Starting phenix.real_space_refine on Thu Nov 20 00:17:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mdr_9104/11_2025/6mdr_9104.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mdr_9104/11_2025/6mdr_9104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mdr_9104/11_2025/6mdr_9104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mdr_9104/11_2025/6mdr_9104.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mdr_9104/11_2025/6mdr_9104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mdr_9104/11_2025/6mdr_9104.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 80 5.16 5 C 18688 2.51 5 N 5232 2.21 5 O 5456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29456 Number of models: 1 Model: "" Number of chains: 2 Chain: "a" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1852 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain: "b" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1830 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Restraints were copied for chains: c, e, g, i, k, m, o, d, f, h, j, l, n, p Time building chain proxies: 3.47, per 1000 atoms: 0.12 Number of scatterers: 29456 At special positions: 0 Unit cell: (155.1, 155.1, 100.1, 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 80 16.00 O 5456 8.00 N 5232 7.00 C 18688 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: 2.14 Conformation dependent library (CDL) restraints added in 981.0 milliseconds 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6672 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 16 sheets defined 11.7% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'a' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG a 10 " --> pdb=" O ARG a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 60 Processing helix chain 'a' and resid 61 through 66 Processing helix chain 'a' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER a 87 " --> pdb=" O ASP a 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 11 removed outlier: 3.533A pdb=" N PHE b 10 " --> pdb=" O GLU b 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR b 11 " --> pdb=" O GLU b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL b 63 " --> pdb=" O PRO b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 74 removed outlier: 4.184A pdb=" N PHE b 73 " --> pdb=" O VAL b 70 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS b 81 " --> pdb=" O ASP b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 89 removed outlier: 3.629A pdb=" N SER b 88 " --> pdb=" O ASP b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 158 through 161 Processing helix chain 'c' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG c 10 " --> pdb=" O ARG c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 57 through 60 Processing helix chain 'c' and resid 61 through 66 Processing helix chain 'c' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER c 87 " --> pdb=" O ASP c 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 11 removed outlier: 3.533A pdb=" N PHE d 10 " --> pdb=" O GLU d 7 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR d 11 " --> pdb=" O GLU d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL d 63 " --> pdb=" O PRO d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 74 removed outlier: 4.185A pdb=" N PHE d 73 " --> pdb=" O VAL d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS d 81 " --> pdb=" O ASP d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 89 removed outlier: 3.630A pdb=" N SER d 88 " --> pdb=" O ASP d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 158 through 161 Processing helix chain 'e' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG e 10 " --> pdb=" O ARG e 7 " (cutoff:3.500A) Processing helix chain 'e' and resid 57 through 60 Processing helix chain 'e' and resid 61 through 66 Processing helix chain 'e' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER e 87 " --> pdb=" O ASP e 83 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 11 removed outlier: 3.533A pdb=" N PHE f 10 " --> pdb=" O GLU f 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR f 11 " --> pdb=" O GLU f 8 " (cutoff:3.500A) Processing helix chain 'f' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL f 63 " --> pdb=" O PRO f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 74 removed outlier: 4.185A pdb=" N PHE f 73 " --> pdb=" O VAL f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 81 removed outlier: 3.870A pdb=" N LYS f 81 " --> pdb=" O ASP f 78 " (cutoff:3.500A) Processing helix chain 'f' and resid 84 through 89 removed outlier: 3.629A pdb=" N SER f 88 " --> pdb=" O ASP f 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 158 through 161 Processing helix chain 'g' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG g 10 " --> pdb=" O ARG g 7 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 60 Processing helix chain 'g' and resid 61 through 66 Processing helix chain 'g' and resid 83 through 88 removed outlier: 3.776A pdb=" N SER g 87 " --> pdb=" O ASP g 83 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 11 removed outlier: 3.532A pdb=" N PHE h 10 " --> pdb=" O GLU h 7 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR h 11 " --> pdb=" O GLU h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL h 63 " --> pdb=" O PRO h 60 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 74 removed outlier: 4.184A pdb=" N PHE h 73 " --> pdb=" O VAL h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS h 81 " --> pdb=" O ASP h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 89 removed outlier: 3.629A pdb=" N SER h 88 " --> pdb=" O ASP h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 158 through 161 Processing helix chain 'i' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG i 10 " --> pdb=" O ARG i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 57 through 60 Processing helix chain 'i' and resid 61 through 66 Processing helix chain 'i' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER i 87 " --> pdb=" O ASP i 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 6 through 11 removed outlier: 3.533A pdb=" N PHE j 10 " --> pdb=" O GLU j 7 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR j 11 " --> pdb=" O GLU j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 63 removed outlier: 3.594A pdb=" N VAL j 63 " --> pdb=" O PRO j 60 " (cutoff:3.500A) Processing helix chain 'j' and resid 70 through 74 removed outlier: 4.185A pdb=" N PHE j 73 " --> pdb=" O VAL j 70 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS j 81 " --> pdb=" O ASP j 78 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 89 removed outlier: 3.630A pdb=" N SER j 88 " --> pdb=" O ASP j 84 " (cutoff:3.500A) Processing helix chain 'j' and resid 158 through 161 Processing helix chain 'k' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG k 10 " --> pdb=" O ARG k 7 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 60 Processing helix chain 'k' and resid 61 through 66 Processing helix chain 'k' and resid 83 through 88 removed outlier: 3.774A pdb=" N SER k 87 " --> pdb=" O ASP k 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 11 removed outlier: 3.533A pdb=" N PHE l 10 " --> pdb=" O GLU l 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR l 11 " --> pdb=" O GLU l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL l 63 " --> pdb=" O PRO l 60 " (cutoff:3.500A) Processing helix chain 'l' and resid 70 through 74 removed outlier: 4.184A pdb=" N PHE l 73 " --> pdb=" O VAL l 70 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS l 81 " --> pdb=" O ASP l 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 84 through 89 removed outlier: 3.630A pdb=" N SER l 88 " --> pdb=" O ASP l 84 " (cutoff:3.500A) Processing helix chain 'l' and resid 158 through 161 Processing helix chain 'm' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG m 10 " --> pdb=" O ARG m 7 " (cutoff:3.500A) Processing helix chain 'm' and resid 57 through 60 Processing helix chain 'm' and resid 61 through 66 Processing helix chain 'm' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER m 87 " --> pdb=" O ASP m 83 " (cutoff:3.500A) Processing helix chain 'n' and resid 6 through 11 removed outlier: 3.532A pdb=" N PHE n 10 " --> pdb=" O GLU n 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR n 11 " --> pdb=" O GLU n 8 " (cutoff:3.500A) Processing helix chain 'n' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL n 63 " --> pdb=" O PRO n 60 " (cutoff:3.500A) Processing helix chain 'n' and resid 70 through 74 removed outlier: 4.184A pdb=" N PHE n 73 " --> pdb=" O VAL n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 77 through 81 removed outlier: 3.870A pdb=" N LYS n 81 " --> pdb=" O ASP n 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 84 through 89 removed outlier: 3.630A pdb=" N SER n 88 " --> pdb=" O ASP n 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 158 through 161 Processing helix chain 'o' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG o 10 " --> pdb=" O ARG o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 57 through 60 Processing helix chain 'o' and resid 61 through 66 Processing helix chain 'o' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER o 87 " --> pdb=" O ASP o 83 " (cutoff:3.500A) Processing helix chain 'p' and resid 6 through 11 removed outlier: 3.532A pdb=" N PHE p 10 " --> pdb=" O GLU p 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR p 11 " --> pdb=" O GLU p 8 " (cutoff:3.500A) Processing helix chain 'p' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL p 63 " --> pdb=" O PRO p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 74 removed outlier: 4.185A pdb=" N PHE p 73 " --> pdb=" O VAL p 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS p 81 " --> pdb=" O ASP p 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 84 through 89 removed outlier: 3.630A pdb=" N SER p 88 " --> pdb=" O ASP p 84 " (cutoff:3.500A) Processing helix chain 'p' and resid 158 through 161 Processing sheet with id=AA1, first strand: chain 'a' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER a 148 " --> pdb=" O ARG a 169 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG a 169 " --> pdb=" O SER a 148 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS a 150 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS a 167 " --> pdb=" O LYS a 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR a 