Starting phenix.real_space_refine on Wed Sep 17 23:23:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f5n_50194/09_2025/9f5n_50194_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f5n_50194/09_2025/9f5n_50194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f5n_50194/09_2025/9f5n_50194_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f5n_50194/09_2025/9f5n_50194_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f5n_50194/09_2025/9f5n_50194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f5n_50194/09_2025/9f5n_50194.map" } resolution = 2.56 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= 0.003 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 25 5.16 5 C 8005 2.51 5 N 2035 2.21 5 O 2205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12270 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2419 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 298} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 98 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.42, per 1000 atoms: 0.20 Number of scatterers: 12270 At special positions: 0 Unit cell: (85.8, 86.45, 122.2, 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 25 16.00 O 2205 8.00 N 2035 7.00 C 8005 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: 1.44 Conformation dependent library (CDL) restraints added in 569.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 41.9% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 43 through 46 Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 246 removed outlier: 3.777A pdb=" N ASP A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 283 Processing helix chain 'A' and resid 285 through 316 removed outlier: 3.868A pdb=" N TYR A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Proline residue: A 301 - end of helix removed outlier: 3.833A pdb=" N TYR A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 46 Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 246 removed outlier: 3.777A pdb=" N ASP C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 283 Processing helix chain 'C' and resid 285 through 316 removed outlier: 3.868A pdb=" N TYR C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Proline residue: C 301 - end of helix removed outlier: 3.833A pdb=" N TYR C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 46 Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 221 through 246 removed outlier: 3.778A pdb=" N ASP B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 283 Processing helix chain 'B' and resid 285 through 316 removed outlier: 3.867A pdb=" N TYR B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.833A pdb=" N TYR B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 46 Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 195 through 202 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 246 removed outlier: 3.778A pdb=" N ASP D 246 " --> pdb=" O THR D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 283 Processing helix chain 'D' and resid 285 through 316 removed outlier: 3.868A pdb=" N TYR D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Proline residue: D 301 - end of helix removed outlier: 3.833A pdb=" N TYR D 304 " --> pdb=" O TYR D 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 46 Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 195 through 202 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 218 through 220 No H-bonds generated for 'chain 'E' and resid 218 through 220' Processing helix chain 'E' and resid 221 through 246 removed outlier: 3.777A pdb=" N ASP E 246 " --> pdb=" O THR E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 283 Processing helix chain 'E' and resid 285 through 316 removed outlier: 3.867A pdb=" N TYR E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Proline residue: E 301 - end of helix removed outlier: 3.833A pdb=" N TYR E 304 " --> pdb=" O TYR E 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 removed outlier: 7.511A pdb=" N GLN A 84 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN A 113 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG A 86 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR A 111 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG A 107 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 92 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 105 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A 94 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET A 103 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 96 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR A 101 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN A 29 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY A 22 " --> pdb=" O ASN A 29 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER A 31 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE A 20 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 33 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG A 41 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP A 10 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER A 9 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN A 145 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 11 " --> pdb=" O GLN A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 60 removed outlier: 7.511A pdb=" N GLN A 84 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN A 113 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG A 86 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR A 111 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG A 107 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 92 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 105 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A 94 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET A 103 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 96 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR A 101 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN A 29 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY A 22 " --> pdb=" O ASN A 29 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER A 31 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE A 20 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 33 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG A 41 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP A 10 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 80 removed outlier: 4.794A pdb=" N SER A 183 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 166 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU A 192 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL A 164 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 56 through 60 removed outlier: 7.512A pdb=" N GLN C 84 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN C 113 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG C 86 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR C 111 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG C 107 " --> pdb=" O GLN C 90 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG C 92 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 105 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE C 94 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET C 103 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU C 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR C 101 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN C 29 " --> pdb=" O GLY C 22 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY C 22 " --> pdb=" O ASN C 29 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER C 31 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE C 20 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL C 33 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG C 41 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP C 10 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SER C 9 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN C 145 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL C 11 " --> pdb=" O GLN C 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 60 removed outlier: 7.512A pdb=" N GLN C 84 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN C 113 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG C 86 