.242 Chirality : 0.039 0.129 3302 Planarity : 0.004 0.040 3822 Dihedral : 3.514 14.281 2782 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.47 % Allowed : 14.74 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.17), residues: 2522 helix: 1.79 (0.11), residues: 2158 sheet: None (None), residues: 0 loop : -0.53 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 81 TYR 0.017 0.001 TYR V 107 PHE 0.009 0.001 PHE H 54 HIS 0.004 0.001 HIS O 139 Details of bonding type rmsd covalent geometry : bond 0.00314 (21944) covalent geometry : angle 0.46783 (29614) hydrogen bonds : bond 0.03255 ( 1197) hydrogen bonds : angle 3.92123 ( 3591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 448 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7808 (mp0) cc_final: 0.7282 (mp0) REVERT: A 108 ASN cc_start: 0.8549 (m-40) cc_final: 0.8282 (m110) REVERT: C 87 LYS cc_start: 0.8039 (tptt) cc_final: 0.7617 (tptm) REVERT: C 118 ASN cc_start: 0.7759 (m-40) cc_final: 0.7552 (m110) REVERT: D 87 LYS cc_start: 0.7930 (tptt) cc_final: 0.7563 (tttt) REVERT: E 87 LYS cc_start: 0.8378 (tptt) cc_final: 0.7895 (tptt) REVERT: E 142 LYS cc_start: 0.7938 (mmtp) cc_final: 0.7546 (mmtt) REVERT: F 142 LYS cc_start: 0.8163 (mmtp) cc_final: 0.7772 (mtmm) REVERT: G 95 SER cc_start: 0.8872 (m) cc_final: 0.8314 (t) REVERT: H 87 LYS cc_start: 0.8188 (tptt) cc_final: 0.7685 (tttt) REVERT: H 95 SER cc_start: 0.8703 (m) cc_final: 0.8389 (t) REVERT: I 59 ARG cc_start: 0.8227 (ttm110) cc_final: 0.7834 (mtp-110) REVERT: I 95 SER cc_start: 0.8663 (m) cc_final: 0.8164 (t) REVERT: I 142 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8136 (mmtt) REVERT: J 69 LYS cc_start: 0.7965 (pttt) cc_final: 0.7470 (pttp) REVERT: J 88 MET cc_start: 0.8205 (tpp) cc_final: 0.7895 (tpp) REVERT: J 95 SER cc_start: 0.8524 (m) cc_final: 0.7986 (t) REVERT: L 59 ARG cc_start: 0.6985 (mmt90) cc_final: 0.6448 (mtm110) REVERT: L 63 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6810 (mt-10) REVERT: L 88 MET cc_start: 0.7764 (tpp) cc_final: 0.7507 (tpt) REVERT: M 136 ASP cc_start: 0.8094 (t70) cc_final: 0.7202 (t0) REVERT: N 91 ASP cc_start: 0.8207 (m-30) cc_final: 0.7765 (t70) REVERT: N 112 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7373 (mm-30) REVERT: O 115 LYS cc_start: 0.8644 (mttp) cc_final: 0.8265 (mtmt) REVERT: O 133 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7867 (mm-30) REVERT: P 76 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: P 131 MET cc_start: 0.8530 (tpp) cc_final: 0.8165 (mpp) REVERT: P 142 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7915 (mmtt) REVERT: Q 87 LYS cc_start: 0.8146 (tptt) cc_final: 0.7847 (tttt) REVERT: S 66 ASN cc_start: 0.7464 (t0) cc_final: 0.7127 (t0) REVERT: T 66 ASN cc_start: 0.8586 (t0) cc_final: 0.8309 (t0) REVERT: T 127 SER cc_start: 0.8162 (t) cc_final: 0.7812 (m) REVERT: W 90 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: W 142 LYS cc_start: 0.8111 (mmtp) cc_final: 0.7801 (mmmt) REVERT: X 87 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8104 (ttpp) REVERT: X 112 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6999 (mm-30) REVERT: X 142 LYS cc_start: 0.8323 (mmtp) cc_final: 0.7332 (mtmt) REVERT: Y 69 LYS cc_start: 0.7801 (pttt) cc_final: 0.7466 (ptmm) REVERT: Y 87 LYS cc_start: 0.8739 (tppt) cc_final: 0.8268 (tmtt) REVERT: Y 131 MET cc_start: 0.7968 (mmm) cc_final: 0.7518 (mpp) REVERT: Y 142 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7404 (mtmt) REVERT: Z 131 MET cc_start: 0.6295 (tpp) cc_final: 0.6045 (mpp) outliers start: 61 outliers final: 47 residues processed: 487 average time/residue: 0.1506 time to fit residues: 114.1948 Evaluate side-chains 484 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 433 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 125 LEU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 76 GLU Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 90 GLU Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 127 SER Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain Z residue 127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 225 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN B 132 GLN B 139 HIS C 60 ASN C 66 ASN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 ASN J 56 HIS L 66 ASN L 132 GLN M 60 ASN N 139 HIS ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 HIS S 132 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.160040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128131 restraints weight = 36268.