152 " --> pdb=" O LYS a 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR a 183 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR a 119 " --> pdb=" O GLU a 116 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN a 122 " --> pdb=" O PRO a 14 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU a 16 " --> pdb=" O ASN a 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE a 124 " --> pdb=" O LEU a 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU a 18 " --> pdb=" O ILE a 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU a 126 " --> pdb=" O GLU a 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS a 20 " --> pdb=" O LEU a 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY a 128 " --> pdb=" O LYS a 20 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP a 22 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 14 through 24 removed outlier: 7.973A pdb=" N ASN b 123 " --> pdb=" O PRO b 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU b 17 " --> pdb=" O ASN b 123 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE b 125 " --> pdb=" O LEU b 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU b 19 " --> pdb=" O ILE b 125 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR b 120 " --> pdb=" O GLU b 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG b 124 " --> pdb=" O GLU b 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 178 through 189 current: chain 'b' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL b 221 " --> pdb=" O SER b 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU b 151 " --> pdb=" O LYS b 168 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS b 168 " --> pdb=" O GLU b 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR b 153 " --> pdb=" O GLU b 166 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU b 166 " --> pdb=" O TYR b 153 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE b 167 " --> pdb=" O HIS b 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 178 through 189 current: chain 'b' and resid 107 through 109 Processing sheet with id=AA3, first strand: chain 'c' and resid 13 through 23 removed outlier: 6.122A pdb=" N SER c 148 " --> pdb=" O ARG c 169 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG c 169 " --> pdb=" O SER c 148 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS c 150 " --> pdb=" O LYS c 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS c 167 " --> pdb=" O LYS c 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR c 152 " --> pdb=" O LYS c 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR c 183 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR c 119 " --> pdb=" O GLU c 116 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN c 122 " --> pdb=" O PRO c 14 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU c 16 " --> pdb=" O ASN c 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE c 124 " --> pdb=" O LEU c 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU c 18 " --> pdb=" O ILE c 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU c 126 " --> pdb=" O GLU c 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS c 20 " --> pdb=" O LEU c 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY c 128 " --> pdb=" O LYS c 20 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP c 22 " --> pdb=" O GLY c 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 14 through 24 removed outlier: 7.974A pdb=" N ASN d 123 " --> pdb=" O PRO d 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU d 17 " --> pdb=" O ASN d 123 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE d 125 " --> pdb=" O LEU d 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU d 19 " --> pdb=" O ILE d 125 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR d 120 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG d 124 " --> pdb=" O GLU d 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 178 through 189 current: chain 'd' and resid 27 through 37 removed outlier: 3.538A pdb=" N VAL d 221 " --> pdb=" O SER d 210 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU d 151 " --> pdb=" O LYS d 168 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS d 168 " --> pdb=" O GLU d 151 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR d 153 " --> pdb=" O GLU d 166 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU d 166 " --> pdb=" O TYR d 153 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE d 167 " --> pdb=" O HIS d 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 178 through 189 current: chain 'd' and resid 107 through 109 Processing sheet with id=AA5, first strand: chain 'e' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER e 148 " --> pdb=" O ARG e 169 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG e 169 " --> pdb=" O SER e 148 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS e 150 " --> pdb=" O LYS e 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS e 167 " --> pdb=" O LYS e 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR e 152 " --> pdb=" O LYS e 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR e 183 " --> pdb=" O THR e 98 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR e 119 " --> pdb=" O GLU e 116 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN e 122 " --> pdb=" O PRO e 14 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU e 16 " --> pdb=" O ASN e 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE e 124 " --> pdb=" O LEU e 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU e 18 " --> pdb=" O ILE e 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU e 126 " --> pdb=" O GLU e 18 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS e 20 " --> pdb=" O LEU e 126 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLY e 128 " --> pdb=" O LYS e 20 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP e 22 " --> pdb=" O GLY e 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 14 through 24 removed outlier: 7.973A pdb=" N ASN f 123 " --> pdb=" O PRO f 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU f 17 " --> pdb=" O ASN f 123 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE f 125 " --> pdb=" O LEU f 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU f 19 " --> pdb=" O ILE f 125 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR f 120 " --> pdb=" O GLU f 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG f 124 " --> pdb=" O GLU f 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 178 through 189 current: chain 'f' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL f 221 " --> pdb=" O SER f 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU f 151 " --> pdb=" O LYS f 168 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS f 168 " --> pdb=" O GLU f 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR f 153 " --> pdb=" O GLU f 166 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU f 166 " --> pdb=" O TYR f 153 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE f 167 " --> pdb=" O HIS f 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 178 through 189 current: chain 'f' and resid 107 through 109 Processing sheet with id=AA7, first strand: chain 'g' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER g 148 " --> pdb=" O ARG g 169 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG g 169 " --> pdb=" O SER g 148 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS g 150 " --> pdb=" O LYS g 167 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS g 167 " --> pdb=" O LYS g 150 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR g 152 " --> pdb=" O LYS g 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR g 183 " --> pdb=" O THR g 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR g 119 " --> pdb=" O GLU g 116 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN g 122 " --> pdb=" O PRO g 14 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU g 16 " --> pdb=" O ASN g 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE g 124 " --> pdb=" O LEU g 16 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU g 18 " --> pdb=" O ILE g 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU g 126 " --> pdb=" O GLU g 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS g 20 " --> pdb=" O LEU g 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY g 128 " --> pdb=" O LYS g 20 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP g 22 " --> pdb=" O GLY g 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 14 through 24 removed outlier: 7.973A pdb=" N ASN h 123 " --> pdb=" O PRO h 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU h 17 " --> pdb=" O ASN h 123 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE h 125 " --> pdb=" O LEU h 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU h 19 " --> pdb=" O ILE h 125 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR h 120 " --> pdb=" O GLU h 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG h 124 " --> pdb=" O GLU h 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 178 through 189 current: chain 'h' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL h 221 " --> pdb=" O SER h 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU h 151 " --> pdb=" O LYS h 168 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS h 168 " --> pdb=" O GLU h 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR h 153 " --> pdb=" O GLU h 166 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU h 166 " --> pdb=" O TYR h 153 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE h 167 " --> pdb=" O HIS h 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 178 through 189 current: chain 'h' and resid 107 through 109 Processing sheet with id=AA9, first strand: chain 'i' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER i 148 " --> pdb=" O ARG i 169 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG i 169 " --> pdb=" O SER i 148 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS i 150 " --> pdb=" O LYS i 167 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS i 167 " --> pdb=" O LYS i 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR i 152 " --> pdb=" O LYS i 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR i 183 " --> pdb=" O THR i 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR i 119 " --> pdb=" O GLU i 116 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN i 122 " --> pdb=" O PRO i 14 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU i 16 " --> pdb=" O ASN i 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE i 124 " --> pdb=" O LEU i 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU i 18 " --> pdb=" O ILE i 124 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU i 126 " --> pdb=" O GLU i 18 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS i 20 " --> pdb=" O LEU i 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY i 128 " --> pdb=" O LYS i 20 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP i 22 " --> pdb=" O GLY i 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'j' and resid 14 through 24 removed outlier: 7.974A pdb=" N ASN j 123 " --> pdb=" O PRO j 15 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU j 17 " --> pdb=" O ASN j 123 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE j 125 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU j 19 " --> pdb=" O ILE j 125 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR j 120 " --> pdb=" O GLU j 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG j 124 " --> pdb=" O GLU j 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 178 through 189 current: chain 'j' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL j 221 " --> pdb=" O SER j 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU j 151 " --> pdb=" O LYS j 168 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS j 168 " --> pdb=" O GLU j 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR j 153 " --> pdb=" O GLU j 166 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU j 166 " --> pdb=" O TYR j 153 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE j 167 " --> pdb=" O HIS j 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 178 through 189 current: chain 'j' and resid 107 through 109 Processing sheet with id=AB2, first strand: chain 'k' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER k 148 " --> pdb=" O ARG k 169 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG k 169 " --> pdb=" O SER k 148 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS k 150 " --> pdb=" O LYS k 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS k 167 " --> pdb=" O LYS k 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR k 152 " --> pdb=" O LYS k 165 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR k 183 " --> pdb=" O THR k 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR k 119 " --> pdb=" O GLU k 116 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN k 122 " --> pdb=" O PRO k 14 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU k 16 " --> pdb=" O ASN k 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE k 124 " --> pdb=" O LEU k 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU k 18 " --> pdb=" O ILE k 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU k 126 " --> pdb=" O GLU k 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS k 20 " --> pdb=" O LEU k 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY k 128 " --> pdb=" O LYS k 20 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP k 22 " --> pdb=" O GLY k 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'l' and resid 14 through 24 removed outlier: 7.974A pdb=" N ASN l 123 " --> pdb=" O PRO l 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU l 17 " --> pdb=" O ASN l 123 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE l 125 " --> pdb=" O LEU l 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU l 19 " --> pdb=" O ILE l 125 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR l 120 " --> pdb=" O GLU l 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG l 124 " --> pdb=" O GLU l 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 178 through 189 current: chain 'l' and resid 27 through 37 removed outlier: 3.538A pdb=" N VAL l 221 " --> pdb=" O SER l 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU l 151 " --> pdb=" O LYS l 168 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS l 168 " --> pdb=" O GLU l 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR l 153 " --> pdb=" O GLU l 166 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU l 166 " --> pdb=" O TYR l 153 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE l 167 " --> pdb=" O HIS l 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 178 through 189 current: chain 'l' and resid 107 through 109 Processing sheet with id=AB4, first strand: chain 'm' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER m 148 " --> pdb=" O ARG m 169 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG m 169 " --> pdb=" O SER m 148 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS m 150 " --> pdb=" O LYS m 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS m 167 " --> pdb=" O LYS m 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR m 152 " --> pdb=" O LYS m 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR m 183 " --> pdb=" O THR m 98 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR m 119 " --> pdb=" O GLU m 116 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN m 122 " --> pdb=" O PRO m 14 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU m 16 " --> pdb=" O ASN m 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE m 124 " --> pdb=" O LEU m 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU m 18 " --> pdb=" O ILE m 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU m 126 " --> pdb=" O GLU m 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS m 20 " --> pdb=" O LEU m 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY m 128 " --> pdb=" O LYS m 20 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP m 22 " --> pdb=" O GLY m 128 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'n' and resid 14 through 24 removed outlier: 7.973A pdb=" N ASN n 123 " --> pdb=" O PRO n 15 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU n 17 " --> pdb=" O ASN n 123 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE n 125 " --> pdb=" O LEU n 17 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU n 19 " --> pdb=" O ILE n 125 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR n 120 " --> pdb=" O GLU n 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG n 124 " --> pdb=" O GLU n 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 178 through 189 current: chain 'n' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL n 221 " --> pdb=" O SER n 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU n 151 " --> pdb=" O LYS n 168 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS n 168 " --> pdb=" O GLU n 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR n 153 " --> pdb=" O GLU n 166 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU n 166 " --> pdb=" O TYR n 153 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE n 167 " --> pdb=" O HIS n 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 178 through 189 current: chain 'n' and resid 107 through 109 Processing sheet with id=AB6, first strand: chain 'o' and resid 13 through 23 removed outlier: 6.122A pdb=" N SER o 148 " --> pdb=" O ARG o 169 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG o 169 " --> pdb=" O SER o 148 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS o 150 " --> pdb=" O LYS o 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS o 167 " --> pdb=" O LYS o 150 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR o 152 " --> pdb=" O LYS o 165 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR o 183 " --> pdb=" O THR o 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR o 119 " --> pdb=" O GLU o 116 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN o 122 " --> pdb=" O PRO o 14 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU o 16 " --> pdb=" O ASN o 122 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE o 124 " --> pdb=" O LEU o 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU o 18 " --> pdb=" O ILE o 124 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU o 126 " --> pdb=" O GLU o 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS o 20 " --> pdb=" O LEU o 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY o 128 " --> pdb=" O LYS o 20 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP o 22 " --> pdb=" O GLY o 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'p' and resid 14 through 24 removed outlier: 7.973A pdb=" N ASN p 123 " --> pdb=" O PRO p 15 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU p 17 " --> pdb=" O ASN p 123 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE p 125 " --> pdb=" O LEU p 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU p 19 " --> pdb=" O ILE p 125 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR p 120 " --> pdb=" O GLU p 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG p 124 " --> pdb=" O GLU p 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 178 through 189 current: chain 'p' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL p 221 " --> pdb=" O SER p 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU p 151 " --> pdb=" O LYS p 168 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS p 168 " --> pdb=" O GLU p 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR p 153 " --> pdb=" O GLU p 166 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU p 166 " --> pdb=" O TYR p 153 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE p 167 " --> pdb=" O HIS p 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 178 through 189 current: chain 'p' and resid 107 through 109 1232 hydrogen bonds defined for protein. 