Starting phenix.real_space_refine on Wed Mar 4 22:06:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lqj_0947/03_2026/6lqj_0947.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lqj_0947/03_2026/6lqj_0947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lqj_0947/03_2026/6lqj_0947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lqj_0947/03_2026/6lqj_0947.map" model { file = "/net/cci-nas-00/data/ceres_data/6lqj_0947/03_2026/6lqj_0947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lqj_0947/03_2026/6lqj_0947.cif" } resolution = 3.24 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= 0.005 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 54 5.16 5 C 10791 2.51 5 N 2925 2.21 5 O 3330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17100 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "a" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Restraints were copied for chains: B, C, D, E, F, G, H, I, b, c, d, e, f, g, h, i Time building chain proxies: 1.76, per 1000 atoms: 0.10 Number of scatterers: 17100 At special positions: 0 Unit cell: (111, 112, 123, 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 54 16.00 O 3330 8.00 N 2925 7.00 C 10791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 886.5 milliseconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 18 sheets defined 26.0% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 226 through 249 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 100 through 115 Processing helix chain 'B' and resid 226 through 249 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 226 through 249 Processing helix chain 'D' and resid 81 through 90 Processing helix chain 'D' and resid 100 through 115 Processing helix chain 'D' and resid 226 through 249 Processing helix chain 'E' and resid 81 through 90 Processing helix chain 'E' and resid 100 through 115 Processing helix chain 'E' and resid 226 through 249 Processing helix chain 'F' and resid 81 through 90 Processing helix chain 'F' and resid 100 through 115 Processing helix chain 'F' and resid 226 through 249 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 100 through 115 Processing helix chain 'G' and resid 226 through 249 Processing helix chain 'H' and resid 81 through 90 Processing helix chain 'H' and resid 100 through 115 Processing helix chain 'H' and resid 226 through 249 Processing helix chain 'I' and resid 81 through 90 Processing helix chain 'I' and resid 100 through 115 Processing helix chain 'I' and resid 226 through 249 Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 37 through 47 Processing helix chain 'b' and resid 34 through 36 No H-bonds generated for 'chain 'b' and resid 34 through 36' Processing helix chain 'b' and resid 37 through 47 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 37 through 47 Processing helix chain 'd' and resid 34 through 36 No H-bonds generated for 'chain 'd' and resid 34 through 36' Processing helix chain 'd' and resid 37 through 47 Processing helix chain 'e' and resid 34 through 36 No H-bonds generated for 'chain 'e' and resid 34 through 36' Processing helix chain 'e' and resid 37 through 47 Processing helix chain 'f' and resid 34 through 36 No H-bonds generated for 'chain 'f' and resid 34 through 36' Processing helix chain 'f' and resid 37 through 47 Processing helix chain 'g' and resid 34 through 36 No H-bonds generated for 'chain 'g' and resid 34 through 36' Processing helix chain 'g' and resid 37 through 47 Processing helix chain 'h' and resid 34 through 36 No H-bonds generated for 'chain 'h' and resid 34 through 36' Processing helix chain 'h' and resid 37 through 47 Processing helix chain 'i' and resid 34 through 36 No H-bonds generated for 'chain 'i' and resid 34 through 36' Processing helix chain 'i' and resid 37 through 47 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE A 49 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 96 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 51 " --> pdb=" O LEU A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.254A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A 139 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A 179 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER A 141 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ARG A 177 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 143 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN A 175 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR A 145 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA A 173 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER A 147 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN A 171 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 169 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 151 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR A 167 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY A 153 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A 165 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 155 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 163 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN A 180 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 186 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL I 149 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN I 57 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY I 144 " --> pdb=" O GLN I 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN I 57 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY I 144 " --> pdb=" O GLN I 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU I 139 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL I 179 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER I 141 " --> pdb=" O ARG I 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG I 177 " --> pdb=" O SER I 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE I 143 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN I 175 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR I 145 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA I 173 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER I 147 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN I 171 " --> pdb=" O SER I 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU I 169 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER I 151 " --> pdb=" O TYR I 167 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR I 167 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY I 153 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR I 165 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY I 155 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA I 163 " --> pdb=" O GLY I 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN I 180 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE I 186 " --> pdb=" O ASN I 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL G 149 " --> pdb=" O ASN I 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU G 139 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL G 179 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER G 141 " --> pdb=" O ARG G 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG G 177 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE G 143 " --> pdb=" O ASN G 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN G 175 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR G 145 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ALA G 173 " --> pdb=" O TYR G 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER G 147 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN G 171 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU G 169 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER G 151 " --> pdb=" O TYR G 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR G 167 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY G 153 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR G 165 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY G 155 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA G 163 " --> pdb=" O