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.127526 restraints weight = 30094.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.128890 restraints weight = 27571.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129461 restraints weight = 21113.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.129568 restraints weight = 20137.369| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21944 Z= 0.112 Angle : 0.445 10.211 29614 Z= 0.233 Chirality : 0.038 0.128 3302 Planarity : 0.004 0.042 3822 Dihedral : 3.447 13.534 2782 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.23 % Allowed : 15.71 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.17), residues: 2522 helix: 1.96 (0.11), residues: 2158 sheet: None (None), residues: 0 loop : -0.62 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 97 TYR 0.008 0.001 TYR T 107 PHE 0.007 0.001 PHE H 54 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00263 (21944) covalent geometry : angle 0.44546 (29614) hydrogen bonds : bond 0.02921 ( 1197) hydrogen bonds : angle 3.80448 ( 3591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 440 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7774 (mp0) cc_final: 0.7296 (mp0) REVERT: A 91 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8179 (t0) REVERT: A 108 ASN cc_start: 0.8574 (m-40) cc_final: 0.8336 (m110) REVERT: C 87 LYS cc_start: 0.7946 (tptt) cc_final: 0.7641 (tptm) REVERT: C 118 ASN cc_start: 0.7768 (m-40) cc_final: 0.7556 (m110) REVERT: D 87 LYS cc_start: 0.7833 (tptt) cc_final: 0.7501 (tttt) REVERT: E 142 LYS cc_start: 0.7894 (mmtp) cc_final: 0.7500 (mmtt) REVERT: F 142 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7771 (mtmm) REVERT: G 95 SER cc_start: 0.8934 (m) cc_final: 0.8375 (t) REVERT: H 87 LYS cc_start: 0.8083 (tptt) cc_final: 0.7596 (tttt) REVERT: H 95 SER cc_start: 0.8739 (m) cc_final: 0.8418 (t) REVERT: I 59 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7839 (mtp-110) REVERT: I 95 SER cc_start: 0.8712 (m) cc_final: 0.8209 (t) REVERT: I 142 LYS cc_start: 0.8362 (mmtp) cc_final: 0.8120 (mmtt) REVERT: J 69 LYS cc_start: 0.7905 (pttt) cc_final: 0.7424 (pttp) REVERT: J 76 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7346 (mp0) REVERT: J 88 MET cc_start: 0.8106 (tpp) cc_final: 0.7775 (tpp) REVERT: J 91 ASP cc_start: 0.8633 (m-30) cc_final: 0.8058 (m-30) REVERT: J 95 SER cc_start: 0.8565 (m) cc_final: 0.7955 (t) REVERT: L 59 ARG cc_start: 0.7122 (mmt90) cc_final: 0.6673 (mtm110) REVERT: L 63 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6884 (mt-10) REVERT: L 88 MET cc_start: 0.7789 (tpp) cc_final: 0.7564 (tpt) REVERT: M 88 MET cc_start: 0.7856 (tpp) cc_final: 0.7520 (tpp) REVERT: M 136 ASP cc_start: 0.8068 (t70) cc_final: 0.7181 (t0) REVERT: N 91 ASP cc_start: 0.8223 (m-30) cc_final: 0.7810 (t70) REVERT: N 112 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7411 (mm-30) REVERT: O 88 MET cc_start: 0.7810 (tpp) cc_final: 0.6713 (tpp) REVERT: O 115 LYS cc_start: 0.8600 (mttp) cc_final: 0.8266 (mtpt) REVERT: O 133 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7916 (mm-30) REVERT: P 76 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: P 131 MET cc_start: 0.8470 (tpp) cc_final: 0.8133 (mpp) REVERT: P 142 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7950 (mmtt) REVERT: Q 87 LYS cc_start: 0.8140 (tptt) cc_final: 0.7863 (tttp) REVERT: S 66 ASN cc_start: 0.7475 (t0) cc_final: 0.7142 (t0) REVERT: S 88 MET cc_start: 