3144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.67 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8946 1.33 - 1.45: 4164 1.45 - 1.57: 16858 1.57 - 1.68: 0 1.68 - 1.80: 128 Bond restraints: 30096 Sorted by residual: bond pdb=" CA TYR j 68 " pdb=" C TYR j 68 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.14e-02 7.69e+03 3.38e+00 bond pdb=" CA TYR d 68 " pdb=" C TYR d 68 " ideal model delta sigma weight residual 1.521 1.501 0.021 1.14e-02 7.69e+03 3.24e+00 bond pdb=" CA TYR n 68 " pdb=" C TYR n 68 " ideal model delta sigma weight residual 1.521 1.501 0.020 1.14e-02 7.69e+03 3.19e+00 bond pdb=" CA TYR h 68 " pdb=" C TYR h 68 " ideal model delta sigma weight residual 1.521 1.501 0.020 1.14e-02 7.69e+03 3.09e+00 bond pdb=" CA TYR f 68 " pdb=" C TYR f 68 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.25e-02 6.40e+03 2.99e+00 ... (remaining 30091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 39528 2.45 - 4.91: 796 4.91 - 7.36: 92 7.36 - 9.81: 64 9.81 - 12.26: 8 Bond angle restraints: 40488 Sorted by residual: angle pdb=" C ASP h 157 " pdb=" N ASP h 158 " pdb=" CA ASP h 158 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" C ASP f 157 " pdb=" N ASP f 158 " pdb=" CA ASP f 158 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 angle pdb=" C ASP d 157 " pdb=" N ASP d 158 " pdb=" CA ASP d 158 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C ASP b 157 " pdb=" N ASP b 158 " pdb=" CA ASP b 158 " ideal model delta sigma weight residual 121.54 129.76 -8.22 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C ASP l 157 " pdb=" N ASP l 158 " pdb=" CA ASP l 158 " ideal model delta sigma weight residual 121.54 129.73 -8.19 1.91e+00 2.74e-01 1.84e+01 ... (remaining 40483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 17229 15.63 - 31.27: 683 31.27 - 46.90: 168 46.90 - 62.53: 0 62.53 - 78.16: 16 Dihedral angle restraints: 18096 sinusoidal: 7624 harmonic: 10472 Sorted by residual: dihedral pdb=" CA THR o 109 " pdb=" C THR o 109 " pdb=" N ARG o 110 " pdb=" CA ARG o 110 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA THR a 109 " pdb=" C THR a 109 " pdb=" N ARG a 110 " pdb=" CA ARG a 110 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA THR i 109 " pdb=" C THR i 109 " pdb=" N ARG i 110 " pdb=" CA ARG i 110 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 18093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2667 0.049 - 0.099: 1207 0.099 - 0.148: 424 0.148 - 0.197: 38 0.197 - 0.247: 8 Chirality restraints: 4344 Sorted by residual: chirality pdb=" CB ILE i 147 " pdb=" CA ILE i 147 " pdb=" CG1 ILE i 147 " pdb=" CG2 ILE i 147 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE a 147 " pdb=" CA ILE a 147 " pdb=" CG1 ILE a 147 " pdb=" CG2 ILE a 147 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE c 147 " pdb=" CA ILE c 147 " pdb=" CG1 ILE c 147 " pdb=" CG2 ILE c 147 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 4341 not shown) Planarity restraints: 5240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP c 67 " -0.028 2.00e-02 2.50e+03 2.08e-02 1.09e+01 pdb=" CG TRP c 67 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP c 67 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP c 67 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP c 67 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP c 67 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP c 67 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 67 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 67 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP c 67 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP e 67 " -0.028 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP e 67 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP e 67 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP e 67 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP e 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP e 67 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP e 67 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP e 67 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP e 67 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP e 67 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP k 67 " -0.028 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP k 67 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP k 67 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP k 67 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP k 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP k 67 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP k 67 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP k 67 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP k 67 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP k 67 " -0.011 2.00e-02 2.50e+03 ... (remaining 5237 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9370 2.86 - 3.37: 22932 3.37 - 3.88: 46523 3.88 - 4.39: 50273 4.39 - 4.90: 95399 Nonbonded interactions: 224497 Sorted by model distance: nonbonded pdb=" O THR b 64 " pdb=" NH1 ARG b 98 " model vdw 2.349 3.120 nonbonded pdb=" O THR n 64 " pdb=" NH1 ARG n 98 " model vdw 2.350 3.120 nonbonded pdb=" O THR f 64 " pdb=" NH1 ARG f 98 " model vdw 2.350 3.120 nonbonded pdb=" O THR d 64 " pdb=" NH1 ARG d 98 " model vdw 2.350 3.120 nonbonded pdb=" O THR h 64 " pdb=" NH1 ARG h 98 " model vdw 2.350 3.120 ... (remaining 224492 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: 0.10 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 22.270 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 30096 Z= 0.299 Angle : 0.929 12.264 40488 Z= 0.486 Chirality : 0.059 0.247 4344 Planarity : 0.006 0.054 5240 Dihedral : 9.548 78.163 11424 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % 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: -3.18 (0.13), residues: 3664 helix: -4.80 (0.21), residues: 56 sheet: -1.67 (0.11), residues: 1880 loop : -2.45 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG o 205 TYR 0.037 0.004 TYR d 68 PHE 0.024 0.004 PHE k 72 TRP 0.052 0.006 TRP e 67 HIS 0.013 0.002 HIS n 183 Details of bonding type rmsd covalent geometry : bond 0.00738 (30096) covalent geometry : angle 0.92860 (40488) hydrogen bonds : bond 0.27526 ( 1232) hydrogen bonds : angle 9.89833 ( 3144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 852 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 89 MET cc_start: 0.8916 (mmt) cc_final: 0.8715 (mmm) REVERT: b 32 ARG cc_start: 0.8348 (ttt90) cc_final: 0.8142 (mtp85) REVERT: c 89 MET cc_start: 0.8919 (mmt) cc_final: 0.8716 (mmm) REVERT: c 106 THR cc_start: 0.9062 (m) cc_final: 0.8836 (p) REVERT: d 32 ARG cc_start: 0.8349 (ttt90) cc_final: 0.8136 (mtp85) REVERT: e 106 THR cc_start: 0.9020 (m) cc_final: 0.8771 (p) REVERT: g 183 TYR cc_start: 0.9138 (m-80) cc_final: 0.8915 (m-80) REVERT: j 32 ARG cc_start: 0.8350 (ttt90) cc_final: 0.8133 (mtp85) REVERT: k 89 MET cc_start: 0.8925 (mmt) cc_final: 0.8702 (mmm) REVERT: o 183 TYR cc_start: 0.9142 (m-80) cc_final: 0.8923 (m-80) REVERT: p 90 MET cc_start: 0.8604 (mmt) cc_final: 0.8402 (mmt) outliers start: 0 outliers final: 0 residues processed: 852 average time/residue: 0.2369 time to fit residues: 299.3096 Evaluate side-chains 496 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 24 ASN ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 123 ASN c 24 ASN c 186 ASN ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 123 ASN e 24 ASN e 145 ASN ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 123 ASN g 24 ASN g 145 ASN ** h 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 ASN i 24 ASN i 95 GLN i 186 ASN ** j 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 123 ASN k 24 ASN k 95 GLN k 186 ASN ** l 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 123 ASN m 24 ASN m 95 GLN m 145 ASN m 186 ASN ** n 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 123 ASN o 24 ASN o 145 ASN o 186 ASN ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 123 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111030 restraints weight = 38645.613| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.37 r_work: 0.2981 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 30096 Z= 0.197 Angle : 0.678 9.620 40488 Z= 0.342 Chirality : 0.050 0.148 4344 Planarity : 0.005 0.035 5240 Dihedral : 4.664 19.766 3992 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.24 % Allowed : 10.72 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % 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 (0.13), residues: 3664 helix: -4.43 (0.20), residues: 152 sheet: -0.89 (0.12), residues: 1832 loop : -1.77 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG g 31 TYR 0.020 0.003 TYR h 68 PHE 0.016 0.002 PHE n 167 TRP 0.020 0.002 TRP g 67 HIS 0.006 0.001 HIS m 82 Details of bonding type rmsd covalent geometry : bond 0.00470 (30096) covalent geometry : angle 0.67794 (40488) hydrogen bonds : bond 0.04703 ( 1232) hydrogen bonds : angle 6.78113 ( 3144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 588 time to evaluate : 1.071 Fit side-chains REVERT: a 81 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.7524 (ttp-110) REVERT: a 89 MET cc_start: 0.9088 (mmt) cc_final: 0.8865 (mmm) REVERT: a 94 VAL cc_start: 0.9245 (t) cc_final: 0.9040 (p) REVERT: b 49 ILE cc_start: 0.8472 (pt) cc_final: 0.8239 (mt) REVERT: b 180 LEU cc_start: 0.8510 (tp) cc_final: 0.8294 (tp) REVERT: c 81 ARG cc_start: 0.7991 (ttp-110) cc_final: 0.7780 (ttp-110) REVERT: c 89 MET cc_start: 0.9097 (mmt) cc_final: 0.8877 (mmm) REVERT: c 94 VAL cc_start: 0.9234 (t) cc_final: 0.9018 (p) REVERT: c 174 ASP cc_start: 0.7910 (t70) cc_final: 0.7635 (t0) REVERT: d 49 ILE cc_start: 0.8467 (pt) cc_final: 0.8241 (mt) REVERT: e 81 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7816 (ttp-110) REVERT: e 94 VAL cc_start: 0.9238 (t) cc_final: 0.8985 (p) REVERT: f 49 ILE cc_start: 0.8434 (pt) cc_final: 0.8229 (mt) REVERT: g 81 ARG cc_start: 0.7853 (ttp-170) cc_final: 0.7327 (ttp-110) REVERT: g 94 VAL cc_start: 0.9237 (t) cc_final: 0.9004 (p) REVERT: h 49 ILE cc_start: 0.8481 (pt) cc_final: 0.8242 (mt) REVERT: h 180 LEU cc_start: 0.8467 (tp) cc_final: 0.8238 (tp) REVERT: i 81 ARG cc_start: 0.7991 (ttp-110) cc_final: 0.7775 (ttp-110) REVERT: j 49 ILE cc_start: 0.8489 (pt) cc_final: 0.8264 (mt) REVERT: j 180 LEU cc_start: 0.8519 (tp) cc_final: 0.8295 (tp) REVERT: k 81 ARG cc_start: 0.7999 (ttp-110) cc_final: 0.7785 (ttp-110) REVERT: k 89 MET cc_start: 0.9129 (mmt) cc_final: 0.8897 (mmm) REVERT: l 49 ILE cc_start: 0.8452 (pt) cc_final: 0.8219 (mt) REVERT: m 81 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7818 (ttp-110) REVERT: o 81 ARG cc_start: 0.8055 (ttp-110) cc_final: 0.7845 (ttp-110) REVERT: o 94 VAL cc_start: 0.9236 (t) cc_final: 0.9033 (p) REVERT: p 49 ILE cc_start: 0.8475 (pt) cc_final: 0.8246 (mt) REVERT: p 90 MET cc_start: 0.8984 (mmt) cc_final: 0.8733 (mmt) REVERT: p 180 LEU cc_start: 0.8498 (tp) cc_final: 0.8286 (tp) outliers start: 72 outliers final: 37 residues processed: 628 average time/residue: 0.1893 time to fit residues: 189.9868 Evaluate side-chains 531 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 494 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 87 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 120 