GLY G 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN G 180 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE G 186 " --> pdb=" O ASN G 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG G 213 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL C 149 " --> pdb=" O ASN G 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU C 139 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C 179 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER C 141 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ARG C 177 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE C 143 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN C 175 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR C 145 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA C 173 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER C 147 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN C 171 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 169 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER C 151 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR C 167 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY C 153 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR C 165 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY C 155 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA C 163 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN C 180 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE C 186 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL D 149 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN D 57 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY D 144 " --> pdb=" O GLN D 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN D 57 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY D 144 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU D 139 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 179 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER D 141 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ARG D 177 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE D 143 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN D 175 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR D 145 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA D 173 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER D 147 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN D 171 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU D 169 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER D 151 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR D 167 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY D 153 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR D 165 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY D 155 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA D 163 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN D 180 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 186 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL F 149 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU F 139 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL F 179 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER F 141 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG F 177 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE F 143 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN F 175 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR F 145 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA F 173 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER F 147 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN F 171 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU F 169 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER F 151 " --> pdb=" O TYR F 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR F 167 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY F 153 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR F 165 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY F 155 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA F 163 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN F 180 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE F 186 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG F 213 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL H 149 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN H 57 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY H 144 " --> pdb=" O GLN H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 56 through 57 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 56 through 57 current: chain 'H' and resid 162 through 180 removed outlier: 6.269A pdb=" N ASN H 180 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE H 186 " --> pdb=" O ASN H 180 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG H 213 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL E 149 " --> pdb=" O ASN H 224 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 56 through 57 removed outlier: 7.254A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU E 139 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL E 179 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER E 141 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG E 177 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 143 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN E 175 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR E 145 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ALA E 173 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER E 147 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN E 171 " --> pdb=" O SER E 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 169 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER E 151 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR E 167 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY E 153 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR E 165 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY E 155 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA E 163 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN E 180 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE E 186 " --> pdb=" O ASN E 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG E 213 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL B 149 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU B 139 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 179 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER B 141 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG B 177 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 143 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN B 175 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR B 145 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA B 173 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER B 147 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN B 171 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 169 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER B 151 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR B 167 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY B 153 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR B 165 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY B 155 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 163 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN B 180 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 186 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL A 149 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE B 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU B 96 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 51 " --> pdb=" O LEU B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE C 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU C 96 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 51 " --> pdb=" O LEU C 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 49 through 52 removed outlier: 6.110A pdb=" N ILE D 49 