Starting phenix.real_space_refine on Thu Mar 5 04:09:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rsl_24674/03_2026/7rsl_24674.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rsl_24674/03_2026/7rsl_24674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rsl_24674/03_2026/7rsl_24674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rsl_24674/03_2026/7rsl_24674.map" model { file = "/net/cci-nas-00/data/ceres_data/7rsl_24674/03_2026/7rsl_24674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rsl_24674/03_2026/7rsl_24674.cif" } resolution = 3.45 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= 0.002 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 90 5.16 5 C 12460 2.51 5 N 3120 2.21 5 O 3480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 19150 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "G" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "H" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "E" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "I" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "J" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "D" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 4.35, per 1000 atoms: 0.23 Number of scatterers: 19150 At special positions: 0 Unit cell: (155.925, 154.275, 85.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3480 8.00 N 3120 7.00 C 12460 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: 1.60 Conformation dependent library (CDL) restraints added in 855.5 milliseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4520 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 40 sheets defined 34.7% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 18 through 45 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 45 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 45 Proline residue: G 31 - end of helix Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'G' and resid 167 through 174 Processing helix chain 'G' and resid 177 through 186 Processing helix chain 'G' and resid 234 through 243 Processing helix chain 'G' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE G 252 " --> pdb=" O TYR G 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 45 Proline residue: H 31 - end of helix Processing helix chain 'H' and resid 56 through 58 No H-bonds generated for 'chain 'H' and resid 56 through 58' Processing helix chain 'H' and resid 167 through 174 Processing helix chain 'H' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU H 187 " --> pdb=" O ASP H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU H 246 " --> pdb=" O ARG H 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 45 Proline residue: E 31 - end of helix Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 177 through 186 Processing helix chain 'E' and resid 234 through 243 Processing helix chain 'E' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 45 Proline residue: F 31 - end of helix Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 167 through 174 Processing helix chain 'F' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU F 187 " --> pdb=" O ASP F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU F 246 " --> pdb=" O ARG F 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 45 Proline residue: I 31 - end of helix Processing helix chain 'I' and resid 56 through 58 No H-bonds generated for 'chain 'I' and resid 56 through 58' Processing helix chain 'I' and resid 167 through 174 Processing helix chain 'I' and resid 177 through 186 Processing helix chain 'I' and resid 234 through 243 Processing helix chain 'I' and resid 243 through 264 removed outlier: 3.856A pdb=" N ILE I 252 " --> pdb=" O TYR I 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 45 Proline residue: J 31 - end of helix Processing helix chain 'J' and resid 56 through 58 No H-bonds generated for 'chain 'J' and resid 56 through 58' Processing helix chain 'J' and resid 167 through 174 Processing helix chain 'J' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU J 187 " --> pdb=" O ASP J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU J 246 " --> pdb=" O ARG J 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 45 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 234 through 243 Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.856A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 45 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.729A pdb=" N LEU D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 264 removed outlier: 3.611A pdb=" N LEU D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE A 196 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU A 107 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP A 194 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 109 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE A 192 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU A 111 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 190 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS A 113 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ASN A 188 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE A 71 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 205 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR A 204 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 132 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG A 131 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS A 149 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.878A pdb=" N MET A 97 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR B 103 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE B 196 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 105 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B 194 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER B 206 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG B 131 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS B 149 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 76 Processing sheet with id=AA9, first strand: chain 'G' and resid 51 through 54 removed outlier: 4.665A pdb=" N ILE G 196 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU G 107 " --> pdb=" O ASP G 194 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASP G 194 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU G 109 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE G 192 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU G 111 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE G 190 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS G 113 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN G 188 " --> pdb=" O CYS G 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE G 71 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE G 205 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR G 204 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY G 132 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG G 131 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS G 149 " --> pdb=" O ARG G 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.823A pdb=" N MET G 97 " --> pdb=" O LYS G 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR H 103 " --> pdb=" O ILE H 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE H 196 " --> pdb=" O TYR H 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU H 105 " --> pdb=" O ASP H 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP H 194 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 50 through 54 Processing sheet with id=AB6, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER H 206 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG H 131 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS H 149 " --> pdb=" O ARG H 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 74 through 76 Processing sheet with id=AB8, first strand: chain 'E' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE E 196 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU E 107 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP E 194 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU E 109 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE E 192 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU E 111 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE E 190 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N CYS E 113 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN E 188 " --> pdb=" O CYS E 113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 59 through 61 removed outlier: 3.618A pdb=" N PHE E 71 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 205 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR E 204 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY E 132 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG E 131 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS E 149 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.823A pdb=" N MET E 97 " --> pdb=" O LYS E 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR F 103 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE F 196 " --> pdb=" O TYR F 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU F 105 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP F 194 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 50 through 54 Processing sheet with id=AC5, first strand: chain 'F' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER F 206 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG F 131 " --> pdb=" O LYS F 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS F 149 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AC7, first strand: chain 'I' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE I 196 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N LEU I 107 " --> pdb=" O ASP I 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP I 194 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU I 109 " --> pdb=" O ILE I 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE I 192 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU I 111 " --> pdb=" O ILE I 190 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE I 190 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS I 113 " --> pdb=" O ASN I 188 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ASN I 188 " --> pdb=" O CYS I 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AC9, first strand: chain 'I' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE I 71 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE I 205 " --> pdb=" O GLN I 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR I 204 " --> pdb=" O GLY I 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY I 132 " --> pdb=" O THR I 204 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG I 131 " --> pdb=" O LYS I 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS I 149 " --> pdb=" O ARG I 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 74 through 77 removed outlier: 3.877A pdb=" N MET I 97 " --> pdb=" O LYS I 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR J 103 " --> pdb=" O ILE J 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE J 196 " --> pdb=" O TYR J 103 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU J 105 " --> pdb=" O ASP J 194 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP J 194 " --> pdb=" O LEU J 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 50 through 54 Processing sheet with id=AD4, first strand: chain 'J' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER J 206 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG J 131 " --> pdb=" O LYS J 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS J 149 " --> pdb=" O ARG J 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 74 through 76 Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE C 196 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU C 107 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP C 194 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU C 109 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 192 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU C 111 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE C 190 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N CYS C 113 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN C 188 " --> pdb=" O CYS C 113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AD8, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE C 71 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 205 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR C 204 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 132 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG C 131 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LYS C 149 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.878A pdb=" N MET C 97 " --> pdb=" O LYS C 75 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 50 through 54 removed outlier: 7.215A pdb=" N TYR D 103 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE D 196 " --> pdb=" O TYR D 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU D 105 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP D 194 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 50 through 54 Processing sheet with id=AE3, first strand: chain 'D' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER D 206 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG D 131 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS D 149 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 74 through 76 1070 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4854 1.33 - 1.45: 3393 1.45 - 1.57: 11153 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 19540 Sorted by residual: bond pdb=" N ILE B 150 " pdb=" CA ILE B 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE J 150 " pdb=" CA ILE J 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE H 150 " pdb=" CA ILE H 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE D 150 " pdb=" CA ILE D 150 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.06e-02 8.90e+03 1.25e+01 bond pdb=" N ILE F 150 " pdb=" CA ILE F 150 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.06e-02 8.90e+03 1.24e+01 ... (remaining 19535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 25402 1.97 - 3.93: 972 3.93 - 5.90: 105 5.90 - 7.86: 6 7.86 - 9.83: 5 Bond angle restraints: 26490 Sorted by residual: angle pdb=" N HIS J 119 " pdb=" CA HIS J 119 " pdb=" C HIS J 119 " ideal model delta sigma weight residual 110.50 100.67 9.83 1.41e+00 5.03e-01 4.86e+01 angle pdb=" N HIS H 119 " pdb=" CA HIS H 119 " pdb=" C HIS H 119 " ideal model delta sigma weight residual 110.50 100.70 9.80 1.41e+00 5.03e-01 4.83e+01 angle pdb=" N HIS B 119 " pdb=" CA HIS B 119 " pdb=" C HIS B 119 " ideal model delta sigma weight residual 110.50 100.73 9.77 1.41e+00 5.03e-01 4.80e+01 angle pdb=" N HIS D 119 " pdb=" CA HIS D 119 " pdb=" C HIS D 119 " ideal model delta sigma weight residual 110.50 100.73 9.77 1.41e+00 5.03e-01 4.80e+01 angle pdb=" N HIS F 119 " pdb=" CA HIS F 119 " pdb=" C HIS F 119 " ideal model delta sigma weight residual 110.50 100.76 9.74 1.41e+00 5.03e-01 4.77e+01 ... (remaining 26485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 10796 17.74 - 35.48: 872 35.48 - 53.22: 119 53.22 - 70.96: 47 70.96 - 88.70: 16 Dihedral angle restraints: 11850 sinusoidal: 4910 harmonic: 6940 Sorted by residual: dihedral pdb=" CA MET J 101 " pdb=" C MET J 101 " pdb=" N GLU J 102 " pdb=" CA GLU J 102 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA MET D 101 " pdb=" C MET D 101 " pdb=" N GLU D 102 " pdb=" CA GLU D 102 " ideal model delta harmonic sigma weight residual -180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA MET B 101 " pdb=" C MET B 101 " pdb=" N