LEU Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 120 LEU Chi-restraints excluded: chain p residue 45 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 305 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 306 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 186 ASN b 71 GLN c 145 ASN d 71 GLN e 145 ASN f 71 GLN g 24 ASN g 145 ASN g 186 ASN h 71 GLN i 178 GLN j 71 GLN k 145 ASN l 71 GLN m 24 ASN m 145 ASN n 71 GLN o 145 ASN p 71 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.105031 restraints weight = 38928.646| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.46 r_work: 0.2999 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 30096 Z= 0.214 Angle : 0.661 10.122 40488 Z= 0.331 Chirality : 0.050 0.164 4344 Planarity : 0.004 0.033 5240 Dihedral : 4.550 18.145 3992 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.93 % Allowed : 12.38 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % 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 (0.14), residues: 3664 helix: -4.16 (0.21), residues: 200 sheet: -0.61 (0.12), residues: 1832 loop : -1.48 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG g 31 TYR 0.020 0.003 TYR b 202 PHE 0.016 0.002 PHE j 167 TRP 0.017 0.002 TRP a 67 HIS 0.005 0.001 HIS o 82 Details of bonding type rmsd covalent geometry : bond 0.00522 (30096) covalent geometry : angle 0.66124 (40488) hydrogen bonds : bond 0.04173 ( 1232) hydrogen bonds : angle 6.35330 ( 3144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 519 time to evaluate : 1.123 Fit side-chains REVERT: a 89 MET cc_start: 0.9096 (mmt) cc_final: 0.8837 (mmm) REVERT: a 104 ASP cc_start: 0.8999 (t0) cc_final: 0.8742 (t0) REVERT: a 160 ASN cc_start: 0.8846 (t0) cc_final: 0.8606 (t0) REVERT: c 81 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7702 (ttp-110) REVERT: c 89 MET cc_start: 0.9120 (mmt) cc_final: 0.8847 (mmm) REVERT: c 160 ASN cc_start: 0.8848 (t0) cc_final: 0.8608 (t0) REVERT: c 174 ASP cc_start: 0.7831 (t70) cc_final: 0.7516 (t0) REVERT: e 81 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.7666 (ttp-110) REVERT: e 160 ASN cc_start: 0.8837 (t0) cc_final: 0.8582 (t0) REVERT: g 160 ASN cc_start: 0.8886 (t0) cc_final: 0.8630 (t0) REVERT: i 81 ARG cc_start: 0.7945 (ttp-110) cc_final: 0.7707 (ttp-110) REVERT: i 104 ASP cc_start: 0.9003 (t0) cc_final: 0.8762 (t0) REVERT: i 160 ASN cc_start: 0.8827 (t0) cc_final: 0.8598 (t0) REVERT: k 81 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7703 (ttp-110) REVERT: k 89 MET cc_start: 0.9109 (mmt) cc_final: 0.8824 (mmm) REVERT: k 160 ASN cc_start: 0.8853 (t0) cc_final: 0.8617 (t0) REVERT: m 81 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7680 (ttp-110) REVERT: m 94 VAL cc_start: 0.9219 (t) cc_final: 0.8990 (p) REVERT: m 160 ASN cc_start: 0.8859 (t0) cc_final: 0.8616 (t0) REVERT: o 81 ARG cc_start: 0.7956 (ttp-110) cc_final: 0.7723 (ttp-110) REVERT: o 160 ASN cc_start: 0.8870 (t0) cc_final: 0.8625 (t0) outliers start: 94 outliers final: 51 residues processed: 578 average time/residue: 0.1989 time to fit residues: 181.6936 Evaluate side-chains 523 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 472 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LYS Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 90 MET Chi-restraints excluded: chain c residue 40 ASN Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 187 THR Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 35 LYS Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 90 MET Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain i residue 35 LYS Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 87 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain k residue 35 LYS Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 187 THR Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 90 MET Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 35 LYS Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain o residue 35 LYS Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 210 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 221 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 292 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 chunk 241 optimal weight: 0.6980 chunk 346 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 289 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 71 GLN d 71 GLN f 71 GLN g 24 ASN h 71 GLN j 71 GLN l 71 GLN m 24 ASN n 71 GLN n 186 GLN o 145 ASN p 71 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.126807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.104910 restraints weight = 38401.969| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.42 r_work: 0.3046 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 30096 Z= 0.116 Angle : 0.581 8.796 40488 Z= 0.288 Chirality : 0.047 0.162 4344 Planarity : 0.003 0.030 5240 Dihedral : 4.204 17.232 3992 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.78 % Allowed : 14.03 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % 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: -1.44 (0.14), residues: 3664 helix: -3.80 (0.27), residues: 152 sheet: -0.31 (0.12), residues: 1824 loop : -1.35 (0.16), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 31 TYR 0.016 0.002 TYR i 107 PHE 0.010 0.001 PHE d 167 TRP 0.012 0.001 TRP e 67 HIS 0.004 0.001 HIS m 182 Details of bonding type rmsd covalent geometry : bond 0.00268 (30096) covalent geometry : angle 0.58110 (40488) hydrogen bonds : bond 0.03449 ( 1232) hydrogen bonds : angle 5.92712 ( 3144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 568 time to evaluate : 1.058 Fit side-chains REVERT: a 81 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7438 (ttp-110) REVERT: a 104 ASP cc_start: 0.8989 (t0) cc_final: 0.8765 (t0) REVERT: a 145 ASN cc_start: 0.8730 (m-40) cc_final: 0.8335 (t0) REVERT: b 49 ILE cc_start: 0.8332 (pt) cc_final: 0.8124 (mt) REVERT: b 84 ASP cc_start: 0.8327 (t0) cc_final: 0.7905 (t70) REVERT: c 81 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7578 (ttp-110) REVERT: c 104 ASP cc_start: 0.9013 (t0) cc_final: 0.8695 (t0) REVERT: d 84 ASP cc_start: 0.8338 (t0) cc_final: 0.7907 (t70) REVERT: e 81 ARG cc_start: 0.7863 (ttp-110) cc_final: 0.7599 (ttp-110) REVERT: e 104 ASP cc_start: 0.9015 (t0) cc_final: 0.8692 (t0) REVERT: f 84 ASP cc_start: 0.8322 (t0) cc_final: 0.7865 (t70) REVERT: g 81 ARG cc_start: 0.7881 (ttp-170) cc_final: 0.7452 (ttp-110) REVERT: h 49 ILE cc_start: 0.8387 (pt) cc_final: 0.8177 (mt) REVERT: h 84 ASP cc_start: 0.8297 (t0) cc_final: 0.7906 (t70) REVERT: i 81 ARG cc_start: 0.7836 (ttp-110) cc_final: 0.7571 (ttp-110) REVERT: i 104 ASP cc_start: 0.8932 (t0) cc_final: 0.8683 (t0) REVERT: i 145 ASN cc_start: 0.8742 (m-40) cc_final: 0.8336 (t0) REVERT: j 84 ASP cc_start: 0.8303 (t0) cc_final: 0.7879 (t70) REVERT: k 81 ARG cc_start: 0.7839 (ttp-110) cc_final: 0.7580 (ttp-110) REVERT: k 104 ASP cc_start: 0.9018 (t0) cc_final: 0.8692 (t0) REVERT: l 49 ILE cc_start: 0.8323 (pt) cc_final: 0.8110 (mt) REVERT: l 84 ASP cc_start: 0.8352 (t0) cc_final: 0.7914 (t70) REVERT: m 81 ARG cc_start: 0.7856 (ttp-110) cc_final: 0.7594 (ttp-110) REVERT: m 104 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8691 (t0) REVERT: n 84 ASP cc_start: 0.8368 (t0) cc_final: 0.7906 (t70) REVERT: o 81 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7569 (ttp-110) REVERT: p 84 ASP cc_start: 0.8330 (t0) cc_final: 0.7918 (t70) outliers start: 57 outliers final: 39 residues processed: 597 average time/residue: 0.1982 time to fit residues: 186.2648 Evaluate side-chains 533 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 493 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 104 ASP Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 210 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 72 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 346 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 145 ASN g 24 ASN h 186 GLN ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 145 ASN ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.106977 restraints weight = 38676.914| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.44 r_work: 0.3017 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30096 Z= 0.160 Angle : 0.609 8.628 40488 Z= 0.302 Chirality : 0.048 0.170 4344 Planarity : 0.003 0.030 5240 Dihedral : 4.185 15.973 3992 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.40 % Allowed : 14.28 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % 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: -1.35 (0.14), residues: 3664 helix: -3.40 (0.22), residues: 248 sheet: -0.26 (0.12), residues: 1832 loop : -1.11 (0.17), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 123 TYR 0.017 0.002 TYR e 107 PHE 0.012 0.001 PHE p 167 TRP 0.011 0.001 TRP g 67 HIS 0.003 0.001 HIS d 171 Details of bonding type rmsd covalent geometry : bond 0.00390 (30096) covalent geometry : angle 0.60940 (40488) hydrogen bonds : bond 0.03539 ( 1232) hydrogen bonds : angle 5.87311 ( 3144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 494 time to evaluate : 0.971 Fit side-chains REVERT: a 81 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.7451 (ttp-110) REVERT: a 104 ASP cc_start: 0.8964 (t0) cc_final: 0.8721 (t0) REVERT: b 49 ILE cc_start: 0.8377 (pt) cc_final: 0.8154 (mt) REVERT: b 84 ASP cc_start: 0.8388 (t0) cc_final: 0.8017 (t70) REVERT: c 81 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7539 (ttp-110) REVERT: c 104 ASP cc_start: 0.9019 (t0) cc_final: 0.8702 (t0) REVERT: d 84 ASP cc_start: 0.8354 (t0) cc_final: 0.7997 (t70) REVERT: e 81 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7535 (ttp-110) REVERT: e 104 ASP cc_start: 0.9037 (t0) cc_final: 0.8720 (t0) REVERT: f 84 ASP cc_start: 0.8323 (t0) cc_final: 0.7945 (t70) REVERT: g 81 ARG cc_start: 0.7883 (ttp-170) cc_final: 0.7404 (ttp-110) REVERT: h 49 ILE cc_start: 0.8350 (pt) cc_final: 0.8140 (mt) REVERT: h 84 ASP cc_start: 0.8369 (t0) cc_final: 0.8005 (t70) REVERT: h 186 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: i 81 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7530 (ttp-110) REVERT: i 104 ASP cc_start: 0.8980 (t0) cc_final: 0.8730 (t0) REVERT: i 145 ASN cc_start: 0.8800 (m-40) cc_final: 0.8468 (t0) REVERT: j 84 ASP cc_start: 0.8376 (t0) cc_final: 0.8010 (t70) REVERT: k 81 ARG cc_start: 0.7836 (ttp-110) cc_final: 0.7532 (ttp-110) REVERT: k 104 ASP cc_start: 