0.7161 (tpp) cc_final: 0.6893 (tpp) REVERT: T 66 ASN cc_start: 0.8581 (t0) cc_final: 0.8333 (t0) REVERT: T 127 SER cc_start: 0.8170 (t) cc_final: 0.7906 (m) REVERT: V 112 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7175 (mm-30) REVERT: W 60 ASN cc_start: 0.8451 (m-40) cc_final: 0.8213 (m-40) REVERT: W 90 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: W 142 LYS cc_start: 0.8119 (mmtp) cc_final: 0.7737 (mttt) REVERT: X 87 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8060 (ttpp) REVERT: X 112 GLU cc_start: 0.7242 (mm-30) cc_final: 0.7000 (mm-30) REVERT: X 142 LYS cc_start: 0.8332 (mmtp) cc_final: 0.7334 (mtmt) REVERT: Y 69 LYS cc_start: 0.7744 (pttt) cc_final: 0.7449 (ptmm) REVERT: Y 87 LYS cc_start: 0.8653 (tppt) cc_final: 0.8227 (tmtt) REVERT: Y 131 MET cc_start: 0.7948 (mmm) cc_final: 0.7594 (mpp) REVERT: Y 142 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7327 (mtmt) REVERT: Z 131 MET cc_start: 0.6398 (tpp) cc_final: 0.6113 (mpp) outliers start: 55 outliers final: 45 residues processed: 478 average time/residue: 0.1477 time to fit residues: 109.2470 Evaluate side-chains 478 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 428 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 125 LEU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 76 GLU Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 90 GLU Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain Z residue 127 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 224 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 139 HIS B 132 GLN B 139 HIS C 66 ASN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS I 66 ASN L 66 ASN L 132 GLN M 60 ASN N 139 HIS O 139 HIS ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 HIS S 132 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.157711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.126520 restraints weight = 36437.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124498 restraints weight = 30125.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.125913 restraints weight = 30564.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.128761 restraints weight = 22900.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.128715 restraints weight = 17299.917| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21944 Z= 0.151 Angle : 0.498 11.121 29614 Z= 0.258 Chirality : 0.040 0.129 3302 Planarity : 0.004 0.039 3822 Dihedral : 3.551 14.455 2782 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.71 % Allowed : 15.95 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.17), residues: 2522 helix: 1.83 (0.11), residues: 2158 sheet: None (None), residues: 0 loop : -0.56 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 97 TYR 0.009 0.001 TYR T 107 PHE 0.010 0.001 PHE H 54 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00368 (21944) covalent geometry : angle 0.49787 (29614) hydrogen bonds : bond 0.03352 ( 1197) hydrogen bonds : angle 3.95382 ( 3591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 446 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7830 (mp0) cc_final: 0.7316 (mp0) REVERT: A 91 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8173 (t0) REVERT: A 108 ASN cc_start: 0.8582 (m-40) cc_final: 0.8345 (m110) REVERT: C 87 LYS cc_start: 0.8008 (tptt) cc_final: 0.7604 (tptm) REVERT: C 118 ASN cc_start: 0.7793 (m-40) cc_final: 0.7585 (m110) REVERT: D 87 LYS cc_start: 0.7874 (tptt) cc_final: 0.7534 (tttt) REVERT: E 91 ASP cc_start: 0.8546 (m-30) cc_final: 0.8297 (m-30) REVERT: E 142 LYS cc_start: 0.7939 (mmtp) cc_final: 0.7543 (mmtt) REVERT: F 142 LYS cc_start: 0.8190 (mmtp) cc_final: 0.7784 (mtmm) REVERT: G 95 SER cc_start: 0.8901 (m) cc_final: 0.8339 (t) REVERT: H 87 LYS cc_start: 0.8152 (tptt) cc_final: 0.7590 (tttt) REVERT: H 95 SER cc_start: 0.8736 (m) cc_final: 0.8433 (t) REVERT: I 59 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7748 (mtp180) REVERT: I 95 SER cc_start: 0.8739 (m) cc_final: 0.8254 (t) REVERT: I 142 LYS cc_start: 0.8421 (mmtp) cc_final: 0.8135 (mmtt) REVERT: J 69 LYS cc_start: 0.8000 (pttt) cc_final: 0.7519 (pttp) REVERT: J 88 MET cc_start: 0.8209 (tpp) cc_final: 0.7970 (tpp) REVERT: J 95 SER cc_start: 0.8546 (m) cc_final: 0.8007 (t) REVERT: L 59 ARG cc_start: 0.7071 (mmt90) cc_final: 0.6618 (mtm110) REVERT: L 63 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: L 88 MET cc_start: 0.7791 (tpp) cc_final: 0.7555 (tpt) REVERT: M 132 GLN cc_start: 0.8149 (tt0) cc_final: 0.7641 (tm-30) REVERT: N 91 ASP cc_start: 0.8218 (m-30) cc_final: 0.7810 (t70) REVERT: N 112 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7375 (mm-30) REVERT: O 115 LYS cc_start: 0.8634 (mttp) cc_final: 0.8354 (mtpt) REVERT: O 133 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7902 (mm-30) REVERT: P 76 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: P 131 MET cc_start: 0.8455 (tpp) cc_final: 0.8145 (mpp) REVERT: Q 63 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: Q 87 LYS cc_start: 0.8142 (tptt) cc_final: 0.7852 (tttt) REVERT: S 66 ASN cc_start: 0.7407 (t0) cc_final: 0.7077 (t0) REVERT: S 88 MET cc_start: 0.7132 (tpp) cc_final: 0.6879 (tpp) REVERT: T 66 ASN cc_start: 0.8588 (t0) cc_final: 0.8324 (t0) REVERT: T 127 SER cc_start: 0.8183 (t) cc_final: 0.7792 (m) REVERT: W 142 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7782 (mttt) REVERT: X 112 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7135 (mm-30) REVERT: X 142 LYS cc_start: 0.8414 (mmtp) cc_final: 0.7357 (mtmt) REVERT: Y 69 LYS cc_start: 0.7789 (pttt) cc_final: 0.7467 (ptmm) REVERT: Y 87 LYS cc_start: 0.8707 (tppt) cc_final: 0.8274 (tmtt) REVERT: Y 131 MET cc_start: 0.7959 (mmm) cc_final: 0.7584 (mpp) REVERT: Y 142 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7334 (mtmt) REVERT: Z 131 MET cc_start: 0.6342 (tpp) cc_final: 0.6095 (mpp) outliers start: 67 outliers final: 50 residues processed: 491 average time/residue: 0.1460 time to fit residues: 111.1609 Evaluate side-chains 490 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 436 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 125 LEU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 76 GLU Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 90 GLU Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 127 SER Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain Z residue 127 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 123 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 205 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN B 132 GLN B 139 HIS C 66 ASN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS D 103 GLN L 132 GLN M 60 ASN N 139 HIS ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 66 ASN X 103 GLN AA 66 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.154508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.122521 restraints weight = 36453.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.119926 restraints weight = 29967.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120893 restraints weight = 33142.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123572 restraints weight = 24890.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.123762 restraints weight = 18529.316| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 21944 Z= 0.227 Angle : 0.596 11.882 29614 Z= 0.303 Chirality : 0.044 0.132 3302 Planarity : 0.005 0.037 3822 Dihedral : 3.879 16.602 2782 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.71 % Allowed : 16.36 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.16), residues: 2522 helix: 1.44 (0.11), residues: 2106 sheet: None (None), residues: 0 loop : -0.89 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 59 TYR 0.011 0.001 TYR P 107 PHE 0.015 0.001 PHE H 54 HIS 0.005 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00558 (21944) covalent geometry : angle 0.59557 (29614) hydrogen bonds : bond 0.04138 ( 1197) hydrogen bonds : angle 4.29130 ( 