GLU B 102 " pdb=" CA GLU B 102 " ideal model delta harmonic sigma weight residual 180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 11847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2091 0.041 - 0.082: 623 0.082 - 0.122: 315 0.122 - 0.163: 60 0.163 - 0.204: 21 Chirality restraints: 3110 Sorted by residual: chirality pdb=" CA LEU J 91 " pdb=" N LEU J 91 " pdb=" C LEU J 91 " pdb=" CB LEU J 91 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE G 28 " pdb=" N ILE G 28 " pdb=" C ILE G 28 " pdb=" CB ILE G 28 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA ILE D 205 " pdb=" N ILE D 205 " pdb=" C ILE D 205 " pdb=" CB ILE D 205 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 3107 not shown) Planarity restraints: 3340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP H 118 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" CG ASP H 118 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP H 118 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP H 118 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 118 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" CG ASP J 118 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP J 118 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP J 118 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 118 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" CG ASP D 118 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP D 118 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP D 118 " 0.015 2.00e-02 2.50e+03 ... (remaining 3337 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1643 2.74 - 3.28: 19652 3.28 - 3.82: 30021 3.82 - 4.36: 37019 4.36 - 4.90: 64414 Nonbonded interactions: 152749 Sorted by model distance: nonbonded pdb=" OD1 ASP I 194 " pdb=" NH2 ARG I 229 " model vdw 2.200 3.120 nonbonded pdb=" OD1 ASP C 194 " pdb=" NH2 ARG C 229 " model vdw 2.200 3.120 nonbonded pdb=" OD1 ASP A 194 " pdb=" NH2 ARG A 229 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASP E 194 " pdb=" NH2 ARG E 229 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASP G 194 " pdb=" NH2 ARG G 229 " model vdw 2.202 3.120 ... (remaining 152744 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 19.510 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 0.041 19540 Z= 0.406 Angle : 0.818 9.828 26490 Z= 0.528 Chirality : 0.051 0.204 3110 Planarity : 0.005 0.043 3340 Dihedral : 13.619 88.702 7330 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.23 % Allowed : 1.71 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.17), residues: 2310 helix: 0.67 (0.19), residues: 725 sheet: -2.21 (0.18), residues: 735 loop : -1.63 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 229 TYR 0.019 0.002 TYR G 103 PHE 0.017 0.002 PHE E 40 TRP 0.012 0.003 TRP F 186 HIS 0.005 0.001 HIS F 152 Details of bonding type rmsd covalent geometry : bond 0.00689 (19540) covalent geometry : angle 0.81757 (26490) hydrogen bonds : bond 0.19751 ( 980) hydrogen bonds : angle 9.51906 ( 2985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 515 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8707 (mmtt) REVERT: A 173 GLN cc_start: 0.8963 (mt0) cc_final: 0.8646 (mt0) REVERT: B 104 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8960 (tptp) REVERT: B 184 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 212 GLU cc_start: 0.8465 (tt0) cc_final: 0.8261 (tt0) REVERT: B 227 LYS cc_start: 0.9394 (mtpt) cc_final: 0.9175 (ttmm) REVERT: G 173 GLN cc_start: 0.8534 (mt0) cc_final: 0.8048 (mt0) REVERT: H 104 LYS cc_start: 0.9281 (ttmm) cc_final: 0.8962 (tptp) REVERT: H 184 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8285 (mm-30) REVERT: E 173 GLN cc_start: 0.7977 (mt0) cc_final: 0.7385 (mt0) REVERT: E 202 TYR cc_start: 0.8810 (m-80) cc_final: 0.8502 (m-80) REVERT: F 103 TYR cc_start: 0.8091 (m-80) cc_final: 0.7859 (m-80) REVERT: F 183 ASP cc_start: 0.8909 (t70) cc_final: 0.8692 (t0) REVERT: F 184 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8255 (mm-30) REVERT: F 195 LYS cc_start: 0.9268 (mmtp) cc_final: 0.8968 (mmmm) REVERT: F 212 GLU cc_start: 0.8506 (tt0) cc_final: 0.8293 (tt0) REVERT: F 227 LYS cc_start: 0.9395 (mtpt) cc_final: 0.9178 (tppp) REVERT: F 234 GLN cc_start: 0.9588 (mm-40) cc_final: 0.9354 (tp40) REVERT: I 97 MET cc_start: 0.7895 (ptm) cc_final: 0.7639 (ptm) REVERT: I 202 TYR cc_start: 0.8316 (m-80) cc_final: 0.8083 (m-80) REVERT: J 104 LYS cc_start: 0.9230 (ttmm) cc_final: 0.9000 (tptp) REVERT: J 184 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8285 (mm-30) REVERT: C 173 GLN cc_start: 0.8167 (mt0) cc_final: 0.7706 (mt0) REVERT: D 104 LYS cc_start: 0.9230 (ttmm) cc_final: 0.8925 (tptp) REVERT: D 184 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8410 (mm-30) REVERT: D 195 LYS cc_start: 0.9238 (mmtp) cc_final: 0.8978 (mmmm) REVERT: D 212 GLU cc_start: 0.8554 (tt0) cc_final: 0.8173 (tt0) REVERT: D 227 LYS cc_start: 0.9424 (mtpt) cc_final: 0.9203 (ttmm) outliers start: 5 outliers final: 0 residues processed: 515 average time/residue: 0.1312 time to fit residues: 102.4119 Evaluate side-chains 308 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 121 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN G 93 GLN G 121 ASN H 114 GLN E 93 GLN E 121 ASN F 114 GLN F 119 HIS I 93 GLN I 121 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 121 ASN D 114 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.053172 restraints weight = 71239.434| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 4.86 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19540 Z= 0.203 Angle : 0.657 11.980 26490 Z= 0.334 Chirality : 0.044 0.157 3110 Planarity : 0.005 0.050 3340 Dihedral : 4.888 23.758 2530 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.31 % Allowed : 11.53 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.18), residues: 2310 helix: 0.92 (0.19), residues: 740 sheet: -1.64 (0.18), residues: 835 loop : -1.10 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 229 TYR 0.024 0.002 TYR G 37 PHE 0.013 0.001 PHE B 228 TRP 0.013 0.002 TRP H 186 HIS 0.011 0.001 HIS F 119 Details of bonding type rmsd covalent geometry : bond 0.00434 (19540) covalent geometry : angle 0.65724 (26490) hydrogen bonds : bond 0.04477 ( 980) hydrogen bonds : angle 6.18363 ( 2985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 325 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.9385 (mp10) cc_final: 0.9140 (pm20) REVERT: B 116 LYS cc_start: 0.9158 (mppt) cc_final: 0.8692 (mttp) REVERT: B 122 LEU cc_start: 0.9673 (tp) cc_final: 0.9446 (tp) REVERT: B 172 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 195 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8636 (mmmm) REVERT: B 212 GLU cc_start: 0.8996 (tt0) cc_final: 0.8672 (tt0) REVERT: B 227 LYS cc_start: 0.9508 (mtpt) cc_final: 0.9174 (ttmm) REVERT: G 101 MET cc_start: 0.7918 (tpt) cc_final: 0.7116 (tpp) REVERT: G 173 GLN cc_start: 0.9226 (mt0) cc_final: 0.8801 (mt0) REVERT: G 202 TYR cc_start: 0.9123 (m-80) cc_final: 0.8910 (m-80) REVERT: G 230 MET cc_start: 0.9067 (ttm) cc_final: 0.8849 (tpp) REVERT: H 103 TYR cc_start: 0.8640 (m-80) cc_final: 0.8196 (m-80) REVERT: H 130 TYR cc_start: 0.9250 (m-10) cc_final: 0.9032 (m-10) REVERT: H 172 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8149 (mt-10) REVERT: H 193 GLU cc_start: 0.9142 (pt0) cc_final: 0.8728 (pm20) REVERT: H 195 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8432 (mmmm) REVERT: E 88 ASP cc_start: 0.8920 (p0) cc_final: 0.8665 (p0) REVERT: E 173 GLN cc_start: 0.9151 (mt0) cc_final: 0.8648 (mt0) REVERT: E 202 TYR cc_start: 0.9266 (m-80) cc_final: 0.8776 (m-80) REVERT: F 17 TYR cc_start: 0.6136 (p90) cc_final: 0.5662 (p90) REVERT: F 169 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8666 (tp-100) REVERT: F 170 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8939 (mt-10) REVERT: F 173 GLN cc_start: 0.9249 (mt0) cc_final: 0.8982 (mt0) REVERT: F 184 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8825 (mm-30) REVERT: F 195 LYS cc_start: 0.9348 (mmtp) cc_final: 0.9035 (mmmm) REVERT: F 212 GLU cc_start: 0.8998 (tt0) cc_final: 0.8696 (tt0) REVERT: I 116 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8506 (tptt) REVERT: I 166 MET cc_start: 0.8954 (tpp) cc_final: 0.8754 (tpp) REVERT: I 173 GLN cc_start: 0.8986 (mt0) cc_final: 0.8545 (mt0) REVERT: I 202 TYR cc_start: 0.8904 (m-80) cc_final: 0.8699 (m-80) REVERT: I 230 MET cc_start: 0.8789 (tmm) cc_final: 0.8388 (tmm) REVERT: J 103 TYR cc_start: 0.8540 (m-80) cc_final: 0.8159 (m-80) REVERT: J 193 GLU cc_start: 0.8563 (pm20) cc_final: 0.8280 (pm20) REVERT: C 88 ASP cc_start: 0.8851 (p0) cc_final: 0.8541 (p0) REVERT: C 116 LYS cc_start: 0.8979 (tptt) cc_final: 0.8640 (tptt) REVERT: C 173 GLN cc_start: 0.9194 (mt0) cc_final: 0.8515 (mt0) REVERT: C 202 TYR cc_start: 0.9194 (m-80) cc_final: 0.8760 (m-80) REVERT: C 230 MET cc_start: 0.8793 (tmm) cc_final: 0.8337 (tmm) REVERT: D 103 TYR cc_start: 0.8768 (m-80) cc_final: 0.8211 (m-80) REVERT: D 170 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8954 (pt0) REVERT: D 184 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8954 (mm-30) REVERT: D 193 GLU cc_start: 0.9067 (pt0) cc_final: 0.8559 (pm20) REVERT: D 195 LYS cc_start: 0.9188 (mmtp) cc_final: 0.8834 (mmmm) REVERT: D 212 GLU cc_start: 0.9000 (tt0) cc_final: 0.8510 (tt0) outliers start: 29 outliers final: 14 residues processed: 342 average time/residue: 0.1252 time to fit residues: 66.2290 Evaluate side-chains 295 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 281 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 205 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 207 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.051701 restraints weight = 73118.965| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 4.90 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19540 Z= 0.240 Angle : 0.625 11.474 26490 Z= 0.313 Chirality : 0.043 0.137 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.720 21.279 2530 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.98 % Allowed : 13.74 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.18), residues: 2310 helix: 1.10 (0.19), residues: 740 sheet: -1.37 (0.17), residues: 865 loop : -1.04 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 229 TYR 0.021 0.002 TYR J 103 PHE 0.011 0.001 PHE B 228 TRP 0.009 0.002 TRP F 186 HIS 0.008 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00514 (19540) covalent geometry : angle 0.62468 (26490) hydrogen bonds : bond 0.03866 ( 980) hydrogen bonds : angle 5.67083 ( 2985) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.9373 (mp10) cc_final: 0.9160 (pm20) REVERT: B 116 LYS cc_start: 0.9147 (mppt) cc_final: 0.8643 (mttp) REVERT: B 170 GLU cc_start: 0.9355 (mt-10) cc_final: 0.8984 (mt-10) REVERT: B 193 GLU cc_start: 0.9116 (pt0) cc_final: 0.8702 (pm20) REVERT: B 202 TYR cc_start: 0.9183 (m-80) cc_final: 0.8981 (m-80) REVERT: B 227 LYS cc_start: 0.9521 (mtpt) cc_final: 0.9186 (ttmm) REVERT: G 101 MET cc_start: 0.8139 (tpt) cc_final: 0.7364 (tpp) REVERT: G 116 LYS cc_start: 0.8929 (tptt) cc_final: 0.8662 (tptt) REVERT: G 230 MET cc_start: 0.9149 (ttm) cc_final: 0.8654 (tpp) REVERT: H 130 TYR cc_start: 0.9265 (m-10) cc_final: 0.9011 (m-10) REVERT: H 227 LYS cc_start: 0.9294 (ttmm) cc_final: 0.8862 (tptp) REVERT: E 88 ASP cc_start: 0.9013 (p0) cc_final: 0.8724 (p0) REVERT: F 17 TYR cc_start: 0.6267 (p90) cc_final: 0.5740 (p90) REVERT: F 169 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8394 (tp-100) REVERT: F 170 GLU cc_start: 0.9362 (mt-10) cc_final: 0.9132 (mt-10) REVERT: F 173 GLN cc_start: 0.9085 (mt0) cc_final: 0.8345 (mt0) REVERT: F 193 GLU cc_start: 0.9148 (pt0) cc_final: 0.8735 (pm20) REVERT: F 195 LYS cc_start: 0.9437 (mmtp) cc_final: 0.9116 (mmmm) REVERT: F 227 LYS cc_start: 0.9445 (ttmm) cc_final: 0.9121 (tmtt) REVERT: I 173 GLN cc_start: 0.8962 (mt0) cc_final: 0.8711 (mt0) REVERT: I 202 TYR cc_start: 0.8897 (m-80) cc_final: 0.8666 (m-80) REVERT: I 230 MET cc_start: 0.8867 (tmm) cc_final: 0.8360 (tmm) REVERT: J 103 TYR cc_start: 0.8451 (m-80) cc_final: 0.8164 (m-80) REVERT: C 88 ASP cc_start: 0.8993 (p0) cc_final: 0.8664 (p0) REVERT: C 230 MET cc_start: 0.8919 (tmm) cc_final: 0.8313 (tmm) REVERT: D 103 TYR cc_start: 0.8952 (m-80) cc_final: 0.8151 (m-10) REVERT: D 195 LYS cc_start: 0.9250 (mmtp) cc_final: 0.8847 (mmmm) outliers start: 44 outliers final: 24 residues processed: 298 average time/residue: 0.1276 time to fit residues: 58.3093 Evaluate side-chains 280 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 115 optimal weight: 2.9990 chunk 182 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 228 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.051331 restraints weight = 73350.155| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 4.81 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 19540 Z= 0.283 Angle : 0.641 9.103 26490 Z= 0.319 Chirality : 0.043 0.138 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.638 20.450 2530 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.52 % Allowed : 14.91 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2310 helix: 1.22 (0.19), residues: 740 sheet: -1.17 (0.17), residues: 865 loop : -1.03 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 229 TYR 0.024 0.002 TYR H 103 PHE 0.011 0.001 PHE D 40 TRP 0.008 0.002 TRP F 186 HIS 0.013 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00605 (19540) covalent geometry : angle 0.64147 (26490) hydrogen bonds : bond 0.03659 ( 980) hydrogen bonds : angle 5.48552 ( 2985) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.9397 (mp10) cc_final: 0.9170 (pm20) REVERT: B 116 LYS cc_start: 0.9137 (mppt) cc_final: 0.8621 (mttp) REVERT: B 193 GLU cc_start: 0.9117 (pt0) cc_final: 0.8739 (pm20) REVERT: B 202 TYR cc_start: 0.9247 (m-80) cc_final: 0.9038 (m-80) REVERT: B 227 LYS cc_start: 0.9527 (mtpt) cc_final: 0.9220 (ttmm) REVERT: G 101 MET cc_start: 0.8244 (tpt) cc_final: 0.7702 (tpp) REVERT: G 116 LYS cc_start: 0.8963 (tptt) cc_final: 0.8654 (tptt) REVERT: H 97 MET cc_start: 0.9427 (ttm) cc_final: 0.9170 (mtp) REVERT: H 116 LYS cc_start: 0.9120 (mppt) cc_final: 0.8668 (mttp) REVERT: H 130 TYR cc_start: 0.9283 (m-10) cc_final: 0.9044 (m-10) REVERT: H 184 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8704 (mm-30) REVERT: H 193 GLU cc_start: 0.9142 (pt0) cc_final: 0.8747 (pm20) REVERT: H 221 HIS cc_start: 0.9376 (OUTLIER) cc_final: 0.9145 (t-90) REVERT: E 88 ASP cc_start: 0.9061 (p0) cc_final: 0.8757 (p0) REVERT: E 116 LYS cc_start: 0.8924 (tptt) cc_final: 0.8578 (tptt) REVERT: E 230 MET cc_start: 0.9224 (tpp) cc_final: 0.9004 (tpp) REVERT: F 17 TYR cc_start: 0.6389 (p90) cc_final: 0.5845 (p90) REVERT: F 116 LYS cc_start: 0.9141 (mttp) cc_final: 0.8746 (mttp) REVERT: F 166 MET cc_start: 0.8645 (mmp) cc_final: 0.8289 (mmp) REVERT: F 170 GLU cc_start: 0.9421 (mt-10) cc_final: 0.8803 (mt-10) REVERT: F 173 GLN cc_start: 0.8907 (mt0) cc_final: 0.8496 (mt0) REVERT: F 184 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8692 (mm-30) REVERT: F 193 GLU cc_start: 0.9156 (pt0) cc_final: 0.8721 (pm20) REVERT: F 195 LYS cc_start: 0.9476 (mmtp) cc_final: 0.9148 (mmmm) REVERT: F 221 HIS cc_start: 0.9346 (OUTLIER) cc_final: 0.9081 (t-90) REVERT: I 202 TYR cc_start: 0.8987 (m-80) cc_final: 0.8751 (m-80) REVERT: I 230 MET cc_start: 0.8826 (tmm) cc_final: 0.8318 (tmm) REVERT: J 122 LEU cc_start: 0.9587 (tp) cc_final: 0.9290 (mp) REVERT: J 221 HIS cc_start: 0.9357 (OUTLIER) cc_final: 0.9116 (t-90) REVERT: J 227 LYS cc_start: 0.9285 (ttmm) cc_final: 0.8831 (tptp) REVERT: C 88 ASP cc_start: 0.9000 (p0) cc_final: 0.8737 (p0) REVERT: C 100 ASN cc_start: 0.8728 (m-40) cc_final: 0.8483 (m110) REVERT: C 230 MET cc_start: 0.8908 (tmm) cc_final: 0.8156 (tmm) REVERT: D 103 TYR cc_start: 0.9081 (m-80) cc_final: 0.8108 (m-10) REVERT: D 195 LYS cc_start: 0.9236 (mmtp) cc_final: 0.8814 (mmmm) REVERT: D 221 HIS cc_start: 0.9390 (OUTLIER) cc_final: 0.8999 (t-90) outliers start: 56 outliers final: 32 residues processed: 296 average time/residue: 0.1293 time to fit residues: 58.8680 Evaluate side-chains 284 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 221 HIS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 221 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 78 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 164 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 185 optimal weight: 30.0000 chunk 43 optimal weight: 0.0770 chunk 183 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 173 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN E 119 HIS ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.080076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.052750 restraints weight = 72128.945| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 4.73 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19540 Z= 0.153 Angle : 0.587 11.825 26490 Z= 0.288 Chirality : 0.042 0.136 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.406 22.713 2530 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.25 % Allowed : 16.44 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 2310 helix: 1.28 (0.19), residues: 750 sheet: -0.96 (0.18), residues: 845 loop : -0.88 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 229 TYR 0.015 0.001 TYR G 130 PHE 0.010 0.001 PHE F 40 TRP 0.008 0.002 TRP F 186 HIS 0.011 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00325 (19540) covalent geometry : angle 0.58723 (26490) hydrogen bonds : bond 0.03303 ( 980) hydrogen bonds : angle 5.25554 ( 2985) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 277 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8778 (m-80) REVERT: A 248 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: B 116 LYS cc_start: 0.9184 (mppt) cc_final: 0.8643 (mttp) REVERT: B 193 GLU cc_start: 0.9118 (pt0) cc_final: 0.8712 (pm20) REVERT: B 221 HIS cc_start: 0.9266 (OUTLIER) cc_final: 0.8993 (t-90) REVERT: B 227 LYS cc_start: 0.9526 (mtpt) cc_final: 0.9238 (ttmm) REVERT: G 101 MET cc_start: 0.8314 (tpt) cc_final: 0.7436 (tpp) REVERT: G 116 LYS cc_start: 0.8988 (tptt) cc_final: 0.8672 (tptt) REVERT: G 202 TYR cc_start: 0.9014 (m-80) cc_final: 0.8636 (m-10) REVERT: G 230 MET cc_start: 0.9120 (ttm) cc_final: 0.8395 (tpp) REVERT: H 101 MET cc_start: 0.8151 (ptm) cc_final: 0.7803 (ppp) REVERT: H 116 LYS cc_start: 0.9118 (mppt) cc_final: 0.8750 (mttp) REVERT: H 130 TYR cc_start: 0.9259 (m-10) cc_final: 0.8997 (m-10) REVERT: H 184 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8621 (mm-30) REVERT: H 193 GLU cc_start: 0.9145 (pt0) cc_final: 0.8782 (pm20) REVERT: E 42 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8848 (pp) REVERT: E 88 ASP cc_start: 0.9001 (p0) cc_final: 0.8664 (p0) REVERT: E 101 MET cc_start: 0.8626 (tpp) cc_final: 0.8194 (tpp) REVERT: E 116 LYS cc_start: 0.8910 (tptt) cc_final: 0.8617 (tptt) REVERT: E 202 TYR cc_start: 0.9057 (m-80) cc_final: 0.8580 (m-80) REVERT: E 230 MET cc_start: 0.9222 (tpp) cc_final: 0.8755 (tpp) REVERT: E 248 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: F 17 TYR cc_start: 0.6266 (p90) cc_final: 0.5706 (p90) REVERT: F 104 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8845 (mmmt) REVERT: F 116 LYS cc_start: 0.9148 (mttp) cc_final: 0.8719 (mttp) REVERT: F 169 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8446 (tp-100) REVERT: F 170 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9125 (mt-10) REVERT: F 193 GLU cc_start: 0.9174 (pt0) cc_final: 0.8711 (pm20) REVERT: F 195 LYS cc_start: 0.9452 (mmtp) cc_final: 0.9072 (mmmm) REVERT: F 227 LYS cc_start: 0.9356 (ttmm) cc_final: 0.8872 (tptp) REVERT: I 101 MET cc_start: 0.8323 (tpp) cc_final: 0.8117 (tpp) REVERT: I 202 TYR cc_start: 0.8980 (m-80) cc_final: 0.8753 (m-80) REVERT: I 230 MET cc_start: 0.8758 (tmm) cc_final: 0.8309 (tmm) REVERT: J 184 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8588 (mm-30) REVERT: J 221 HIS cc_start: 0.9327 (OUTLIER) cc_final: 0.8745 (t-90) REVERT: C 42 LEU cc_start: 0.9158 (mm) cc_final: 0.8789 (pp) REVERT: C 88 ASP cc_start: 0.8945 (p0) cc_final: 0.8650 (p0) REVERT: C 100 ASN cc_start: 0.8704 (m-40) cc_final: 0.8369 (m110) REVERT: C 101 MET cc_start: 0.8456 (tpp) cc_final: 0.8110 (ttm) REVERT: C 230 MET cc_start: 0.8881 (tmm) cc_final: 0.8405 (tmm) REVERT: C 248 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: D 103 TYR cc_start: 0.8941 (m-80) cc_final: 0.8070 (m-10) REVERT: D 195 LYS cc_start: 0.9184 (mmtp) cc_final: 0.8742 (mmmm) REVERT: D 227 LYS cc_start: 0.9453 (ttmm) cc_final: 0.9004 (tttp) outliers start: 50 outliers final: 26 residues processed: 301 average time/residue: 0.1311 time to fit residues: 60.4518 Evaluate side-chains 292 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 132 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 229 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS H 72 GLN E 93 GLN F 72 GLN F 119 HIS I 100 ASN I 119 HIS I 173 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.079940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.052377 restraints weight = 72533.812| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 4.75 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 19540 Z= 0.169 Angle : 0.587 11.468 26490 Z= 0.290 Chirality : 0.042 0.134 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.323 20.124 2530 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.52 % Allowed : 16.49 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.18), residues: 2310 helix: 1.36 (0.19), residues: 750 sheet: -0.80 (0.18), residues: 845 loop : -0.83 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 229 TYR 0.014 0.001 TYR G 130 PHE 0.010 0.001 PHE D 40 TRP 0.007 0.002 TRP F 186 HIS 0.014 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00363 (19540) covalent geometry : angle 0.58650 (26490) hydrogen bonds : bond 0.03187 ( 980) hydrogen bonds : angle 5.14895 ( 2985) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 288 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8791 (m-80) REVERT: A 100 ASN cc_start: 0.8780 (m-40) cc_final: 0.8551 (m110) REVERT: A 116 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8708 (tptt) REVERT: A 248 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: B 116 LYS cc_start: 0.9179 (mppt) cc_final: 0.8655 (mttp) REVERT: B 170 GLU cc_start: 0.9351 (mt-10) cc_final: 0.9071 (mt-10) REVERT: B 184 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.9008 (mm-30) REVERT: B 193 GLU cc_start: 0.9120 (pt0) cc_final: 0.8715 (pm20) REVERT: B 227 LYS cc_start: 0.9519 (mtpt) cc_final: 0.9222 (ttmm) REVERT: B 230 MET cc_start: 0.9067 (tpp) cc_final: 0.8839 (tpp) REVERT: G 101 MET cc_start: 0.8436 (tpt) cc_final: 0.7987 (tpp) REVERT: G 116 LYS cc_start: 0.8949 (tptt) cc_final: 0.8681 (tptt) REVERT: G 202 TYR cc_start: 0.9014 (m-80) cc_final: 0.8604 (m-10) REVERT: G 248 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: H 101 MET cc_start: 0.7914 (ptm) cc_final: 0.7368 (ppp) REVERT: H 116 LYS cc_start: 0.9104 (mppt) cc_final: 0.8720 (mtmm) REVERT: H 130 TYR cc_start: 0.9253 (m-10) cc_final: 0.8995 (m-10) REVERT: H 184 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8653 (mm-30) REVERT: H 193 GLU cc_start: 0.9146 (pt0) cc_final: 0.8781 (pm20) REVERT: H 227 LYS cc_start: 0.9447 (ttmm) cc_final: 0.9091 (tttp) REVERT: E 42 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8844 (pp) REVERT: E 88 ASP cc_start: 0.9022 (p0) cc_final: 0.8671 (p0) REVERT: E 101 MET cc_start: 0.8603 (tpp) cc_final: 0.8100 (tpp) REVERT: E 116 LYS cc_start: 0.8892 (tptt) cc_final: 