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU D 96 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 51 " --> pdb=" O LEU D 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE E 49 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU E 96 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL E 51 " --> pdb=" O LEU E 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.110A pdb=" N ILE F 49 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 96 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL F 51 " --> pdb=" O LEU F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 49 through 52 removed outlier: 6.110A pdb=" N ILE G 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU G 96 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL G 51 " --> pdb=" O LEU G 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE H 49 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU H 96 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 51 " --> pdb=" O LEU H 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE I 49 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU I 96 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL I 51 " --> pdb=" O LEU I 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 755 hydrogen bonds defined for protein. 2238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5751 1.34 - 1.45: 2233 1.45 - 1.57: 9314 1.57 - 1.68: 0 1.68 - 1.80: 99 Bond restraints: 17397 Sorted by residual: bond pdb=" CA ASP B 164 " pdb=" CB ASP B 164 " ideal model delta sigma weight residual 1.534 1.512 0.023 1.77e-02 3.19e+03 1.65e+00 bond pdb=" CG PRO D 67 " pdb=" CD PRO D 67 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.59e+00 bond pdb=" CA ASP H 164 " pdb=" CB ASP H 164 " ideal model delta sigma weight residual 1.534 1.512 0.022 1.77e-02 3.19e+03 1.58e+00 bond pdb=" CG PRO A 67 " pdb=" CD PRO A 67 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.57e+00 bond pdb=" CG PRO E 67 " pdb=" CD PRO E 67 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.55e+00 ... (remaining 17392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 22055 1.35 - 2.70: 1271 2.70 - 4.05: 227 4.05 - 5.40: 36 5.40 - 6.75: 9 Bond angle restraints: 23598 Sorted by residual: angle pdb=" CA PHE f 31 " pdb=" CB PHE f 31 " pdb=" CG PHE f 31 " ideal model delta sigma weight residual 113.80 116.91 -3.11 1.00e+00 1.00e+00 9.66e+00 angle pdb=" CA PHE i 31 " pdb=" CB PHE i 31 " pdb=" CG PHE i 31 " ideal model delta sigma weight residual 113.80 116.90 -3.10 1.00e+00 1.00e+00 9.58e+00 angle pdb=" CA PHE a 31 " pdb=" CB PHE a 31 " pdb=" CG PHE a 31 " ideal model delta sigma weight residual 113.80 116.88 -3.08 1.00e+00 1.00e+00 9.51e+00 angle pdb=" CA PHE d 31 " pdb=" CB PHE d 31 " pdb=" CG PHE d 31 " ideal model delta sigma weight residual 113.80 116.88 -3.08 1.00e+00 1.00e+00 9.49e+00 angle pdb=" CA PHE e 31 " pdb=" CB PHE e 31 " pdb=" CG PHE e 31 " ideal model delta sigma weight residual 113.80 116.86 -3.06 1.00e+00 1.00e+00 9.35e+00 ... (remaining 23593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 8896 15.66 - 31.31: 1010 31.31 - 46.97: 291 46.97 - 62.62: 135 62.62 - 78.28: 18 Dihedral angle restraints: 10350 sinusoidal: 4032 harmonic: 6318 Sorted by residual: dihedral pdb=" CA GLY f 32 " pdb=" C GLY f 32 " pdb=" N GLY f 33 " pdb=" CA GLY f 33 " ideal model delta harmonic sigma weight residual 180.00 148.98 31.02 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLY d 32 " pdb=" C GLY d 32 " pdb=" N GLY d 33 " pdb=" CA GLY d 33 " ideal model delta harmonic sigma weight residual 180.00 148.98 31.02 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLY e 32 " pdb=" C GLY e 32 " pdb=" N GLY e 33 " pdb=" CA GLY e 33 " ideal model delta harmonic sigma weight residual 180.00 149.02 30.98 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1530 0.036 - 0.072: 831 0.072 - 0.108: 179 0.108 - 0.145: 102 0.145 - 0.181: 13 Chirality restraints: 2655 Sorted by residual: chirality pdb=" CA PHE h 31 " pdb=" N PHE h 31 " pdb=" C PHE h 31 " pdb=" CB PHE h 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA PHE i 31 " pdb=" N PHE i 31 " pdb=" C PHE i 31 " pdb=" CB PHE i 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA PHE e 31 " pdb=" N PHE e 31 " pdb=" C PHE e 31 " pdb=" CB PHE e 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 2652 not shown) Planarity restraints: 3123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE g 31 " -0.019 2.00e-02 2.50e+03 1.74e-02 5.29e+00 pdb=" CG PHE g 31 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE g 31 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE g 31 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE g 31 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE g 31 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE g 31 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE e 31 " 0.019 2.00e-02 2.50e+03 1.73e-02 5.27e+00 pdb=" CG PHE e 31 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE e 31 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE e 31 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE e 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE e 31 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE e 31 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE c 31 " -0.019 2.00e-02 2.50e+03 1.73e-02 5.25e+00 pdb=" CG PHE c 31 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE c 31 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE c 31 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE c 31 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE c 31 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE c 31 " -0.003 2.00e-02 2.50e+03 ... (remaining 3120 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2731 2.75 - 3.29: 16427 3.29 - 3.83: 29104 3.83 - 4.36: 35687 4.36 - 4.90: 64804 Nonbonded interactions: 148753 Sorted by model distance: nonbonded pdb=" OD1 ASN I 224 " pdb=" N MET i 22 " model vdw 2.216 3.120 nonbonded pdb=" O GLN A 102 " pdb=" ND2 ASN A 106 " model vdw 2.226 3.120 nonbonded pdb=" O GLN H 102 " pdb=" ND2 ASN H 106 " model vdw 2.226 3.120 nonbonded pdb=" O GLN G 102 " pdb=" ND2 ASN G 106 " model vdw 2.227 3.120 nonbonded pdb=" O GLN I 102 " pdb=" ND2 ASN I 106 " model vdw 2.227 3.120 ... (remaining 148748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } 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: 1.400 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.930 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 0.044 17397 Z= 0.319 Angle : 0.739 6.750 23598 Z= 0.435 Chirality : 0.048 0.181 2655 Planarity : 0.004 0.039 3123 Dihedral : 16.291 78.277 6318 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 5.34 % Allowed : 15.53 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -3.28 (0.16), residues: 2178 helix: -1.56 (0.17), residues: 603 sheet: -1.31 (0.21), residues: 693 loop : -3.29 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG b 27 TYR 0.015 0.001 TYR B 158 PHE 0.040 0.003 PHE g 31 TRP 0.006 0.002 TRP C 252 Details of bonding type rmsd covalent geometry : bond 0.00701 (17397) covalent geometry : angle 0.73928 (23598) hydrogen bonds : bond 0.16207 ( 755) hydrogen bonds : angle 8.11394 ( 2238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 287 time to evaluate : 0.806 Fit side-chains REVERT: A 215 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8303 (tp) REVERT: B 146 GLU cc_start: 0.7309 (tp30) cc_final: 0.7076 (tp30) REVERT: C 59 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7926 (mt-10) REVERT: C 137 MET cc_start: 0.8214 (ttm) cc_final: 0.7706 (ttm) REVERT: C 139 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7327 (mm-30) REVERT: C 213 ARG cc_start: 0.8682 (mmt-90) cc_final: 0.8279 (mpt180) REVERT: C 228 MET cc_start: 0.8442 (ptt) cc_final: 0.8102 (ptp) REVERT: D 75 VAL cc_start: 0.9147 (t) cc_final: 0.8879 (m) REVERT: D 107 GLU cc_start: 0.8490 (tp30) cc_final: 0.8243 (tp30) REVERT: D 131 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7890 (mp) REVERT: D 139 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7211 (mm-30) REVERT: F 59 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8069 (mt-10) REVERT: F 75 VAL cc_start: 0.9158 (t) cc_final: 0.8893 (m) REVERT: F 139 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7112 (mm-30) REVERT: F 146 GLU cc_start: 0.7236 (tp30) cc_final: 0.6864 (tp30) REVERT: F 240 ILE cc_start: 0.8747 (mm) cc_final: 0.8499 (mm) REVERT: G 59 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8062 (mt-10) REVERT: G 75 VAL cc_start: 0.9142 (t) cc_final: 0.8887 (m) REVERT: G 137 MET cc_start: 0.8192 (ttm) cc_final: 0.7933 (ttp) REVERT: G 207 ARG cc_start: 0.7469 (ptt90) cc_final: 0.7268 (ptm-80) REVERT: G 213 ARG cc_start: 0.8586 (mmt-90) cc_final: 0.8328 (mpt180) REVERT: H 75 VAL cc_start: 0.9101 (t) cc_final: 0.8842 (m) REVERT: H 213 ARG cc_start: 0.8620 (mmt-90) cc_final: 0.8255 (mmt180) REVERT: I 170 ASP cc_start: 0.8151 (m-30) cc_final: 0.7889 (m-30) REVERT: I 213 ARG cc_start: 0.8552 (mmt-90) cc_final: 0.8195 (mpt180) REVERT: I 215 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8165 (tt) REVERT: a 22 MET cc_start: 0.8715 (mtt) cc_final: 0.8450 (mtt) REVERT: a 52 LYS cc_start: 0.8528 (mppt) cc_final: 0.8101 (mppt) REVERT: e 22 MET cc_start: 0.8679 (mtt) cc_final: 0.8424 (mtt) REVERT: e 52 LYS cc_start: 0.8508 (mppt) cc_final: 0.8304 (mtmm) REVERT: f 52 LYS cc_start: 0.8402 (mppt) cc_final: 0.8164 (mtmm) REVERT: i 22 MET cc_start: 0.8843 (mtt) cc_final: 0.8575 (mtp) outliers start: 99 outliers final: 51 residues processed: 371 average time/residue: 0.1474 time to fit residues: 81.0012 Evaluate side-chains 307 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 237 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 77 GLN A 148 ASN A 244 ASN B 77 GLN B 148 ASN B 244 ASN C 62 GLN C 77 GLN C 106 ASN C 148 ASN C 244 ASN D 62 GLN D 77 GLN D 106 ASN D 135 ASN D 148 ASN D 244 ASN E 62 GLN E 77 GLN E 106 ASN E 148 ASN E 244 ASN F 62 GLN F 77 GLN F 106 ASN F 148 ASN F 244 ASN G 62 GLN G 70 ASN G 77 GLN G 106 ASN G 148 ASN G 244 ASN H 62 GLN H 77 GLN H 106 ASN H 148 ASN H 244 ASN I 77 GLN I 106 ASN I 148 ASN I 244 ASN a 28 ASN b 28 ASN b 36 ASN c 28 ASN d 28 ASN e 28 ASN f 28 ASN g 28 ASN h 28 ASN i 28 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.131345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.111301 restraints weight = 18409.446| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.14 r_work: 0.3115 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17397 Z= 0.194 Angle : 0.611 8.658 23598 Z= 0.332 Chirality : 0.046 0.150 2655 Planarity : 0.004 0.041 3123 Dihedral : 8.491 57.253 2467 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.26 % Allowed : 16.67 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.18), residues: 2178 helix: -0.13 (0.20), residues: 603 sheet: -1.04 (0.22), residues: 693 loop : -2.86 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 157 TYR 0.013 0.001 TYR E 158 PHE 0.029 0.002 PHE h 31 TRP 0.008 0.001 TRP F 252 Details of bonding type rmsd covalent geometry : bond 0.00437 (17397) covalent geometry : angle 0.61104 (23598) hydrogen bonds : bond 0.03585 ( 755) hydrogen bonds : angle 5.57906 ( 2238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 263 time to evaluate : 0.719 Fit side-chains REVERT: A 109 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8586 (mtmt) REVERT: A 137 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8061 (ttm) REVERT: A 139 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 48 LYS cc_start: 0.7601 (mttp) cc_final: 0.7347 (mttm) REVERT: B 59 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8233 (mt-10) REVERT: B 131 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7806 (mp) REVERT: B 139 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 215 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8328 (tp) REVERT: B 218 GLU cc_start: 0.7903 (pt0) cc_final: 0.7688 (pt0) REVERT: C 59 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8216 (mt-10) REVERT: C 137 MET cc_start: 0.8528 (ttm) cc_final: 0.8038 (ttm) REVERT: C 139 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7596 (mm-30) REVERT: C 213 ARG cc_start: 0.8834 (mmt-90) cc_final: 0.8597 (mpt180) REVERT: C 228 MET cc_start: 0.8332 (ptt) cc_final: 0.8096 (ptp) REVERT: D 131 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7858 (mp) REVERT: D 139 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7443 (mm-30) REVERT: F 59 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8278 (mt-10) REVERT: F 139 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7498 (mm-30) REVERT: F 225 GLU cc_start: 0.8784 (tt0) cc_final: 0.8377 (tt0) REVERT: F 240 ILE cc_start: 0.8608 (mm) cc_final: 0.8299 (mm) REVERT: G 131 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7964 (mp) REVERT: G 139 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7620 (mm-30) REVERT: G 218 GLU cc_start: 0.7921 (pt0) cc_final: 0.7682 (pt0) REVERT: G 240 ILE cc_start: 0.8492 (mm) cc_final: 0.8273 (mt) REVERT: H 59 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8186 (mt-10) REVERT: H 131 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7996 (mp) REVERT: H 137 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8085 (ttm) REVERT: H 139 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7601 (mm-30) REVERT: H 215 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8388 (tp) REVERT: H 249 ARG cc_start: 0.7242 (ptm-80) cc_final: 0.7031 (ptm-80) REVERT: I 48 LYS cc_start: 0.7707 (mttm) cc_final: 0.7493 (mttm) REVERT: I 109 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8710 (mtmt) REVERT: I 213 ARG cc_start: 0.8855 (mmt-90) cc_final: 0.8568 (mpt180) REVERT: I 232 MET cc_start: 0.8885 (tpt) cc_final: 0.8104 (tpt) REVERT: a 22 MET cc_start: 0.8874 (mtt) cc_final: 0.8605 (mtt) REVERT: e 28 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7621 (t0) REVERT: e 52 LYS cc_start: 0.8349 (mppt) cc_final: 0.8112 (mtmm) REVERT: i 22 MET cc_start: 0.9018 (mtt) cc_final: 0.8802 (mtp) REVERT: i 28 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7732 (t0) outliers start: 79 outliers final: 55 residues processed: 316 average time/residue: 0.1519 time to fit residues: 71.0334 Evaluate side-chains 302 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 135 ASN Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 ASN Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain i residue 28 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 140 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 68 optimal weight: 0.0040 chunk 53 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 48 GLN e 28 ASN f 28 ASN f 48 GLN i 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.129644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.109316 restraints weight = 18644.045| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.16 r_work: 0.3032 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17397 Z= 0.224 Angle : 0.619 8.561 23598 Z= 0.334 Chirality : 0.047 0.162 2655 Planarity : 0.004 0.041 3123 Dihedral : 8.276 58.196 2440 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 5.29 % Allowed : 16.77 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.18), residues: 2178 helix: 0.42 (0.20), residues: 603 sheet: -0.85 (0.22), residues: 693 loop : -2.71 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 213 TYR 0.014 0.001 TYR B 158 PHE 0.036 0.002 PHE i 31 TRP 0.007 0.001 TRP F 252 Details of bonding type rmsd covalent geometry : bond 0.00511 (17397) covalent geometry : angle 0.61906 (23598) hydrogen bonds : bond 0.03355 ( 755) hydrogen bonds : angle 5.32715 ( 2238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 242 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7751 (mt-10) REVERT: A 137 MET cc_start: 0.8429 (ttm) cc_final: 0.7857 (ttm) REVERT: A 139 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 215 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8424 (tp) REVERT: A 218 GLU cc_start: 0.7989 (pt0) cc_final: 0.7763 (pt0) REVERT: A 225 