3591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 457 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7870 (mp0) cc_final: 0.7318 (mp0) REVERT: A 108 ASN cc_start: 0.8620 (m-40) cc_final: 0.8361 (m110) REVERT: A 115 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8614 (mttp) REVERT: B 63 GLU cc_start: 0.7447 (mp0) cc_final: 0.7082 (mp0) REVERT: B 82 ASP cc_start: 0.8435 (t0) cc_final: 0.8159 (t0) REVERT: C 76 GLU cc_start: 0.8075 (mp0) cc_final: 0.7864 (mp0) REVERT: C 87 LYS cc_start: 0.8115 (tptt) cc_final: 0.7849 (tptm) REVERT: D 87 LYS cc_start: 0.7927 (tptt) cc_final: 0.7628 (tttt) REVERT: E 87 LYS cc_start: 0.8432 (tptt) cc_final: 0.8089 (tppt) REVERT: E 91 ASP cc_start: 0.8691 (m-30) cc_final: 0.8369 (m-30) REVERT: E 142 LYS cc_start: 0.8019 (mmtp) cc_final: 0.7634 (mmtt) REVERT: F 60 ASN cc_start: 0.8308 (m-40) cc_final: 0.8070 (m-40) REVERT: F 142 LYS cc_start: 0.8202 (mmtp) cc_final: 0.7793 (mtmm) REVERT: G 95 SER cc_start: 0.8975 (m) cc_final: 0.8408 (t) REVERT: H 87 LYS cc_start: 0.8284 (tptt) cc_final: 0.7735 (tttt) REVERT: H 95 SER cc_start: 0.8812 (m) cc_final: 0.8468 (t) REVERT: I 59 ARG cc_start: 0.8382 (ttm110) cc_final: 0.7795 (mtp180) REVERT: I 95 SER cc_start: 0.8746 (m) cc_final: 0.8359 (t) REVERT: J 69 LYS cc_start: 0.8069 (pttt) cc_final: 0.7580 (pttp) REVERT: J 88 MET cc_start: 0.8256 (tpp) cc_final: 0.8001 (tpp) REVERT: J 95 SER cc_start: 0.8626 (m) cc_final: 0.8120 (t) REVERT: L 59 ARG cc_start: 0.6934 (mmt90) cc_final: 0.6436 (mtm110) REVERT: L 88 MET cc_start: 0.7810 (tpp) cc_final: 0.7545 (tpt) REVERT: M 132 GLN cc_start: 0.8283 (tt0) cc_final: 0.7749 (tm-30) REVERT: M 136 ASP cc_start: 0.8169 (t70) cc_final: 0.7258 (t0) REVERT: N 91 ASP cc_start: 0.8307 (m-30) cc_final: 0.7865 (t70) REVERT: N 112 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7348 (mm-30) REVERT: O 115 LYS cc_start: 0.8704 (mttp) cc_final: 0.8464 (mtpt) REVERT: O 133 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7903 (mm-30) REVERT: P 76 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: P 131 MET cc_start: 0.8406 (tpp) cc_final: 0.8082 (mpp) REVERT: Q 63 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: Q 87 LYS cc_start: 0.8069 (tptt) cc_final: 0.7600 (tttt) REVERT: Q 91 ASP cc_start: 0.8589 (m-30) cc_final: 0.8323 (m-30) REVERT: R 59 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7430 (ttm110) REVERT: S 66 ASN cc_start: 0.7486 (t0) cc_final: 0.7133 (t0) REVERT: T 66 ASN cc_start: 0.8627 (t0) cc_final: 0.8367 (t0) REVERT: T 127 SER cc_start: 0.8196 (t) cc_final: 0.7829 (m) REVERT: T 128 ASP cc_start: 0.7303 (t0) cc_final: 0.7076 (t0) REVERT: V 112 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7127 (mm-30) REVERT: W 90 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: W 142 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7808 (mttt) REVERT: X 142 LYS cc_start: 0.8415 (mmtp) cc_final: 0.7373 (mtmt) REVERT: Y 69 LYS cc_start: 0.7892 (pttt) cc_final: 0.7559 (ptmm) REVERT: Y 87 LYS cc_start: 0.8700 (tppt) cc_final: 0.8282 (tmtt) REVERT: Y 112 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7119 (mm-30) REVERT: Y 131 MET cc_start: 0.7848 (mmm) cc_final: 0.7488 (mpp) REVERT: Y 142 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7346 (mtmt) REVERT: AA 88 MET cc_start: 0.6500 (tpp) cc_final: 0.6225 (tpp) outliers start: 67 outliers final: 54 residues processed: 504 average time/residue: 0.1462 time to fit residues: 114.1894 Evaluate side-chains 501 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 444 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 125 LEU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 76 GLU Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 90 GLU Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain Y residue 127 SER Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain Z residue 127 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 164 optimal weight: 0.4980 chunk 168 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS B 132 GLN B 139 HIS ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS H 66 ASN I 66 ASN L 66 ASN L 132 GLN M 60 ASN N 139 HIS O 139 HIS ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 HIS R 66 ASN ** T 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN AA 66 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.159094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127591 restraints weight = 36326.