0.8679 (tptt) REVERT: E 202 TYR cc_start: 0.9040 (m-80) cc_final: 0.8536 (m-80) REVERT: E 230 MET cc_start: 0.9259 (tpp) cc_final: 0.8783 (tpp) REVERT: E 248 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: F 17 TYR cc_start: 0.6277 (p90) cc_final: 0.5714 (p90) REVERT: F 104 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8718 (mmmt) REVERT: F 116 LYS cc_start: 0.9149 (mttp) cc_final: 0.8843 (mtmm) REVERT: F 170 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9146 (mt-10) REVERT: F 173 GLN cc_start: 0.8776 (mt0) cc_final: 0.8521 (mt0) REVERT: F 184 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8717 (mm-30) REVERT: F 193 GLU cc_start: 0.9185 (pt0) cc_final: 0.8720 (pm20) REVERT: F 195 LYS cc_start: 0.9459 (mmtp) cc_final: 0.9006 (mmmm) REVERT: F 212 GLU cc_start: 0.9110 (tt0) cc_final: 0.8866 (tt0) REVERT: F 227 LYS cc_start: 0.9354 (ttmm) cc_final: 0.8884 (tptp) REVERT: I 101 MET cc_start: 0.8381 (tpp) cc_final: 0.7660 (tpp) REVERT: I 202 TYR cc_start: 0.8994 (m-80) cc_final: 0.8760 (m-80) REVERT: J 122 LEU cc_start: 0.9598 (tp) cc_final: 0.9341 (mp) REVERT: J 172 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8705 (tm-30) REVERT: J 173 GLN cc_start: 0.9022 (mt0) cc_final: 0.8623 (mt0) REVERT: J 184 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8606 (mm-30) REVERT: J 220 ILE cc_start: 0.9645 (OUTLIER) cc_final: 0.9425 (mm) REVERT: J 221 HIS cc_start: 0.9264 (OUTLIER) cc_final: 0.8959 (t-90) REVERT: J 227 LYS cc_start: 0.9409 (ttmm) cc_final: 0.8925 (tptp) REVERT: C 42 LEU cc_start: 0.9155 (mm) cc_final: 0.8801 (pp) REVERT: C 88 ASP cc_start: 0.8969 (p0) cc_final: 0.8667 (p0) REVERT: C 100 ASN cc_start: 0.8749 (m-40) cc_final: 0.8501 (m110) REVERT: C 202 TYR cc_start: 0.9233 (m-80) cc_final: 0.8884 (m-80) REVERT: C 230 MET cc_start: 0.8904 (tmm) cc_final: 0.8211 (tmm) REVERT: C 248 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8166 (m-80) REVERT: D 103 TYR cc_start: 0.8852 (m-80) cc_final: 0.7822 (m-10) REVERT: D 184 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8573 (mm-30) REVERT: D 195 LYS cc_start: 0.9188 (mmtp) cc_final: 0.8719 (mmmm) REVERT: D 227 LYS cc_start: 0.9433 (ttmm) cc_final: 0.8916 (tttp) outliers start: 56 outliers final: 33 residues processed: 318 average time/residue: 0.1300 time to fit residues: 63.5113 Evaluate side-chains 304 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 184 optimal weight: 50.0000 chunk 167 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN E 119 HIS F 231 ASN I 100 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.051750 restraints weight = 72403.753| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 4.71 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19540 Z= 0.220 Angle : 0.623 12.438 26490 Z= 0.307 Chirality : 0.042 0.138 3110 Planarity : 0.004 0.039 3340 Dihedral : 4.391 20.976 2530 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.61 % Allowed : 17.39 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2310 helix: 1.34 (0.19), residues: 750 sheet: -0.72 (0.18), residues: 855 loop : -0.87 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 229 TYR 0.016 0.002 TYR A 182 PHE 0.010 0.001 PHE D 40 TRP 0.005 0.002 TRP H 186 HIS 0.019 0.002 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00472 (19540) covalent geometry : angle 0.62307 (26490) hydrogen bonds : bond 0.03252 ( 980) hydrogen bonds : angle 5.14996 ( 2985) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: A 100 ASN cc_start: 0.8791 (m-40) cc_final: 0.8563 (m110) REVERT: A 101 MET cc_start: 0.8705 (tpp) cc_final: 0.8385 (tpp) REVERT: A 248 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: B 116 LYS cc_start: 0.9161 (mppt) cc_final: 0.8627 (mttp) REVERT: B 170 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9086 (mt-10) REVERT: B 193 GLU cc_start: 0.9111 (pt0) cc_final: 0.8704 (pm20) REVERT: B 227 LYS cc_start: 0.9507 (mtpt) cc_final: 0.9193 (ttmm) REVERT: G 101 MET cc_start: 0.8381 (tpt) cc_final: 0.8005 (tpp) REVERT: G 116 LYS cc_start: 0.8959 (tptt) cc_final: 0.8656 (tptt) REVERT: G 166 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8788 (mpp) REVERT: G 202 TYR cc_start: 0.9015 (m-80) cc_final: 0.8640 (m-10) REVERT: G 230 MET cc_start: 0.9234 (ttm) cc_final: 0.8504 (tpp) REVERT: G 248 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8325 (m-80) REVERT: H 116 LYS cc_start: 0.9022 (mppt) cc_final: 0.8638 (mtmm) REVERT: H 172 GLU cc_start: 0.9258 (tt0) cc_final: 0.9021 (tm-30) REVERT: H 173 GLN cc_start: 0.8917 (mt0) cc_final: 0.8482 (mt0) REVERT: H 184 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8673 (mm-30) REVERT: H 193 GLU cc_start: 0.9132 (pt0) cc_final: 0.8784 (pm20) REVERT: E 42 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8845 (pp) REVERT: E 88 ASP cc_start: 0.9003 (p0) cc_final: 0.8629 (p0) REVERT: E 101 MET cc_start: 0.8636 (tpp) cc_final: 0.8291 (tpp) REVERT: E 202 TYR cc_start: 0.9061 (m-80) cc_final: 0.8557 (m-80) REVERT: E 230 MET cc_start: 0.9286 (tpp) cc_final: 0.8986 (tpp) REVERT: E 248 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: F 17 TYR cc_start: 0.6282 (p90) cc_final: 0.5714 (p90) REVERT: F 116 LYS cc_start: 0.9098 (mttp) cc_final: 0.8781 (mtmm) REVERT: F 170 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9100 (mt-10) REVERT: F 193 GLU cc_start: 0.9169 (pt0) cc_final: 0.8729 (pm20) REVERT: F 195 LYS cc_start: 0.9334 (mmtp) cc_final: 0.8906 (mmmm) REVERT: I 202 TYR cc_start: 0.8981 (m-80) cc_final: 0.8721 (m-80) REVERT: I 248 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8222 (m-80) REVERT: J 116 LYS cc_start: 0.9092 (mttp) cc_final: 0.8858 (mtmm) REVERT: J 122 LEU cc_start: 0.9590 (tp) cc_final: 0.9354 (mp) REVERT: J 172 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8748 (tm-30) REVERT: J 184 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8628 (mm-30) REVERT: J 220 ILE cc_start: 0.9657 (OUTLIER) cc_final: 0.9439 (mm) REVERT: J 221 HIS cc_start: 0.9273 (OUTLIER) cc_final: 0.8893 (t-90) REVERT: J 227 LYS cc_start: 0.9416 (ttmm) cc_final: 0.8920 (tptp) REVERT: C 42 LEU cc_start: 0.9168 (mm) cc_final: 0.8817 (pp) REVERT: C 88 ASP cc_start: 0.8969 (p0) cc_final: 0.8683 (p0) REVERT: C 100 ASN cc_start: 0.8777 (m-40) cc_final: 0.8477 (m110) REVERT: C 101 MET cc_start: 0.8505 (tpp) cc_final: 0.8144 (ttm) REVERT: C 202 TYR cc_start: 0.9230 (m-80) cc_final: 0.8894 (m-80) REVERT: C 230 MET cc_start: 0.8946 (tmm) cc_final: 0.8336 (tmm) REVERT: C 248 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: D 101 MET cc_start: 0.9012 (ptm) cc_final: 0.8740 (ptm) REVERT: D 103 TYR cc_start: 0.8871 (m-80) cc_final: 0.7778 (m-10) REVERT: D 184 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8613 (mm-30) REVERT: D 195 LYS cc_start: 0.9202 (mmtp) cc_final: 0.8726 (mmmm) REVERT: D 227 LYS cc_start: 0.9429 (ttmm) cc_final: 0.8929 (tttp) outliers start: 58 outliers final: 35 residues processed: 303 average time/residue: 0.1251 time to fit residues: 58.3356 Evaluate side-chains 302 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 243 LYS Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 105 optimal weight: 0.0570 chunk 5 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN J 72 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.080737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.053670 restraints weight = 71428.911| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 4.70 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19540 Z= 0.125 Angle : 0.607 16.128 26490 Z= 0.294 Chirality : 0.043 0.136 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.223 21.574 2530 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.94 % Allowed : 18.24 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.18), residues: 2310 helix: 1.22 (0.19), residues: 780 sheet: -0.46 (0.18), residues: 795 loop : -0.77 