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7839 (tt0) REVERT: B 48 LYS cc_start: 0.7572 (mttp) cc_final: 0.7318 (mttm) REVERT: B 131 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7808 (mp) REVERT: B 139 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 164 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7789 (p0) REVERT: B 218 GLU cc_start: 0.7952 (pt0) cc_final: 0.7720 (pt0) REVERT: C 59 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8193 (mt-10) REVERT: C 139 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7598 (mm-30) REVERT: C 213 ARG cc_start: 0.8855 (mmt-90) cc_final: 0.8582 (mpt180) REVERT: D 107 GLU cc_start: 0.8863 (tp30) cc_final: 0.8590 (tp30) REVERT: D 131 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7918 (mp) REVERT: D 139 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7462 (mm-30) REVERT: F 59 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8278 (mt-10) REVERT: F 139 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7441 (mm-30) REVERT: F 225 GLU cc_start: 0.8789 (tt0) cc_final: 0.8406 (tt0) REVERT: F 240 ILE cc_start: 0.8528 (mm) cc_final: 0.8215 (mm) REVERT: G 131 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7929 (mp) REVERT: G 146 GLU cc_start: 0.7598 (tp30) cc_final: 0.7355 (tp30) REVERT: H 59 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8168 (mt-10) REVERT: H 131 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7968 (mp) REVERT: H 137 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7925 (ttm) REVERT: H 139 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7648 (mm-30) REVERT: H 215 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8386 (tp) REVERT: H 225 GLU cc_start: 0.8792 (tt0) cc_final: 0.8375 (tt0) REVERT: I 139 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7602 (mm-30) REVERT: I 213 ARG cc_start: 0.8917 (mmt-90) cc_final: 0.8707 (mpt180) REVERT: I 232 MET cc_start: 0.8819 (tpt) cc_final: 0.8053 (tpt) REVERT: a 22 MET cc_start: 0.8920 (mtt) cc_final: 0.8674 (mtt) REVERT: e 28 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7547 (t0) REVERT: e 52 LYS cc_start: 0.8303 (mppt) cc_final: 0.8076 (mtmm) REVERT: i 22 MET cc_start: 0.8972 (mtt) cc_final: 0.8725 (mtp) REVERT: i 28 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7632 (t0) outliers start: 98 outliers final: 75 residues processed: 314 average time/residue: 0.1418 time to fit residues: 66.1588 Evaluate side-chains 324 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 239 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain i residue 28 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN e 28 ASN f 28 ASN i 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.127679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.107156 restraints weight = 18563.010| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.15 r_work: 0.3000 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 17397 Z= 0.290 Angle : 0.666 8.565 23598 Z= 0.359 Chirality : 0.048 0.168 2655 Planarity : 0.004 0.041 3123 Dihedral : 8.510 59.880 2439 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 6.47 % Allowed : 17.53 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.18), residues: 2178 helix: 0.54 (0.20), residues: 603 sheet: -0.71 (0.23), residues: 648 loop : -2.74 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG i 27 TYR 0.016 0.001 TYR B 158 PHE 0.043 0.003 PHE f 31 TRP 0.006 0.002 TRP F 252 Details of bonding type rmsd covalent geometry : bond 0.00665 (17397) covalent geometry : angle 0.66645 (23598) hydrogen bonds : bond 0.03401 ( 755) hydrogen bonds : angle 5.35406 ( 2238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 236 time to evaluate : 0.672 Fit side-chains REVERT: A 137 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7883 (ttm) REVERT: A 139 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 215 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8438 (tp) REVERT: A 218 GLU cc_start: 0.8022 (pt0) cc_final: 0.7805 (pt0) REVERT: A 225 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7870 (tt0) REVERT: B 48 LYS cc_start: 0.7613 (mttp) cc_final: 0.7329 (mttm) REVERT: B 59 GLU cc_start: 0.8624 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 106 ASN cc_start: 0.7891 (m-40) cc_final: 0.7580 (m-40) REVERT: B 109 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8470 (mtmt) REVERT: B 131 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7870 (mp) REVERT: B 139 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7765 (mm-30) REVERT: B 218 GLU cc_start: 0.7998 (pt0) cc_final: 0.7787 (pt0) REVERT: C 137 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8116 (ttm) REVERT: C 139 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7646 (mm-30) REVERT: C 213 ARG cc_start: 0.8910 (mmt-90) cc_final: 0.8470 (mpt180) REVERT: D 59 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8349 (mt-10) REVERT: D 107 GLU cc_start: 0.8872 (tp30) cc_final: 0.8604 (tp30) REVERT: D 131 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7911 (mp) REVERT: D 139 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7506 (mm-30) REVERT: E 139 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7769 (mm-30) REVERT: E 146 GLU cc_start: 0.7737 (tp30) cc_final: 0.7405 (tp30) REVERT: E 170 ASP cc_start: 0.8510 (m-30) cc_final: 0.8289 (m-30) REVERT: E 215 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8583 (tp) REVERT: F 59 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8182 (mt-10) REVERT: F 109 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8645 (mtmt) REVERT: F 139 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7561 (mm-30) REVERT: F 176 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8674 (mt) REVERT: F 225 GLU cc_start: 0.8783 (tt0) cc_final: 0.8523 (tt0) REVERT: G 131 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7986 (mp) REVERT: G 164 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8100 (p0) REVERT: G 215 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8537 (tp) REVERT: H 59 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8152 (mt-10) REVERT: H 131 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8005 (mp) REVERT: H 139 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7699 (mm-30) REVERT: H 164 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8079 (p0) REVERT: H 215 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8412 (tp) REVERT: H 225 GLU cc_start: 0.8746 (tt0) cc_final: 0.8335 (tt0) REVERT: I 139 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7653 (mm-30) REVERT: I 176 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8763 (mt) REVERT: I 213 ARG cc_start: 0.8966 (mmt-90) cc_final: 0.8750 (mpt180) REVERT: I 215 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8489 (tt) REVERT: I 232 MET cc_start: 0.8827 (tpt) cc_final: 0.8153 (tpt) REVERT: e 28 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7546 (t0) REVERT: e 52 LYS cc_start: 0.8359 (mppt) cc_final: 0.8084 (mtmm) REVERT: i 22 MET cc_start: 0.9008 (mtt) cc_final: 0.8793 (mtp) REVERT: i 28 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7745 (t0) outliers start: 120 outliers final: 86 residues processed: 323 average time/residue: 0.1451 time to fit residues: 70.1679 Evaluate side-chains 333 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 230 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 135 ASN Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 ASN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain e residue 21 THR Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain i residue 28 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 167 optimal weight: 0.0270 chunk 130 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 28 ASN f 28 ASN i 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.115636 restraints weight = 18190.307| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.10 r_work: 0.3169 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17397 Z= 0.126 Angle : 0.551 9.224 23598 Z= 0.296 Chirality : 0.044 0.148 2655 Planarity : 0.003 