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126689 restraints weight = 27890.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.128333 restraints weight = 27762.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128857 restraints weight = 20076.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129155 restraints weight = 18839.611| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21944 Z= 0.120 Angle : 0.484 12.657 29614 Z= 0.254 Chirality : 0.038 0.134 3302 Planarity : 0.004 0.042 3822 Dihedral : 3.621 14.968 2782 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.23 % Allowed : 17.17 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.16), residues: 2522 helix: 1.75 (0.11), residues: 2106 sheet: None (None), residues: 0 loop : -0.85 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 59 TYR 0.008 0.001 TYR Q 141 PHE 0.007 0.001 PHE G 54 HIS 0.005 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00283 (21944) covalent geometry : angle 0.48443 (29614) hydrogen bonds : bond 0.03030 ( 1197) hydrogen bonds : angle 3.96309 ( 3591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 441 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7834 (mp0) cc_final: 0.7319 (mp0) REVERT: A 108 ASN cc_start: 0.8558 (m-40) cc_final: 0.8295 (m110) REVERT: A 112 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7181 (tt0) REVERT: B 131 MET cc_start: 0.8022 (mmt) cc_final: 0.7791 (mmt) REVERT: D 87 LYS cc_start: 0.7779 (tptt) cc_final: 0.7493 (tttt) REVERT: E 142 LYS cc_start: 0.7890 (mmtp) cc_final: 0.7452 (mmtt) REVERT: F 142 LYS cc_start: 0.8147 (mmtp) cc_final: 0.7742 (mtmm) REVERT: G 95 SER cc_start: 0.8877 (m) cc_final: 0.8291 (t) REVERT: H 87 LYS cc_start: 0.7995 (tptt) cc_final: 0.7481 (tttt) REVERT: H 95 SER cc_start: 0.8700 (m) cc_final: 0.8357 (t) REVERT: I 59 ARG cc_start: 0.8259 (ttm110) cc_final: 0.7705 (mtp-110) REVERT: I 95 SER cc_start: 0.8663 (m) cc_final: 0.8180 (t) REVERT: I 142 LYS cc_start: 0.8345 (mmtp) cc_final: 0.8103 (mmtt) REVERT: J 69 LYS cc_start: 0.7964 (pttt) cc_final: 0.7583 (pttp) REVERT: J 76 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7549 (mp0) REVERT: J 88 MET cc_start: 0.8106 (tpp) cc_final: 0.7779 (tpp) REVERT: J 91 ASP cc_start: 0.8718 (m-30) cc_final: 0.8118 (m-30) REVERT: J 95 SER cc_start: 0.8580 (m) cc_final: 0.7980 (t) REVERT: L 59 ARG cc_start: 0.7025 (mmt90) cc_final: 0.6587 (mtm110) REVERT: L 63 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6441 (mt-10) REVERT: M 132 GLN cc_start: 0.8259 (tt0) cc_final: 0.7793 (tm-30) REVERT: N 91 ASP cc_start: 0.8209 (m-30) cc_final: 0.7837 (t70) REVERT: N 112 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7374 (mm-30) REVERT: O 115 LYS cc_start: 0.8659 (mttp) cc_final: 0.8437 (mtpt) REVERT: O 133 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7898 (mm-30) REVERT: P 76 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: P 131 MET cc_start: 0.8337 (tpp) cc_final: 0.8054 (mpp) REVERT: Q 63 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: Q 87 LYS cc_start: 0.8089 (tptt) cc_final: 0.7780 (tttt) REVERT: R 59 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7471 (ttm110) REVERT: S 66 ASN cc_start: 0.7438 (t0) cc_final: 0.7107 (t0) REVERT: S 88 MET cc_start: 0.7332 (tpp) cc_final: 0.7086 (tpp) REVERT: S 128 ASP cc_start: 0.7094 (t0) cc_final: 0.6761 (t0) REVERT: T 66 ASN cc_start: 0.8575 (t0) cc_final: 0.8332 (t0) REVERT: V 112 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7187 (mm-30) REVERT: W 60 ASN cc_start: 0.8429 (m-40) cc_final: 0.8153 (m-40) REVERT: W 142 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7737 (mttt) REVERT: X 142 LYS cc_start: 0.8360 (mmtp) cc_final: 0.7332 (mtmt) REVERT: Y 69 LYS cc_start: 0.7760 (pttt) cc_final: 0.7456 (ptmm) REVERT: Y 87 LYS cc_start: 0.8566 (tppt) cc_final: 0.8173 (tmtt) REVERT: Y 112 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7126 (mm-30) REVERT: Y 131 MET cc_start: 0.7752 (mmm) cc_final: 0.7492 (mpp) REVERT: Y 142 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7325 (mtmt) outliers start: 55 outliers final: 44 residues processed: 483 average time/residue: 0.1455 time to fit residues: 109.4134 Evaluate side-chains 477 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 431 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 125 LEU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 76 GLU Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 90 GLU Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain Z residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 58 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 216 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 139 HIS ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS I 66 ASN L 66 ASN L 132 GLN M 60 ASN N 139 HIS ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 HIS R 66 ASN T 66 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.157147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125211 restraints weight = 36546.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.122469 restraints weight = 29683.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.123839 restraints weight = 29819.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125273 restraints weight = 22972.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.125444 restraints weight = 19987.544| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21944 Z= 0.155 Angle : 0.525 12.975 29614 Z= 0.273 Chirality : 0.040 0.129 3302 Planarity : 0.004 0.041 3822 Dihedral : 3.706 15.549 2782 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.15 % Allowed : 17.00 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.16), residues: 2522 helix: 1.66 (0.11), residues: 2106 sheet: None (None), residues: 0 loop : -0.86 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 59 TYR 0.009 0.001 TYR P 107 PHE 0.009 0.001 PHE H 54 HIS 0.004 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00377 (21944) covalent geometry : angle 0.52462 (29614) hydrogen bonds : bond 0.03435 ( 1197) hydrogen bonds : angle 4.08824 ( 3591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 433 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7866 (mp0) cc_final: 0.7353 (mp0) REVERT: A 108 ASN cc_start: 0.8612 (m-40) cc_final: 0.8389 (m110) REVERT: A 112 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7168 (tt0) REVERT: B 82 ASP cc_start: 0.8350 (t0) cc_final: 0.8090 (t0) REVERT: D 87 LYS cc_start: 0.7792 (tptt) cc_final: 0.7535 (tttt) REVERT: E 91 ASP cc_start: 0.8562 (m-30) cc_final: 0.8245 (m-30) REVERT: E 142 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7518 (mmtt) REVERT: F 142 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7747 (mtmm) REVERT: G 95 SER cc_start: 0.8914 (m) cc_final: 0.8364 (t) REVERT: H 87 LYS cc_start: 0.8069 (tptt) cc_final: 0.7545 (tttt) REVERT: H 95 SER cc_start: 0.8743 (m) cc_final: 0.8447 (t) REVERT: I 59 ARG cc_start: 0.8268 (ttm110) cc_final: 0.7705 (mtp-110) REVERT: I 95 SER cc_start: 0.8764 (m) cc_final: 0.8294 (t) REVERT: I 142 LYS cc_start: 0.8380 (mmtp) cc_final: 0.8141 (mmtt) REVERT: J 69 LYS cc_start: 0.8033 (pttt) cc_final: 0.7572 (pttp) REVERT: J 88 MET cc_start: 0.8074 (tpp) cc_final: 0.7793 (tpp) REVERT: J 91 ASP cc_start: 0.8742 (m-30) cc_final: 0.8141 (m-30) REVERT: J 95 SER cc_start: 0.8581 (m) cc_final: 0.8025 (t) REVERT: L 59 ARG cc_start: 0.6970 (mmt90) cc_final: 0.6494 (mtm110) REVERT: L 63 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6376 (mt-10) REVERT: M 132 GLN cc_start: 0.8345 (tt0) cc_final: 