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 229 TYR 0.016 0.001 TYR A 182 PHE 0.010 0.001 PHE D 40 TRP 0.009 0.002 TRP B 186 HIS 0.019 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00271 (19540) covalent geometry : angle 0.60690 (26490) hydrogen bonds : bond 0.02997 ( 980) hydrogen bonds : angle 4.99496 ( 2985) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 295 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8813 (m-80) REVERT: A 100 ASN cc_start: 0.8812 (m-40) cc_final: 0.8583 (m110) REVERT: A 101 MET cc_start: 0.8730 (tpp) cc_final: 0.8458 (tpp) REVERT: A 248 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: B 116 LYS cc_start: 0.9214 (mppt) cc_final: 0.8672 (mttp) REVERT: B 170 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9129 (mt-10) REVERT: B 184 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8646 (mm-30) REVERT: B 193 GLU cc_start: 0.9115 (pt0) cc_final: 0.8630 (pm20) REVERT: B 194 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: B 227 LYS cc_start: 0.9509 (mtpt) cc_final: 0.9213 (ttmm) REVERT: G 101 MET cc_start: 0.8509 (tpt) cc_final: 0.8185 (tpp) REVERT: G 116 LYS cc_start: 0.9005 (tptt) cc_final: 0.8697 (tptt) REVERT: G 172 GLU cc_start: 0.9253 (tt0) cc_final: 0.9002 (tt0) REVERT: G 202 TYR cc_start: 0.8996 (m-80) cc_final: 0.8451 (m-80) REVERT: G 230 MET cc_start: 0.9134 (ttm) cc_final: 0.8575 (tpp) REVERT: G 248 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: H 116 LYS cc_start: 0.9090 (mppt) cc_final: 0.8726 (mtmm) REVERT: H 130 TYR cc_start: 0.9270 (m-10) cc_final: 0.9033 (m-10) REVERT: H 172 GLU cc_start: 0.9268 (tt0) cc_final: 0.9036 (tm-30) REVERT: H 173 GLN cc_start: 0.9067 (mt0) cc_final: 0.8659 (mt0) REVERT: H 193 GLU cc_start: 0.9108 (pt0) cc_final: 0.8721 (pm20) REVERT: H 227 LYS cc_start: 0.9437 (ttmm) cc_final: 0.8940 (tptp) REVERT: E 42 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8819 (pp) REVERT: E 88 ASP cc_start: 0.8947 (p0) cc_final: 0.8661 (p0) REVERT: E 101 MET cc_start: 0.8648 (tpp) cc_final: 0.8349 (tpp) REVERT: E 202 TYR cc_start: 0.9009 (m-80) cc_final: 0.8522 (m-80) REVERT: E 230 MET cc_start: 0.9231 (tpp) cc_final: 0.9004 (tpp) REVERT: E 248 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: F 116 LYS cc_start: 0.9125 (mttp) cc_final: 0.8804 (mtmm) REVERT: F 170 GLU cc_start: 0.9461 (mt-10) cc_final: 0.9234 (mt-10) REVERT: F 193 GLU cc_start: 0.9165 (pt0) cc_final: 0.8690 (pm20) REVERT: F 195 LYS cc_start: 0.9237 (mmtp) cc_final: 0.8998 (mmtm) REVERT: F 212 GLU cc_start: 0.9115 (tt0) cc_final: 0.8871 (tt0) REVERT: I 182 TYR cc_start: 0.9194 (m-80) cc_final: 0.8933 (m-80) REVERT: I 202 TYR cc_start: 0.8962 (m-80) cc_final: 0.8711 (m-80) REVERT: I 248 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: J 116 LYS cc_start: 0.9114 (mttp) cc_final: 0.8892 (mtmm) REVERT: J 122 LEU cc_start: 0.9598 (tp) cc_final: 0.9277 (mp) REVERT: J 172 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8774 (tm-30) REVERT: J 184 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8603 (mm-30) REVERT: J 193 GLU cc_start: 0.8945 (pm20) cc_final: 0.8534 (pm20) REVERT: J 221 HIS cc_start: 0.9276 (OUTLIER) cc_final: 0.8982 (t-90) REVERT: J 227 LYS cc_start: 0.9410 (ttmm) cc_final: 0.8855 (tptp) REVERT: C 42 LEU cc_start: 0.9162 (mm) cc_final: 0.8816 (pp) REVERT: C 88 ASP cc_start: 0.8919 (p0) cc_final: 0.8630 (p0) REVERT: C 100 ASN cc_start: 0.8767 (m-40) cc_final: 0.8474 (m110) REVERT: C 101 MET cc_start: 0.8519 (tpp) cc_final: 0.8314 (ttm) REVERT: C 170 GLU cc_start: 0.9261 (mt-10) cc_final: 0.9004 (mt-10) REVERT: C 202 TYR cc_start: 0.9214 (m-80) cc_final: 0.8859 (m-80) REVERT: C 230 MET cc_start: 0.8858 (tmm) cc_final: 0.8381 (tmm) REVERT: C 248 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: D 103 TYR cc_start: 0.8807 (m-80) cc_final: 0.7828 (m-10) REVERT: D 195 LYS cc_start: 0.9138 (mmtp) cc_final: 0.8660 (mmmm) REVERT: D 227 LYS cc_start: 0.9442 (ttmm) cc_final: 0.8958 (tttp) outliers start: 43 outliers final: 28 residues processed: 314 average time/residue: 0.1267 time to fit residues: 61.2013 Evaluate side-chains 312 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 205 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 127 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 229 optimal weight: 40.0000 chunk 134 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 185 optimal weight: 30.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.081023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053809 restraints weight = 71458.576| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.73 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19540 Z= 0.128 Angle : 0.628 15.996 26490 Z= 0.303 Chirality : 0.043 0.178 3110 Planarity : 0.004 0.039 3340 Dihedral : 4.180 21.998 2530 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.80 % Allowed : 18.74 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.18), residues: 2310 helix: 1.23 (0.19), residues: 780 sheet: -0.35 (0.18), residues: 795 loop : -0.67 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 229 TYR 0.029 0.001 TYR A 41 PHE 0.010 0.001 PHE A 255 TRP 0.008 0.002 TRP B 186 HIS 0.019 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00280 (19540) covalent geometry : angle 0.62760 (26490) hydrogen bonds : bond 0.02987 ( 980) hydrogen bonds : angle 4.95792 ( 2985) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 296 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.9357 (t80) cc_final: 0.9056 (m-80) REVERT: A 40 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8848 (m-80) REVERT: A 100 ASN cc_start: 0.8833 (m-40) cc_final: 0.8602 (m110) REVERT: A 101 MET cc_start: 0.8745 (tpp) cc_final: 0.8506 (tpp) REVERT: A 202 TYR cc_start: 0.9073 (m-80) cc_final: 0.8842 (m-80) REVERT: B 116 LYS cc_start: 0.9231 (mppt) cc_final: 0.8686 (mttp) REVERT: B 170 GLU cc_start: 0.9329 (mt-10) cc_final: 0.9111 (mt-10) REVERT: B 193 GLU cc_start: 0.9150 (pt0) cc_final: 0.8729 (pm20) REVERT: B 195 LYS cc_start: 0.9216 (mmtm) cc_final: 0.8953 (mmmm) REVERT: G 37 TYR cc_start: 0.9223 (t80) cc_final: 0.9008 (m-80) REVERT: G 101 MET cc_start: 0.8509 (tpt) cc_final: 0.8190 (tpp) REVERT: G 116 LYS cc_start: 0.9004 (tptt) cc_final: 0.8705 (tptt) REVERT: G 172 GLU cc_start: 0.9270 (tt0) cc_final: 0.9023 (tt0) REVERT: G 202 TYR cc_start: 0.8966 (m-80) cc_final: 0.8384 (m-80) REVERT: G 230 MET cc_start: 0.9167 (ttm) cc_final: 0.8641 (tpp) REVERT: G 248 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: H 116 LYS cc_start: 0.9101 (mppt) cc_final: 0.8739 (mtmm) REVERT: H 130 TYR cc_start: 0.9265 (m-10) cc_final: 0.9056 (m-10) REVERT: H 172 GLU cc_start: 0.9267 (tt0) cc_final: 0.9039 (tm-30) REVERT: H 173 GLN cc_start: 0.9048 (mt0) cc_final: 0.8676 (mt0) REVERT: H 184 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8676 (mm-30) REVERT: H 193 GLU cc_start: 0.9138 (pt0) cc_final: 0.8778 (pm20) REVERT: H 195 LYS cc_start: 0.9220 (mmtm) cc_final: 0.8898 (mmmm) REVERT: H 227 LYS cc_start: 0.9425 (ttmm) cc_final: 0.8934 (tptp) REVERT: E 42 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8830 (pp) REVERT: E 101 MET cc_start: 0.8708 (tpp) cc_final: 0.8438 (tpp) REVERT: E 202 TYR cc_start: 0.9009 (m-80) cc_final: 0.8502 (m-80) REVERT: E 248 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: F 17 TYR cc_start: 0.6323 (p90) cc_final: 0.5758 (p90) REVERT: F 101 MET cc_start: 0.8492 (ptm) cc_final: 0.8171 (ptm) REVERT: F 116 LYS cc_start: 0.9122 (mttp) cc_final: 0.8813 (mtmm) REVERT: F 169 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8543 (tp-100) REVERT: F 193 GLU cc_start: 0.9177 (pt0) cc_final: 0.8645 (pm20) REVERT: F 212 GLU cc_start: 0.9120 (tt0) cc_final: 0.8863 (tt0) REVERT: I 42 LEU cc_start: 0.9164 (mm) cc_final: 0.8821 (pp) REVERT: I 101 MET cc_start: 0.8787 (tpp) cc_final: 0.8479 (tpp) REVERT: I 202 TYR cc_start: 0.8939 (m-80) cc_final: 