0.038 3123 Dihedral : 8.047 59.957 2439 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 5.18 % Allowed : 19.31 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2178 helix: 1.14 (0.21), residues: 603 sheet: -0.62 (0.24), residues: 558 loop : -2.14 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 27 TYR 0.008 0.001 TYR B 199 PHE 0.028 0.002 PHE f 31 TRP 0.010 0.001 TRP F 252 Details of bonding type rmsd covalent geometry : bond 0.00288 (17397) covalent geometry : angle 0.55115 (23598) hydrogen bonds : bond 0.02864 ( 755) hydrogen bonds : angle 5.02046 ( 2238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 238 time to evaluate : 0.637 Fit side-chains REVERT: A 137 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8239 (ttm) REVERT: A 215 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8475 (tp) REVERT: A 225 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7868 (tt0) REVERT: B 106 ASN cc_start: 0.7876 (m-40) cc_final: 0.7617 (m-40) REVERT: B 131 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7912 (mp) REVERT: B 139 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7591 (mm-30) REVERT: B 164 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7899 (p0) REVERT: C 228 MET cc_start: 0.8391 (ptt) cc_final: 0.8154 (ptp) REVERT: D 131 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7853 (mp) REVERT: D 139 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7460 (mm-30) REVERT: E 109 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8816 (mtpt) REVERT: E 146 GLU cc_start: 0.7354 (tp30) cc_final: 0.7148 (tp30) REVERT: F 139 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7472 (mm-30) REVERT: F 240 ILE cc_start: 0.8644 (mm) cc_final: 0.8389 (mm) REVERT: G 131 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7757 (mp) REVERT: H 131 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7799 (mp) REVERT: H 137 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7727 (ttp) REVERT: H 139 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7638 (mm-30) REVERT: H 146 GLU cc_start: 0.7418 (tp30) cc_final: 0.7137 (tp30) REVERT: H 164 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8033 (p0) REVERT: H 225 GLU cc_start: 0.8674 (tt0) cc_final: 0.8313 (tt0) REVERT: I 131 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7852 (mp) REVERT: I 139 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7686 (mm-30) REVERT: I 213 ARG cc_start: 0.8810 (mmt-90) cc_final: 0.8599 (mpt180) REVERT: I 215 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8513 (tp) REVERT: I 232 MET cc_start: 0.8848 (tpt) cc_final: 0.8296 (tpt) REVERT: b 22 MET cc_start: 0.8859 (mtp) cc_final: 0.8593 (mtp) REVERT: i 22 MET cc_start: 0.8986 (mtt) cc_final: 0.8712 (mtp) REVERT: i 28 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7475 (t0) outliers start: 96 outliers final: 59 residues processed: 304 average time/residue: 0.1415 time to fit residues: 65.0515 Evaluate side-chains 287 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 216 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 ASN Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain d residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain i residue 28 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 88 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 211 optimal weight: 0.0870 chunk 144 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN f 28 ASN i 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.133009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113139 restraints weight = 18239.779| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.11 r_work: 0.3137 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17397 Z= 0.165 Angle : 0.563 8.244 23598 Z= 0.303 Chirality : 0.045 0.154 2655 Planarity : 0.004 0.037 3123 Dihedral : 7.934 59.608 2436 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.91 % Allowed : 20.01 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.19), residues: 2178 helix: 1.30 (0.21), residues: 603 sheet: -0.45 (0.23), residues: 648 loop : -2.46 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 249 TYR 0.010 0.001 TYR B 158 PHE 0.029 0.002 PHE i 31 TRP 0.008 0.001 TRP F 252 Details of bonding type rmsd covalent geometry : bond 0.00377 (17397) covalent geometry : angle 0.56325 (23598) hydrogen bonds : bond 0.02879 ( 755) hydrogen bonds : angle 4.97717 ( 2238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 214 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8097 (ttm) REVERT: A 139 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7758 (mm-30) REVERT: A 164 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.8094 (p0) REVERT: A 215 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8500 (tp) REVERT: A 225 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7891 (tt0) REVERT: A 228 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8277 (ptp) REVERT: B 106 ASN cc_start: 0.7891 (m-40) cc_final: 0.7650 (m-40) REVERT: B 131 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8017 (mp) REVERT: B 139 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 164 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7795 (p0) REVERT: C 137 MET cc_start: 0.8590 (ttm) cc_final: 0.8141 (ttm) REVERT: C 139 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7651 (mm-30) REVERT: D 139 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7495 (mm-30) REVERT: F 139 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7506 (mm-30) REVERT: F 225 GLU cc_start: 0.8724 (tt0) cc_final: 0.8400 (tt0) REVERT: F 240 ILE cc_start: 0.8600 (mm) cc_final: 0.8346 (mm) REVERT: G 57 GLN cc_start: 0.8031 (tt0) cc_final: 0.7754 (mm-40) REVERT: G 146 GLU cc_start: 0.7582 (tp30) cc_final: 0.7268 (tp30) REVERT: G 215 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8544 (tp) REVERT: H 131 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7869 (mp) REVERT: H 139 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7710 (mm-30) REVERT: H 164 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8049 (p0) REVERT: H 225 GLU cc_start: 0.8685 (tt0) cc_final: 0.8420 (tt0) REVERT: I 131 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7951 (mp) REVERT: I 139 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7641 (mm-30) REVERT: I 213 ARG cc_start: 0.8856 (mmt-90) cc_final: 0.8652 (mpt180) REVERT: I 215 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8520 (tp) REVERT: I 232 MET cc_start: 0.8830 (tpt) cc_final: 0.8298 (tpt) REVERT: b 22 MET cc_start: 0.8821 (mtp) cc_final: 0.8511 (mtp) REVERT: i 22 MET cc_start: 0.8997 (mtt) cc_final: 0.8713 (mtp) REVERT: i 28 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7628 (t0) outliers start: 91 outliers final: 65 residues processed: 284 average time/residue: 0.1441 time to fit residues: 61.2104 Evaluate side-chains 287 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 210 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 ASN Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain i residue 28 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 192 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 87 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 135 ASN f 28 ASN i 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.127790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.107828 restraints weight = 18521.117| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.09 r_work: 0.3192 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 17397 Z= 0.300 Angle : 0.663 7.928 23598 Z= 0.358 Chirality : 0.049 0.168 2655 Planarity : 0.004 0.041 3123 Dihedral : 8.087 59.841 2430 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 5.45 % Allowed : 19.58 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.18), residues: 2178 helix: 1.00 (0.20), residues: 603 sheet: -0.50 (0.23), residues: 648 loop : -2.59 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.017 0.001 TYR G 158 PHE 0.049 0.003 PHE i 31 TRP 0.005 0.001 TRP I 252 Details of bonding type rmsd covalent geometry : bond 