0.7843 (tm-30) REVERT: N 91 ASP cc_start: 0.8247 (m-30) cc_final: 0.7881 (t70) REVERT: N 112 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7344 (mm-30) REVERT: O 133 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7946 (mm-30) REVERT: P 76 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: P 131 MET cc_start: 0.8340 (tpp) cc_final: 0.8067 (mpp) REVERT: Q 63 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7102 (mt-10) REVERT: Q 87 LYS cc_start: 0.8104 (tptt) cc_final: 0.7778 (tttt) REVERT: R 59 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7393 (ttm110) REVERT: S 66 ASN cc_start: 0.7384 (t0) cc_final: 0.7061 (t0) REVERT: S 88 MET cc_start: 0.7166 (tpp) cc_final: 0.6944 (tpp) REVERT: S 128 ASP cc_start: 0.7073 (t0) cc_final: 0.6693 (t0) REVERT: S 132 GLN cc_start: 0.8534 (mp10) cc_final: 0.8195 (mp10) REVERT: T 66 ASN cc_start: 0.8588 (t0) cc_final: 0.8320 (t0) REVERT: V 112 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7145 (mm-30) REVERT: W 60 ASN cc_start: 0.8457 (m-40) cc_final: 0.8177 (m-40) REVERT: W 142 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7783 (mttt) REVERT: X 87 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8110 (ttpp) REVERT: X 141 TYR cc_start: 0.8543 (t80) cc_final: 0.8214 (t80) REVERT: X 142 LYS cc_start: 0.8394 (mmtp) cc_final: 0.7347 (mtmt) REVERT: Y 69 LYS cc_start: 0.7822 (pttt) cc_final: 0.7503 (ptmm) REVERT: Y 87 LYS cc_start: 0.8587 (tppt) cc_final: 0.8170 (tmtt) REVERT: Y 131 MET cc_start: 0.7735 (mmm) cc_final: 0.7488 (mpp) REVERT: Y 142 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7280 (mtmt) outliers start: 53 outliers final: 47 residues processed: 473 average time/residue: 0.1477 time to fit residues: 108.4247 Evaluate side-chains 480 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 430 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 125 LEU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 76 GLU Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 90 GLU Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 85 THR Chi-restraints excluded: chain Y residue 127 SER Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain Z residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 2 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 90 optimal weight: 40.0000 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS B 139 HIS ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS I 66 ASN L 66 ASN L 132 GLN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 HIS O 139 HIS ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 HIS T 66 ASN Y 60 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.157547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126153 restraints weight = 36468.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.123502 restraints weight = 29937.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.124951 restraints weight = 29956.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127639 restraints weight = 22334.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127675 restraints weight = 16862.077| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 21944 Z= 0.156 Angle : 0.684 59.200 29614 Z= 0.386 Chirality : 0.040 0.354 3302 Planarity : 0.005 0.071 3822 Dihedral : 3.712 21.656 2782 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.98 % Rotamer: Outliers : 2.27 % Allowed : 17.45 % Favored : 80.28 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.17), residues: 2522 helix: 1.67 (0.11), residues: 2106 sheet: None (None), residues: 0 loop : -0.85 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 59 TYR 0.009 0.001 TYR P 107 PHE 0.008 0.001 PHE H 54 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00357 (21944) covalent geometry : angle 0.68364 (29614) hydrogen bonds : bond 0.03443 ( 1197) hydrogen bonds : angle 4.10220 ( 3591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3556.05 seconds wall clock time: 62 minutes 6.33 seconds (3726.33 seconds total)