0.9010 (t0) cc_final: 0.8689 (t0) REVERT: l 84 ASP cc_start: 0.8376 (t0) cc_final: 0.8012 (t70) REVERT: m 81 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.7589 (ttp-110) REVERT: m 104 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8715 (t0) REVERT: n 84 ASP cc_start: 0.8355 (t0) cc_final: 0.7978 (t70) REVERT: o 81 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.7581 (ttp-110) REVERT: p 84 ASP cc_start: 0.8379 (t0) cc_final: 0.8003 (t70) outliers start: 77 outliers final: 62 residues processed: 524 average time/residue: 0.1955 time to fit residues: 161.9993 Evaluate side-chains 532 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 468 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 187 THR Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 187 THR Chi-restraints excluded: chain c residue 195 LEU Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 187 THR Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 186 GLN Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 187 THR Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 104 ASP Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 187 THR Chi-restraints excluded: chain o residue 195 LEU Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 210 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 209 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 260 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 136 ASN a 178 GLN ** c 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 136 ASN c 178 GLN ** c 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 136 ASN e 178 GLN g 24 ASN g 136 ASN g 178 GLN ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 136 ASN ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 ASN k 178 GLN ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 136 ASN m 178 GLN ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 136 ASN o 178 GLN ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.098418 restraints weight = 39311.382| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.65 r_work: 0.2901 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 30096 Z= 0.251 Angle : 0.683 9.190 40488 Z= 0.340 Chirality : 0.051 0.171 4344 Planarity : 0.004 0.033 5240 Dihedral : 4.454 15.274 3992 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.99 % Allowed : 14.87 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % 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: -1.43 (0.14), residues: 3664 helix: -3.31 (0.24), residues: 248 sheet: -0.44 (0.11), residues: 1872 loop : -1.01 (0.17), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG k 97 TYR 0.021 0.003 TYR j 202 PHE 0.017 0.002 PHE p 167 TRP 0.012 0.002 TRP a 67 HIS 0.004 0.001 HIS k 200 Details of bonding type rmsd covalent geometry : bond 0.00619 (30096) covalent geometry : angle 0.68255 (40488) hydrogen bonds : bond 0.03935 ( 1232) hydrogen bonds : angle 6.05327 ( 3144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 444 time to evaluate : 1.340 Fit side-chains REVERT: a 104 ASP cc_start: 0.8989 (t0) cc_final: 0.8731 (t0) REVERT: a 145 ASN cc_start: 0.8926 (m-40) cc_final: 0.8569 (t0) REVERT: b 68 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.5799 (t80) REVERT: b 105 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8390 (m-30) REVERT: c 81 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7598 (ttp-110) REVERT: c 104 ASP cc_start: 0.9049 (t0) cc_final: 0.8721 (t0) REVERT: c 145 ASN cc_start: 0.8915 (m-40) cc_final: 0.8553 (t0) REVERT: d 68 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.5831 (t80) REVERT: e 81 ARG cc_start: 0.8003 (ttp-110) cc_final: 0.7613 (ttp-110) REVERT: e 104 ASP cc_start: 0.9066 (t0) cc_final: 0.8738 (t0) REVERT: e 145 ASN cc_start: 0.8994 (m-40) cc_final: 0.8648 (t0) REVERT: f 68 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.5836 (t80) REVERT: g 81 ARG cc_start: 0.8023 (ttp-170) cc_final: 0.7701 (ttp-110) REVERT: g 145 ASN cc_start: 0.8961 (m-40) cc_final: 0.8620 (t0) REVERT: h 68 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.5881 (t80) REVERT: h 105 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8388 (m-30) REVERT: i 81 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.7565 (ttp-110) REVERT: i 104 ASP cc_start: 0.8979 (t0) cc_final: 0.8721 (t0) REVERT: i 145 ASN cc_start: 0.8902 (m-40) cc_final: 0.8548 (t0) REVERT: j 68 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.5835 (t80) REVERT: j 105 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8434 (m-30) REVERT: k 81 ARG cc_start: 0.7989 (ttp-110) cc_final: 0.7606 (ttp-110) REVERT: k 104 ASP cc_start: 0.9054 (t0) cc_final: 0.8725 (t0) REVERT: k 145 ASN cc_start: 0.8931 (m-40) cc_final: 0.8569 (t0) REVERT: l 68 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.5791 (t80) REVERT: m 81 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7593 (ttp-110) REVERT: m 104 ASP cc_start: 0.9069 (OUTLIER) cc_final: 0.8743 (t0) REVERT: m 145 ASN cc_start: 0.8919 (m-40) cc_final: 0.8558 (t0) REVERT: n 68 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.5857 (t80) REVERT: o 81 ARG cc_start: 0.7984 (ttp-110) cc_final: 0.7598 (ttp-110) REVERT: o 145 ASN cc_start: 0.8948 (m-40) cc_final: 0.8597 (t0) REVERT: p 68 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.5843 (t80) REVERT: p 105 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8422 (m-30) outliers start: 96 outliers final: 72 residues processed: 486 average time/residue: 0.2004 time to fit residues: 153.1558 Evaluate side-chains 520 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 435 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 68 TYR Chi-restraints excluded: chain b residue 90 MET Chi-restraints excluded: chain b residue 105 ASP Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 187 THR Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 68 TYR Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 158 ASP Chi-restraints excluded: chain f residue 190 ILE Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 105 ASP Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 68 TYR Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 105 ASP Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 187 THR Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 190 ILE Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 40 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 104 ASP Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 68 TYR Chi-restraints excluded: chain n residue 158 ASP Chi-restraints excluded: chain n residue 190 ILE Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 187 THR Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 295 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 204 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 71 GLN g 24 ASN ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100332 restraints weight = 39095.417| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.65 r_work: 0.2911 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 30096 Z= 0.168 Angle : 0.617 8.613 40488 Z= 0.308 Chirality : 0.048 0.163 4344 Planarity : 0.003 0.032 5240 Dihedral : 4.233 15.274 3992 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.99 % Allowed : 14.74 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % 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: -1.26 (0.14), residues: 3664 helix: -2.98 (0.26), residues: 248 sheet: -0.31 (0.11), residues: 1864 loop : -0.98 (0.17), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 123 TYR 0.017 0.002 TYR k 107 PHE 0.013 0.001 PHE f 167 TRP 0.011 0.002 TRP a 67 HIS 0.004 0.001 HIS m 182 Details of bonding type rmsd covalent geometry : bond 0.00408 (30096) covalent geometry : angle 0.61715 (40488) hydrogen bonds : bond 0.03497 ( 1232) hydrogen bonds : angle 5.88013 ( 3144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 459 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 104 ASP cc_start: 0.8972 (t0) cc_final: 0.8705 (t0) REVERT: a 145 ASN cc_start: 0.8910 (m-40) cc_final: 0.8572 (t0) REVERT: b 68 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.5704 (t80) REVERT: b 105 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8367 (m-30) REVERT: c 81 ARG cc_start: 0.7946 (ttp-110) cc_final: 0.7564 (ttp-110) REVERT: c 104 ASP cc_start: 0.9029 (t0) cc_final: 0.8703 (t0) REVERT: c 145 ASN cc_start: 0.8898 (m-40) cc_final: 0.8556 (t0) REVERT: d 68 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.5858 (t80) REVERT: e 81 ARG cc_start: 0.7948 (ttp-110) cc_final: 0.7560 (ttp-110) REVERT: e 104 ASP cc_start: 0.9044 (t0) cc_final: 0.8716 (t0) REVERT: e 145 ASN cc_start: 0.8918 (m-40) cc_final: 0.8566 (t0) REVERT: f 68 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.5779 (t80) REVERT: g 81 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7710 (ttp-110) REVERT: g 145 ASN cc_start: 0.8877 (m-40) cc_final: 0.8534 (t0) REVERT: h 68 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.5878 (t80) REVERT: h 105 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8432 (m-30) REVERT: i 81 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7512 (ttp-110) REVERT: i 104 ASP cc_start: 0.9047 (t0) cc_final: 0.8774 (t0) REVERT: i 145 ASN cc_start: 0.8901 (m-40) cc_final: 0.8564 (t0) REVERT: j 68 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.5829 (t80) REVERT: j 105 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8459 (m-30) REVERT: k 81 ARG cc_start: 0.7924 (ttp-110) cc_final: 0.7551 (ttp-110) REVERT: k 104 ASP cc_start: 0.9027 (t0) cc_final: 0.8697 (t0) REVERT: k 145 ASN cc_start: 0.8927 (m-40) cc_final: 0.8586 (t0) REVERT: l 68 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.5754 (t80) REVERT: m 81 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7545 (ttp-110) REVERT: m 104 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8731 (t0) REVERT: m 145 ASN cc_start: 0.8903 (m-40) cc_final: 0.8554 (t0) REVERT: n 68 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.5968 (t80) REVERT: o 81 ARG cc_start: 0.7914 (ttp-110) cc_final: 0.7532 (ttp-110) REVERT: o 145 ASN cc_start: 0.8958 (m-40) cc_final: 0.8630 (t0) REVERT: p 68 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.5796 (t80) REVERT: p 105 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8393 (m-30) outliers start: 96 outliers final: 77 residues processed: 503 average time/residue: 0.2089 time to fit residues: 163.5201 Evaluate