0.00688 (17397) covalent geometry : angle 0.66256 (23598) hydrogen bonds : bond 0.03275 ( 755) hydrogen bonds : angle 5.23823 ( 2238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 218 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8057 (ttm) REVERT: A 139 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 215 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8518 (tp) REVERT: A 225 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7917 (tt0) REVERT: B 106 ASN cc_start: 0.7935 (m-40) cc_final: 0.7703 (m-40) REVERT: B 131 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7989 (mp) REVERT: B 139 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7851 (mm-30) REVERT: B 164 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7783 (p0) REVERT: B 218 GLU cc_start: 0.7873 (pt0) cc_final: 0.7660 (pt0) REVERT: D 139 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7562 (mm-30) REVERT: E 139 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7884 (mm-30) REVERT: E 215 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8657 (tp) REVERT: F 59 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8200 (mt-10) REVERT: F 139 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7568 (mm-30) REVERT: F 146 GLU cc_start: 0.7738 (tp30) cc_final: 0.7517 (tp30) REVERT: F 225 GLU cc_start: 0.8728 (tt0) cc_final: 0.8410 (tt0) REVERT: G 131 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8068 (mp) REVERT: G 139 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7691 (mm-30) REVERT: G 146 GLU cc_start: 0.7698 (tp30) cc_final: 0.7365 (tp30) REVERT: G 215 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8584 (tp) REVERT: H 59 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8084 (mt-10) REVERT: H 131 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7977 (mp) REVERT: H 139 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7696 (mm-30) REVERT: H 146 GLU cc_start: 0.7672 (tp30) cc_final: 0.7442 (tp30) REVERT: H 164 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8144 (p0) REVERT: I 139 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7563 (mm-30) REVERT: I 176 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8798 (mt) REVERT: I 213 ARG cc_start: 0.8966 (mmt-90) cc_final: 0.8748 (mpt180) REVERT: I 215 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8511 (tt) REVERT: I 232 MET cc_start: 0.8806 (tpt) cc_final: 0.8220 (tpt) REVERT: c 25 GLN cc_start: 0.8459 (mt0) cc_final: 0.8229 (mt0) REVERT: e 52 LYS cc_start: 0.8397 (mppt) cc_final: 0.8162 (mtmm) REVERT: i 28 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7798 (t0) outliers start: 101 outliers final: 70 residues processed: 295 average time/residue: 0.1454 time to fit residues: 64.0633 Evaluate side-chains 294 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 212 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 135 ASN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 ASN Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain i residue 28 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 55 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 147 optimal weight: 0.0040 chunk 111 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 28 ASN i 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.134812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.115500 restraints weight = 18218.771| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.09 r_work: 0.3118 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17397 Z= 0.125 Angle : 0.549 9.047 23598 Z= 0.295 Chirality : 0.044 0.151 2655 Planarity : 0.003 0.036 3123 Dihedral : 7.580 59.899 2430 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.31 % Allowed : 20.87 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.19), residues: 2178 helix: 1.61 (0.21), residues: 603 sheet: -0.40 (0.25), residues: 558 loop : -2.00 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 27 TYR 0.008 0.001 TYR A 158 PHE 0.031 0.002 PHE i 31 TRP 0.011 0.001 TRP C 252 Details of bonding type rmsd covalent geometry : bond 0.00282 (17397) covalent geometry : angle 0.54936 (23598) hydrogen bonds : bond 0.02792 ( 755) hydrogen bonds : angle 4.95775 ( 2238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 228 time to evaluate : 0.679 Fit side-chains REVERT: A 137 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8049 (ttm) REVERT: A 139 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 146 GLU cc_start: 0.7638 (tp30) cc_final: 0.7319 (tp30) REVERT: A 215 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8481 (tp) REVERT: A 225 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7801 (tt0) REVERT: B 106 ASN cc_start: 0.7894 (m-40) cc_final: 0.7595 (m-40) REVERT: B 131 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7891 (mp) REVERT: B 139 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7678 (mm-30) REVERT: B 164 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7949 (p0) REVERT: C 170 ASP cc_start: 0.8386 (m-30) cc_final: 0.8054 (m-30) REVERT: D 139 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7444 (mm-30) REVERT: D 164 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7922 (p0) REVERT: E 215 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8558 (tp) REVERT: F 139 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7382 (mm-30) REVERT: F 225 GLU cc_start: 0.8665 (tt0) cc_final: 0.8282 (tt0) REVERT: G 48 LYS cc_start: 0.7185 (mtpp) cc_final: 0.6782 (mttp) REVERT: G 57 GLN cc_start: 0.7944 (tt0) cc_final: 0.7606 (mm110) REVERT: G 131 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7654 (mp) REVERT: G 146 GLU cc_start: 0.7522 (tp30) cc_final: 0.7208 (tp30) REVERT: H 131 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7728 (mp) REVERT: H 139 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7617 (mm-30) REVERT: H 146 GLU cc_start: 0.7489 (tp30) cc_final: 0.7179 (tp30) REVERT: H 164 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8115 (p0) REVERT: H 225 GLU cc_start: 0.8693 (tt0) cc_final: 0.8221 (tt0) REVERT: I 131 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7776 (mp) REVERT: I 139 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7552 (mm-30) REVERT: I 213 ARG cc_start: 0.8872 (mmt-90) cc_final: 0.8670 (mpt180) REVERT: I 215 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8572 (tp) REVERT: I 232 MET cc_start: 0.8661 (tpt) cc_final: 0.8100 (tpt) REVERT: b 22 MET cc_start: 0.8832 (mtp) cc_final: 0.8542 (mtp) REVERT: d 22 MET cc_start: 0.8927 (mtp) cc_final: 0.8596 (mtp) REVERT: g 52 LYS cc_start: 0.8235 (mppt) cc_final: 0.7973 (mtmm) REVERT: i 28 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7584 (t0) outliers start: 80 outliers final: 59 residues processed: 284 average time/residue: 0.1446 time to fit residues: 61.7807 Evaluate side-chains 285 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 214 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 ASN Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain i residue 28 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 204 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN f 28 ASN i 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.130214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.110480 restraints weight = 18453.543| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.10 r_work: 0.3050 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17397 Z= 0.225 Angle : 0.605 7.974 23598 Z= 0.327 Chirality : 0.047 0.160 2655 Planarity : 0.004 0.036 3123 Dihedral : 7.715 59.378 2429 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 5.02 % Allowed : 20.55 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.19), residues: 2178 helix: 1.49 (0.21), residues: 603 sheet: -0.45 (0.24), residues: 594 loop : -1.92 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 207 TYR 0.015 0.001 TYR B 158 PHE 0.040 0.003 PHE i 31 TRP 0.006 0.001 TRP F 252 Details of bonding type rmsd covalent geometry : bond 0.00516 (17397) covalent geometry : angle 0.60542 (23598) hydrogen bonds : bond 0.03031 ( 