0.8661 (m-80) REVERT: I 248 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: J 116 LYS cc_start: 0.9085 (mttp) cc_final: 0.8875 (mtmm) REVERT: J 122 LEU cc_start: 0.9602 (tp) cc_final: 0.9315 (mp) REVERT: J 172 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8804 (tm-30) REVERT: J 184 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8595 (mm-30) REVERT: J 195 LYS cc_start: 0.9312 (mmtp) cc_final: 0.8964 (mmmm) REVERT: J 221 HIS cc_start: 0.9266 (OUTLIER) cc_final: 0.8951 (t-90) REVERT: J 227 LYS cc_start: 0.9411 (ttmm) cc_final: 0.8855 (tptp) REVERT: C 42 LEU cc_start: 0.9162 (mm) cc_final: 0.8813 (pp) REVERT: C 88 ASP cc_start: 0.8904 (p0) cc_final: 0.8687 (p0) REVERT: C 100 ASN cc_start: 0.8747 (m-40) cc_final: 0.8450 (m110) REVERT: C 170 GLU cc_start: 0.9262 (mt-10) cc_final: 0.9059 (mt-10) REVERT: C 202 TYR cc_start: 0.9204 (m-80) cc_final: 0.8824 (m-80) REVERT: C 230 MET cc_start: 0.8854 (tmm) cc_final: 0.8379 (tmm) REVERT: C 248 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: D 103 TYR cc_start: 0.8781 (m-80) cc_final: 0.7838 (m-10) REVERT: D 193 GLU cc_start: 0.9162 (pt0) cc_final: 0.8619 (pm20) REVERT: D 195 LYS cc_start: 0.9133 (mmtp) cc_final: 0.8925 (mmtm) REVERT: D 212 GLU cc_start: 0.8945 (tt0) cc_final: 0.8424 (tt0) REVERT: D 227 LYS cc_start: 0.9443 (ttmm) cc_final: 0.8964 (tttp) outliers start: 40 outliers final: 27 residues processed: 312 average time/residue: 0.1261 time to fit residues: 60.4072 Evaluate side-chains 315 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 205 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 193 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 204 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN H 231 ASN E 173 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.079498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.052289 restraints weight = 71997.602| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.70 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19540 Z= 0.211 Angle : 0.666 13.423 26490 Z= 0.325 Chirality : 0.043 0.193 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.272 21.380 2530 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.94 % Allowed : 19.01 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2310 helix: 1.18 (0.19), residues: 780 sheet: -0.37 (0.18), residues: 805 loop : -0.69 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 229 TYR 0.022 0.002 TYR C 37 PHE 0.014 0.001 PHE A 255 TRP 0.005 0.001 TRP H 186 HIS 0.019 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00458 (19540) covalent geometry : angle 0.66560 (26490) hydrogen bonds : bond 0.03108 ( 980) hydrogen bonds : angle 5.02733 ( 2985) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 272 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.9351 (t80) cc_final: 0.8947 (m-80) REVERT: A 40 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8877 (m-80) REVERT: B 116 LYS cc_start: 0.9186 (mppt) cc_final: 0.8653 (mttp) REVERT: B 170 GLU cc_start: 0.9293 (mt-10) cc_final: 0.9037 (mt-10) REVERT: B 193 GLU cc_start: 0.9204 (pt0) cc_final: 0.8755 (pm20) REVERT: B 195 LYS cc_start: 0.9186 (mmtm) cc_final: 0.8840 (mmmm) REVERT: G 37 TYR cc_start: 0.9223 (t80) cc_final: 0.8958 (m-80) REVERT: G 101 MET cc_start: 0.8575 (tpt) cc_final: 0.8195 (tpp) REVERT: G 116 LYS cc_start: 0.9005 (tptt) cc_final: 0.8676 (tptt) REVERT: G 172 GLU cc_start: 0.9271 (tt0) cc_final: 0.9026 (tt0) REVERT: G 202 TYR cc_start: 0.8968 (m-80) cc_final: 0.8531 (m-80) REVERT: G 230 MET cc_start: 0.9258 (ttm) cc_final: 0.8625 (tpp) REVERT: G 248 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8405 (m-80) REVERT: H 116 LYS cc_start: 0.9033 (mppt) cc_final: 0.8668 (mtmm) REVERT: H 130 TYR cc_start: 0.9290 (m-10) cc_final: 0.9089 (m-10) REVERT: H 172 GLU cc_start: 0.9282 (tt0) cc_final: 0.9057 (tm-30) REVERT: H 173 GLN cc_start: 0.9036 (mt0) cc_final: 0.8679 (mt0) REVERT: H 193 GLU cc_start: 0.9178 (pt0) cc_final: 0.8824 (pm20) REVERT: H 195 LYS cc_start: 0.9235 (mmtm) cc_final: 0.8892 (mmmm) REVERT: H 227 LYS cc_start: 0.9421 (ttmm) cc_final: 0.8915 (tptp) REVERT: E 42 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8825 (pp) REVERT: E 101 MET cc_start: 0.8632 (tpp) cc_final: 0.8343 (tpp) REVERT: E 202 TYR cc_start: 0.9012 (m-80) cc_final: 0.8497 (m-80) REVERT: E 248 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: F 17 TYR cc_start: 0.6365 (p90) cc_final: 0.5810 (p90) REVERT: F 101 MET cc_start: 0.8577 (ptm) cc_final: 0.8268 (ptm) REVERT: F 104 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8719 (mmmt) REVERT: F 116 LYS cc_start: 0.9089 (mttp) cc_final: 0.8791 (mtmm) REVERT: F 170 GLU cc_start: 0.9540 (mt-10) cc_final: 0.9254 (pt0) REVERT: F 193 GLU cc_start: 0.9199 (pt0) cc_final: 0.8764 (pm20) REVERT: F 212 GLU cc_start: 0.9122 (tt0) cc_final: 0.8864 (tt0) REVERT: I 42 LEU cc_start: 0.9176 (mm) cc_final: 0.8843 (pp) REVERT: I 88 ASP cc_start: 0.9162 (p0) cc_final: 0.8792 (p0) REVERT: I 166 MET cc_start: 0.8953 (mmt) cc_final: 0.8514 (mmt) REVERT: I 202 TYR cc_start: 0.8958 (m-80) cc_final: 0.8673 (m-80) REVERT: I 248 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: J 116 LYS cc_start: 0.9080 (mttp) cc_final: 0.8856 (mtmm) REVERT: J 122 LEU cc_start: 0.9593 (tp) cc_final: 0.9304 (mp) REVERT: J 172 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8848 (tm-30) REVERT: J 184 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8652 (mm-30) REVERT: J 195 LYS cc_start: 0.9295 (mmtp) cc_final: 0.8887 (mmmm) REVERT: J 220 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9426 (mm) REVERT: J 221 HIS cc_start: 0.9274 (OUTLIER) cc_final: 0.8935 (t-90) REVERT: J 227 LYS cc_start: 0.9402 (ttmm) cc_final: 0.8849 (tptp) REVERT: C 41 TYR cc_start: 0.9057 (m-10) cc_final: 0.8840 (m-80) REVERT: C 88 ASP cc_start: 0.8946 (p0) cc_final: 0.8741 (p0) REVERT: C 230 MET cc_start: 0.8997 (tmm) cc_final: 0.8227 (tmm) REVERT: C 248 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8361 (m-80) REVERT: D 172 GLU cc_start: 0.9258 (tt0) cc_final: 0.9010 (tm-30) REVERT: D 193 GLU cc_start: 0.9179 (pt0) cc_final: 0.8701 (pm20) REVERT: D 212 GLU cc_start: 0.8964 (tt0) cc_final: 0.8439 (tt0) REVERT: D 227 LYS cc_start: 0.9427 (ttmm) cc_final: 0.8918 (tttp) outliers start: 43 outliers final: 31 residues processed: 298 average time/residue: 0.1276 time to fit residues: 58.0879 Evaluate side-chains 307 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 267 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 220 ILE Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 205 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 82 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 72 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN G 93 GLN H 72 GLN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.078226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.051055 restraints weight = 72819.803| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 4.68 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19540 Z= 0.265 Angle : 0.700 12.913 26490 Z= 0.344 Chirality : 0.044 0.210 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.506 20.966 2530 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.07 % Allowed : 19.14 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2310 helix: 1.42 (0.19), residues: 730 sheet: -0.51 (0.17), residues: 870 loop : -0.83 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 229 TYR 0.020 0.002 TYR A 37 PHE 0.014 0.001 PHE A 255 TRP 0.004 0.001 TRP I 186 HIS 0.019 0.002 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00574 (19540) covalent geometry : angle 0.70043 (26490) hydrogen bonds : bond 0.03270 ( 980) hydrogen bonds : angle 5.18119 ( 2985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.86 seconds wall clock time: 55 minutes 24.32 seconds (3324.32 seconds total)