side-chains 525 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 435 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 68 TYR Chi-restraints excluded: chain b residue 105 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 187 THR Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 68 TYR Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 98 ARG Chi-restraints excluded: chain f residue 190 ILE Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 184 GLN Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 105 ASP Chi-restraints excluded: chain h residue 158 ASP Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 187 THR Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 68 TYR Chi-restraints excluded: chain j residue 105 ASP Chi-restraints excluded: chain j residue 158 ASP Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 187 THR Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 98 ARG Chi-restraints excluded: chain l residue 190 ILE Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 104 ASP Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain m residue 219 MET Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 68 TYR Chi-restraints excluded: chain n residue 190 ILE Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 187 THR Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain o residue 219 MET Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Chi-restraints excluded: chain p residue 217 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 80 optimal weight: 5.9990 chunk 284 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 154 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 365 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 311 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 267 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 71 GLN m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.124510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.102412 restraints weight = 38982.858| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.42 r_work: 0.2996 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30096 Z= 0.140 Angle : 0.596 8.408 40488 Z= 0.298 Chirality : 0.048 0.160 4344 Planarity : 0.003 0.031 5240 Dihedral : 4.099 14.959 3992 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.02 % Allowed : 14.90 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % 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: -1.08 (0.14), residues: 3664 helix: -2.73 (0.27), residues: 248 sheet: -0.23 (0.11), residues: 1904 loop : -0.83 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG o 123 TYR 0.016 0.002 TYR m 107 PHE 0.011 0.001 PHE f 167 TRP 0.011 0.001 TRP e 67 HIS 0.004 0.001 HIS m 26 Details of bonding type rmsd covalent geometry : bond 0.00338 (30096) covalent geometry : angle 0.59593 (40488) hydrogen bonds : bond 0.03311 ( 1232) hydrogen bonds : angle 5.74983 ( 3144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 463 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 104 ASP cc_start: 0.9068 (t0) cc_final: 0.8788 (t0) REVERT: a 145 ASN cc_start: 0.8815 (m-40) cc_final: 0.8434 (t0) REVERT: b 49 ILE cc_start: 0.8364 (pt) cc_final: 0.8123 (mt) REVERT: b 68 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.5696 (t80) REVERT: b 105 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8127 (t0) REVERT: c 104 ASP cc_start: 0.8992 (t0) cc_final: 0.8684 (t0) REVERT: c 145 ASN cc_start: 0.8810 (m-40) cc_final: 0.8430 (t0) REVERT: d 68 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.5785 (t80) REVERT: e 104 ASP cc_start: 0.8996 (t0) cc_final: 0.8688 (t0) REVERT: e 145 ASN cc_start: 0.8827 (m-40) cc_final: 0.8478 (t0) REVERT: f 68 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.5704 (t80) REVERT: g 81 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7624 (ttp-110) REVERT: g 104 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8757 (t0) REVERT: g 145 ASN cc_start: 0.8783 (m-40) cc_final: 0.8446 (t0) REVERT: h 49 ILE cc_start: 0.8373 (pt) cc_final: 0.8161 (mt) REVERT: h 68 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.5807 (t80) REVERT: h 105 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8380 (m-30) REVERT: i 104 ASP cc_start: 0.9073 (t0) cc_final: 0.8794 (t0) REVERT: i 145 ASN cc_start: 0.8806 (m-40) cc_final: 0.8470 (t0) REVERT: j 68 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.5762 (t80) REVERT: j 84 ASP cc_start: 0.8402 (t0) cc_final: 0.8067 (t70) REVERT: j 105 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8435 (m-30) REVERT: k 104 ASP cc_start: 0.8982 (t0) cc_final: 0.8670 (t0) REVERT: k 145 ASN cc_start: 0.8840 (m-40) cc_final: 0.8463 (t0) REVERT: l 49 ILE cc_start: 0.8352 (pt) cc_final: 0.8116 (mt) REVERT: l 68 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.5845 (t80) REVERT: m 104 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8695 (t0) REVERT: m 145 ASN cc_start: 0.8809 (m-40) cc_final: 0.8454 (t0) REVERT: n 68 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.5865 (t80) REVERT: n 84 ASP cc_start: 0.8389 (t0) cc_final: 0.8034 (t70) REVERT: o 81 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7500 (ttp-110) REVERT: o 104 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8712 (t0) REVERT: o 145 ASN cc_start: 0.8862 (m-40) cc_final: 0.8543 (t0) REVERT: p 68 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.5817 (t80) REVERT: p 84 ASP cc_start: 0.8422 (t0) cc_final: 0.8078 (t70) REVERT: p 105 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8411 (m-30) outliers start: 97 outliers final: 82 residues processed: 510 average time/residue: 0.2082 time to fit residues: 165.2656 Evaluate side-chains 544 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 447 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 195 LEU Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 68 TYR Chi-restraints excluded: chain b residue 105 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 187 THR Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 68 TYR Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 98 ARG Chi-restraints excluded: chain f residue 158 ASP Chi-restraints excluded: chain f residue 190 ILE Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 184 GLN Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 105 ASP Chi-restraints excluded: chain h residue 158 ASP Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 187 THR Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 68 TYR Chi-restraints excluded: chain j residue 105 ASP Chi-restraints excluded: chain j residue 158 ASP Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 122 ASN Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 187 THR Chi-restraints excluded: chain k residue 195 LEU Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain k residue 219 MET Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 98 ARG Chi-restraints excluded: chain l residue 190 ILE Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 104 ASP Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 122 ASN Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain m residue 219 MET Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 68 TYR Chi-restraints excluded: chain n residue 190 ILE Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 187 THR Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain o residue 219 MET Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 22 optimal weight: 7.9990 chunk 310 optimal weight: 0.0170 chunk 137 optimal weight: 4.9990 chunk 363 optimal weight: 8.9990 chunk 337 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 chunk 276 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100864 restraints weight = 38945.977| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.53 r_work: 0.2950 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30096 Z= 0.169 Angle : 0.619 8.309 40488 Z= 0.311 Chirality : 0.048 0.160 4344 Planarity : 0.004 0.032 5240 Dihedral : 4.158 15.242 3992 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.21 % Allowed : 14.90 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % 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: -1.07 (0.14), residues: 3664 helix: -2.60 (0.28), residues: 248 sheet: -0.24 (0.11), residues: 1912 loop : -0.83 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG k 81 TYR 0.018 0.002 TYR f 145 PHE 0.013 0.001 PHE l 167 TRP 0.011 0.001 TRP g 67 HIS 0.004 0.001 HIS n 171 Details of bonding type rmsd covalent geometry : bond 0.00415 (30096) covalent geometry : angle 0.61938 (40488) hydrogen bonds : bond 0.03447 ( 1232) hydrogen bonds : angle 5.77652 ( 3144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 445 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 104 ASP cc_start: 0.9091 (t0) cc_final: 0.8807 (t0) REVERT: a 145 ASN cc_start: 0.8881 (m-40) cc_final: 0.8539 (t0) REVERT: b 68 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.5749 (t80) REVERT: b 105 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8067 (t0) REVERT: c 81 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7683 (ttp-110) REVERT: c 104 ASP cc_start: 0.9070 (t0) cc_final: 0.8751 (t0) REVERT: c 145 ASN cc_start: 0.8872 (m-40) cc_final: 0.8531 (t0) REVERT: d 68 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.5796 (t80) REVERT: e 81 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7638 (ttp-110) REVERT: e 104 ASP cc_start: 0.9082 (t0) cc_final: 0.8761 (t0) REVERT: e 145 ASN cc_start: 0.8888 (m-40) cc_final: 0.8532 (t0) REVERT: f 68 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.5824 (t80) REVERT: g 81 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7644 (ttp-110) REVERT: g 104 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8750 (t0) REVERT: g 145 ASN cc_start: 0.8871 (m-40) cc_final: 0.8529 (t0) REVERT: h 68 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.5899 (t80) REVERT: h 105 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: i 81 ARG cc_start: 0.7835 (ttp-110) cc_final: 0.7627 (ttp-110) REVERT: i 104 ASP cc_start: 0.9095 (t0) cc_final: 0.8813 (t0) REVERT: i 145 ASN cc_start: 0.8885 (m-40) cc_final: 0.8544 (t0) REVERT: j 68 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.5858 (t80) REVERT: j 105 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8502 (m-30) REVERT: k 81 ARG cc_start: 0.7916 (ttp-110) cc_final: 0.7665 (ttp-110) REVERT: k 104 ASP cc_start: 0.9063 (t0) cc_final: 0.8740 (t0) REVERT: k 145 ASN cc_start: 0.8913 (m-40) cc_final: 0.8583 (t0) REVERT: l 68 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.5819 (t80) REVERT: m 81 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7645 (ttp-110) REVERT: m 104 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8724 (t0) REVERT: m 145 ASN cc_start: 0.8888 (m-40) cc_final: 0.8536 (t0) REVERT: n 68 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.5948 (t80) REVERT: n 84 ASP cc_start: 0.8404 (t0) cc_final: 0.8058 (t70) REVERT: o 104 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8727 (t0) REVERT: o 145 ASN cc_start: 0.8940 (m-40) cc_final: 0.8629 (t0) REVERT: p 68 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.5801 (t80) REVERT: p 105 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8486 (m-30) outliers start: 103 outliers final: 85 residues processed: 496 average time/residue: 0.2003 time to fit residues: 157.0482 Evaluate side-chains 536 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 436 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 184 GLN Chi-restraints excluded: chain a residue 195 LEU Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain a residue 219 MET Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 68 TYR Chi-restraints excluded: chain b residue 105 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 187 THR Chi-restraints excluded: chain c residue 195 LEU Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 68 TYR Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 98 ARG Chi-restraints excluded: chain f residue 158 ASP Chi-restraints excluded: chain f residue 190 ILE Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 184 GLN Chi-restraints excluded: chain g residue 187 THR Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 105 ASP Chi-restraints excluded: chain h residue 158 ASP Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 187 THR Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain i residue 219 MET Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 68 TYR Chi-restraints excluded: chain j residue 105 ASP Chi-restraints excluded: chain j residue 158 ASP Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 122 ASN Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 187 THR Chi-restraints excluded: chain k residue 195 LEU Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 98 ARG Chi-restraints excluded: chain l residue 190 ILE Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 104 ASP Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 122 ASN Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 68 TYR Chi-restraints excluded: chain n residue 158 ASP Chi-restraints excluded: chain n residue 190 ILE Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 187 THR Chi-restraints excluded: chain o residue 195 LEU Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain o residue 219 MET Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Chi-restraints excluded: chain p residue 217 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 294 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN g 232 HIS ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105740 restraints weight = 38571.707| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.45 r_work: 0.2984 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30096 Z= 0.195 Angle : 0.647 8.292 40488 Z= 0.326 Chirality : 0.049 0.163 4344 Planarity : 0.004 0.033 5240 Dihedral : 4.243 15.372 3992 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.34 % Allowed : 15.06 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % 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: -1.12 (0.14), residues: 3664 helix: -2.53 (0.29), residues: 248 sheet: -0.27 (0.11), residues: 1912 loop : -0.89 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG o 81 TYR 0.022 0.003 TYR h 145 PHE 0.014 0.002 PHE l 167 TRP 0.013 0.002 TRP i 67 HIS 0.006 0.001 HIS g 26 Details of bonding type rmsd covalent geometry : bond 0.00480 (30096) covalent geometry : angle 0.64655 (40488) hydrogen bonds : bond 0.03580 ( 1232) hydrogen bonds : angle 5.82784 ( 3144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 430 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 104 ASP cc_start: 0.9081 (t0) cc_final: 0.8802 (t0) REVERT: a 145 ASN cc_start: 0.8848 (m-40) cc_final: 0.8514 (t0) REVERT: b 68 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.5803 (t80) REVERT: b 105 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8112 (t0) REVERT: c 81 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7665 (ttp-110) REVERT: c 104 ASP cc_start: 0.9120 (t0) cc_final: 0.8785 (t0) REVERT: c 145 ASN cc_start: 0.8852 (m-40) cc_final: 0.8518 (t0) REVERT: d 68 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.5852 (t80) REVERT: e 81 ARG cc_start: 0.7908 (ttp-110) cc_final: 0.7646 (ttp-110) REVERT: e 104 ASP cc_start: 0.9112 (t0) cc_final: 0.8787 (t0) REVERT: e 145 ASN cc_start: 0.8863 (m-40) cc_final: 0.8506 (t0) REVERT: f 68 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.5804 (t80) REVERT: g 81 ARG cc_start: 0.7963 (ttp-170) cc_final: 0.7633 (ttp-110) REVERT: g 104 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8795 (t0) REVERT: g 145 ASN cc_start: 0.8839 (m-40) cc_final: 0.8501 (t0) REVERT: h 68 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.5880 (t80) REVERT: h 105 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8223 (t0) REVERT: i 81 ARG cc_start: 0.7766 (ttp-110) cc_final: 0.7559 (ttp-110) REVERT: i 104 ASP cc_start: 0.9083 (t0) cc_final: 0.8806 (t0) REVERT: i 145 ASN cc_start: 0.8868 (m-40) cc_final: 0.8531 (t0) REVERT: j 68 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.5845 (t80) REVERT: j 105 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8359 (t0) REVERT: k 81 ARG cc_start: 0.7950 (ttp-110) cc_final: 0.7706 (ttp-110) REVERT: k 104 ASP cc_start: 0.9097 (t0) cc_final: 0.8764 (t0) REVERT: k 145 ASN cc_start: 0.8871 (m-40) cc_final: 0.8541 (t0) REVERT: l 68 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.5828 (t80) REVERT: m 81 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7634 (ttp-110) REVERT: m 104 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8720 (t0) REVERT: m 145 ASN cc_start: 0.8847 (m-40) cc_final: 0.8504 (t0) REVERT: n 68 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.5833 (t80) REVERT: o 81 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7689 (ttp-110) REVERT: o 104 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8771 (t0) REVERT: o 145 ASN cc_start: 0.8857 (m-40) cc_final: 0.8517 (t0) REVERT: p 68 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.5816 (t80) REVERT: p 105 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8429 (m-30) outliers start: 107 outliers final: 90 residues processed: 480 average time/residue: 0.1983 time to fit residues: 150.4749 Evaluate side-chains 533 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 428 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 184 GLN Chi-restraints excluded: chain a residue 187 THR Chi-restraints excluded: chain a residue 195 LEU Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain a residue 219 MET Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 68 TYR Chi-restraints excluded: chain b residue 105 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 187 THR Chi-restraints excluded: chain c residue 195 LEU Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain c residue 219 MET Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 68 TYR Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 187 THR Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 98 ARG Chi-restraints excluded: chain f residue 158 ASP Chi-restraints excluded: chain f residue 190 ILE Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 184 GLN Chi-restraints excluded: chain g residue 187 THR Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 105 ASP Chi-restraints excluded: chain h residue 158 ASP Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 187 THR Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain i residue 219 MET Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 68 TYR Chi-restraints excluded: chain j residue 105 ASP Chi-restraints excluded: chain j residue 158 ASP Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 122 ASN Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 187 THR Chi-restraints excluded: chain k residue 195 LEU Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain k residue 219 MET Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 98 ARG Chi-restraints excluded: chain l residue 190 ILE Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 104 ASP Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 122 ASN Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 68 TYR Chi-restraints excluded: chain n residue 158 ASP Chi-restraints excluded: chain n residue 190 ILE Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 187 THR Chi-restraints excluded: chain o residue 195 LEU Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain o residue 219 MET Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 347 optimal weight: 7.9990 chunk 294 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 316 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.098000 restraints weight = 39602.769| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.55 r_work: 0.2899 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 30096 Z= 0.268 Angle : 0.695 9.046 40488 Z= 0.351 Chirality : 0.051 0.165 4344 Planarity : 0.004 0.034 5240 Dihedral : 4.410 15.985 3992 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.46 % Allowed : 14.96 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % 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: -1.29 (0.14), residues: 3664 helix: -2.64 (0.29), residues: 248 sheet: -0.35 (0.11), residues: 1872 loop : -1.04 (0.17), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG o 81 TYR 0.027 0.003 TYR h 145 PHE 0.017 0.002 PHE l 167 TRP 0.012 0.002 TRP i 67 HIS 0.004 0.001 HIS n 171 Details of bonding type rmsd covalent geometry : bond 0.00661 (30096) covalent geometry : angle 0.69541 (40488) hydrogen bonds : bond 0.03879 ( 1232) hydrogen bonds : angle 5.96337 ( 3144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5630.88 seconds wall clock time: 97 minutes 56.85 seconds (5876.85 seconds total)