755) hydrogen bonds : angle 5.06946 ( 2238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 203 time to evaluate : 0.637 Fit side-chains REVERT: A 137 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8020 (ttm) REVERT: A 139 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 215 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8549 (tp) REVERT: A 218 GLU cc_start: 0.7967 (pt0) cc_final: 0.7764 (pt0) REVERT: A 225 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7817 (tt0) REVERT: B 106 ASN cc_start: 0.7887 (m-40) cc_final: 0.7612 (m-40) REVERT: B 131 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7922 (mp) REVERT: B 139 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 164 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7835 (p0) REVERT: C 175 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8786 (t0) REVERT: D 139 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7515 (mm-30) REVERT: E 139 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7780 (mm-30) REVERT: E 215 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8608 (tp) REVERT: F 59 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8131 (mt-10) REVERT: F 139 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7482 (mm-30) REVERT: F 225 GLU cc_start: 0.8704 (tt0) cc_final: 0.8315 (tt0) REVERT: G 48 LYS cc_start: 0.7231 (mtpp) cc_final: 0.6959 (mttp) REVERT: G 131 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7831 (mp) REVERT: G 139 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7675 (mm-30) REVERT: H 131 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7867 (mp) REVERT: H 139 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7661 (mm-30) REVERT: H 164 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8155 (p0) REVERT: H 225 GLU cc_start: 0.8725 (tt0) cc_final: 0.8225 (tt0) REVERT: I 139 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7580 (mm-30) REVERT: I 213 ARG cc_start: 0.8958 (mmt-90) cc_final: 0.8748 (mpt180) REVERT: I 215 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8566 (tp) REVERT: I 232 MET cc_start: 0.8662 (tpt) cc_final: 0.8077 (tpt) REVERT: c 25 GLN cc_start: 0.8468 (mt0) cc_final: 0.8225 (mt0) REVERT: e 52 LYS cc_start: 0.8290 (mppt) cc_final: 0.8053 (mtmm) REVERT: i 28 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7652 (t0) outliers start: 93 outliers final: 67 residues processed: 275 average time/residue: 0.1490 time to fit residues: 61.6799 Evaluate side-chains 277 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 199 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 ASN Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain i residue 28 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 90 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 181 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 21 optimal weight: 0.2980 chunk 93 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 28 ASN i 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.134438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.115200 restraints weight = 18158.853| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.09 r_work: 0.3163 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17397 Z= 0.138 Angle : 0.552 8.678 23598 Z= 0.296 Chirality : 0.044 0.150 2655 Planarity : 0.003 0.036 3123 Dihedral : 7.430 59.786 2429 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 4.15 % Allowed : 21.20 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.19), residues: 2178 helix: 1.89 (0.21), residues: 603 sheet: -0.38 (0.24), residues: 594 loop : -1.82 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 249 TYR 0.009 0.001 TYR A 158 PHE 0.026 0.002 PHE i 31 TRP 0.010 0.001 TRP F 252 Details of bonding type rmsd covalent geometry : bond 0.00314 (17397) covalent geometry : angle 0.55157 (23598) hydrogen bonds : bond 0.02790 ( 755) hydrogen bonds : angle 4.93230 ( 2238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 219 time to evaluate : 0.679 Fit side-chains REVERT: A 137 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8058 (ttm) REVERT: A 139 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7684 (mm-30) REVERT: A 225 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7819 (tt0) REVERT: B 106 ASN cc_start: 0.7900 (m-40) cc_final: 0.7597 (m-40) REVERT: B 131 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7941 (mp) REVERT: B 139 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7707 (mm-30) REVERT: B 164 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7937 (p0) REVERT: C 175 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8717 (t0) REVERT: D 137 MET cc_start: 0.8290 (ttm) cc_final: 0.7799 (ttp) REVERT: D 139 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7489 (mm-30) REVERT: E 139 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7719 (mm-30) REVERT: E 146 GLU cc_start: 0.7386 (tp30) cc_final: 0.7173 (tp30) REVERT: E 215 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8564 (tp) REVERT: F 139 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7480 (mm-30) REVERT: F 164 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7990 (p0) REVERT: F 225 GLU cc_start: 0.8645 (tt0) cc_final: 0.8294 (tt0) REVERT: G 48 LYS cc_start: 0.7094 (mtpp) cc_final: 0.6835 (mttp) REVERT: G 57 GLN cc_start: 0.7970 (tt0) cc_final: 0.7666 (mm110) REVERT: G 131 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7670 (mp) REVERT: G 139 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7611 (mm-30) REVERT: G 146 GLU cc_start: 0.7642 (tp30) cc_final: 0.7332 (tp30) REVERT: H 131 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7809 (mp) REVERT: H 139 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7637 (mm-30) REVERT: H 146 GLU cc_start: 0.7478 (tp30) cc_final: 0.7181 (tp30) REVERT: H 164 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8103 (p0) REVERT: H 225 GLU cc_start: 0.8653 (tt0) cc_final: 0.8184 (tt0) REVERT: I 131 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7838 (mp) REVERT: I 139 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7572 (mm-30) REVERT: I 215 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8598 (tp) REVERT: I 232 MET cc_start: 0.8679 (tpt) cc_final: 0.8148 (tpt) REVERT: b 22 MET cc_start: 0.8839 (mtp) cc_final: 0.8556 (mtp) REVERT: c 25 GLN cc_start: 0.8388 (mt0) cc_final: 0.8172 (mt0) REVERT: g 52 LYS cc_start: 0.8251 (mppt) cc_final: 0.7994 (mtmm) REVERT: i 28 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7661 (t0) outliers start: 77 outliers final: 62 residues processed: 272 average time/residue: 0.1462 time to fit residues: 59.9364 Evaluate side-chains 288 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 214 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 ASN Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain i residue 28 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 73 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 28 ASN i 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.133361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.113971 restraints weight = 18319.515| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.09 r_work: 0.3093 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17397 Z= 0.162 Angle : 0.562 8.192 23598 Z= 0.302 Chirality : 0.045 0.157 2655 Planarity : 0.003 0.034 3123 Dihedral : 7.415 59.984 2429 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 4.21 % Allowed : 21.41 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.19), residues: 2178 helix: 1.90 (0.21), residues: 603 sheet: -0.50 (0.23), residues: 612 loop : -1.73 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 207 TYR 0.009 0.001 TYR A 158 PHE 0.027 0.002 PHE i 31 TRP 0.008 0.001 TRP F 252 Details of bonding type rmsd covalent geometry : bond 0.00371 (17397) covalent geometry : angle 0.56171 (23598) hydrogen bonds : bond 0.02835 ( 755) hydrogen bonds : angle 4.93639 ( 2238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4013.40 seconds wall clock time: 69 minutes 41.48 seconds (4181.48 seconds total)