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR C 111 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG C 107 " --> pdb=" O GLN C 90 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG C 92 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 105 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE C 94 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET C 103 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU C 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR C 101 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN C 29 " --> pdb=" O GLY C 22 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY C 22 " --> pdb=" O ASN C 29 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER C 31 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE C 20 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL C 33 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG C 41 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP C 10 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 78 through 80 removed outlier: 4.795A pdb=" N SER C 183 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 166 " --> pdb=" O HIS C 190 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU C 192 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL C 164 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 60 removed outlier: 7.511A pdb=" N GLN B 84 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN B 113 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG B 86 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR B 111 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG B 107 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG B 92 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 105 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE B 94 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET B 103 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 96 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR B 101 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN B 29 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY B 22 " --> pdb=" O ASN B 29 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER B 31 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE B 20 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 33 " --> pdb=" O ASP B 18 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG B 41 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP B 10 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER B 9 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN B 145 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL B 11 " --> pdb=" O GLN B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 56 through 60 removed outlier: 7.511A pdb=" N GLN B 84 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN B 113 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG B 86 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR B 111 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG B 107 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG B 92 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 105 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE B 94 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET B 103 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 96 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR B 101 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN B 29 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY B 22 " --> pdb=" O ASN B 29 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER B 31 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE B 20 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 33 " --> pdb=" O ASP B 18 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG B 41 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP B 10 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 80 removed outlier: 4.795A pdb=" N SER B 183 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 166 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU B 192 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL B 164 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 60 removed outlier: 7.512A pdb=" N GLN D 84 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN D 113 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG D 86 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR D 111 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG D 107 " --> pdb=" O GLN D 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG D 92 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU D 105 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE D 94 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET D 103 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU D 96 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR D 101 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN D 29 " --> pdb=" O GLY D 22 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY D 22 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER D 31 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE D 20 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL D 33 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG D 41 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP D 10 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SER D 9 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN D 145 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL D 11 " --> pdb=" O GLN D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 56 through 60 removed outlier: 7.512A pdb=" N GLN D 84 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN D 113 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG D 86 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR D 111 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG D 107 " --> pdb=" O GLN D 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG D 92 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU D 105 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE D 94 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET D 103 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU D 96 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR D 101 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN D 29 " --> pdb=" O GLY D 22 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY D 22 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER D 31 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE D 20 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL D 33 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG D 41 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP D 10 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 78 through 80 removed outlier: 4.795A pdb=" N SER D 183 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 166 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU D 192 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL D 164 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 60 removed outlier: 7.512A pdb=" N GLN E 84 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN E 113 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG E 86 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N THR E 111 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG E 107 " --> pdb=" O GLN E 90 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG E 92 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU E 105 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE E 94 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET E 103 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU E 96 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR E 101 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN E 29 " --> pdb=" O GLY E 22 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY E 22 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER E 31 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE E 20 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL E 33 " --> pdb=" O ASP E 18 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG E 41 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP E 10 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER E 9 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN E 145 " --> pdb=" O SER E 9 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL E 11 " --> pdb=" O GLN E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 56 through 60 removed outlier: 7.512A pdb=" N GLN E 84 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN E 113 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG E 86 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N THR E 111 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG E 107 " --> pdb=" O GLN E 90 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG E 92 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU E 105 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE E 94 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET E 103 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU E 96 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR E 101 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN E 29 " --> pdb=" O GLY E 22 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY E 22 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER E 31 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE E 20 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL E 33 " --> pdb=" O ASP E 18 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG E 41 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP E 10 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 78 through 80 removed outlier: 4.795A pdb=" N SER E 183 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU E 166 " --> pdb=" O HIS E 190 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU E 192 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL E 164 " --> pdb=" O GLU E 192 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2475 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3773 1.33 - 1.45: 1986 1.45 - 1.57: 6753 1.57 - 1.68: 23 1.68 - 1.80: 50 Bond restraints: 12585 Sorted by residual: bond pdb=" C5' LMT D 401 " pdb=" O5' LMT D 401 " ideal model delta sigma weight residual 1.411 1.524 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C5' LMT C 401 " pdb=" O5' LMT C 401 " ideal model delta sigma weight residual 1.411 1.524 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C5' LMT A 402 " pdb=" O5' LMT A 402 " ideal model delta sigma weight residual 1.411 1.523 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C5' LMT A 401 " pdb=" O5' LMT A 401 " ideal model delta sigma weight residual 1.411 1.523 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C5' LMT B 401 " pdb=" O5' LMT B 401 " ideal model delta sigma weight residual 1.411 1.523 -0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 12580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 16224 1.45 - 2.90: 729 2.90 - 4.35: 137 4.35 - 5.81: 45 5.81 - 7.26: 5 Bond angle restraints: 17140 Sorted by residual: angle pdb=" C3B LMT D 401 " pdb=" C4B LMT D 401 " pdb=" C5B LMT D 401 " ideal model delta sigma weight residual 109.17 116.43 -7.26 3.00e+00 1.11e-01 5.85e+00 angle pdb=" C3B LMT A 401 " pdb=" C4B LMT A 401 " pdb=" C5B LMT A 401 " ideal model delta sigma weight residual 109.17 116.39 -7.22 3.00e+00 1.11e-01 5.80e+00 angle pdb=" C3B LMT A 402 " pdb=" C4B LMT A 402 " pdb=" C5B LMT A 402 " ideal model delta sigma weight residual 109.17 116.39 -7.22 3.00e+00 1.11e-01 5.79e+00 angle pdb=" C3B LMT C 401 " pdb=" C4B LMT C 401 " pdb=" C5B LMT C 401 " ideal model delta sigma weight residual 109.17 116.37 -7.20 3.00e+00 1.11e-01 5.76e+00 angle pdb=" C3B LMT B 401 " pdb=" C4B LMT B 401 " pdb=" C5B LMT B 401 " ideal model delta sigma weight residual 109.17 116.36 -7.19 3.00e+00 1.11e-01 5.75e+00 ... (remaining 17135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 6830 17.32 - 34.64: 500 34.64 - 51.96: 90 51.96 - 69.28: 30 69.28 - 86.59: 10 Dihedral angle restraints: 7460 sinusoidal: 2955 harmonic: 4505 Sorted by residual: dihedral pdb=" CA TYR B 59 " pdb=" C TYR B 59 " pdb=" N THR B 60 " pdb=" CA THR B 60 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TYR A 59 " pdb=" C TYR A 59 " pdb=" N THR A 60 " pdb=" CA THR A 60 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TYR D 59 " pdb=" C TYR D 59 " pdb=" N THR D 60 " pdb=" CA THR D 60 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 7457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1315 0.047 - 0.093: 557 0.093 - 0.140: 83 0.140 - 0.186: 15 0.186 - 0.233: 10 Chirality restraints: 1980 Sorted by residual: chirality pdb=" C5B LMT D 401 " pdb=" C4B LMT D 401 " pdb=" C6B LMT D 401 " pdb=" O5B LMT D 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.66 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C5B LMT A 401 " pdb=" C4B LMT A 401 " pdb=" C6B LMT A 401 " pdb=" O5B LMT A 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.66 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C5B LMT A 402 " pdb=" C4B LMT A 402 " pdb=" C6B LMT A 402 " pdb=" O5B LMT A 402 " both_signs ideal model delta sigma weight residual False -2.43 -2.66 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1977 not shown) Planarity restraints: 2170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 117 " -0.016 2.00e-02 2.50e+03 1.33e-02 3.09e+00 pdb=" CG PHE A 117 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 117 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 117 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 117 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 117 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 117 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 117 " 0.016 2.00e-02 2.50e+03 1.32e-02 3.07e+00 pdb=" CG PHE E 117 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE E 117 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE E 117 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 117 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 117 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 117 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 117 " 0.016 2.00e-02 2.50e+03 1.32e-02 3.06e+00 pdb=" CG PHE C 117 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE C 117 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 117 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 117 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 117 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 117 " 0.006 2.00e-02 2.50e+03 ... (remaining 2167 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1807 2.76 - 3.29: 11431 3.29 - 3.83: 21263 3.83 - 4.36: 26265 4.36 - 4.90: 43920 Nonbonded interactions: 104686 Sorted by model distance: nonbonded pdb=" OE2 GLU B 161 " pdb=" OH TYR B 198 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU C 161 " pdb=" OH TYR C 198 " model vdw 2.220 3.040 nonbonded pdb=" OE2 GLU A 161 " pdb=" OH TYR A 198 " model vdw 2.220 3.040 nonbonded pdb=" OE2 GLU E 161 " pdb=" OH TYR E 198 " model vdw 2.220 3.040 nonbonded pdb=" OE2 GLU D 161 " pdb=" OH TYR D 198 " model vdw 2.220 3.040 ... (remaining 104681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 316) selection = (chain 'B' and resid 7 through 316) selection = (chain 'C' and resid 7 through 316) selection = (chain 'D' and resid 7 through 316) selection = chain 'E' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.090 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.009 0.113 12585 Z= 0.418 Angle : 0.736 7.258 17140 Z= 0.374 Chirality : 0.052 0.233 1980 Planarity : 0.006 0.049 2170 Dihedral : 13.221 86.594 4540 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 0.22 (0.20), residues: 1540 helix: 1.18 (0.20), residues: 610 sheet: -0.17 (0.23), residues: 480 loop : -0.76 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 57 TYR 0.017 0.002 TYR E 198 PHE 0.030 0.003 PHE A 117 TRP 0.009 0.003 TRP D 40 HIS 0.009 0.003 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00888 (12585) covalent geometry : angle 0.73640 (17140) hydrogen bonds : bond 0.09968 ( 710) hydrogen bonds : angle 6.64338 ( 2475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.568 Fit side-chains REVERT: A 72 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7291 (mm110) REVERT: A 148 GLN cc_start: 0.7485 (mm110) cc_final: 0.7117 (mm110) REVERT: A 228 LEU cc_start: 0.6052 (tp) cc_final: 0.5781 (tt) REVERT: A 235 LEU cc_start: 0.6194 (mt) cc_final: 0.5621 (tt) REVERT: A 299 SER cc_start: 0.5291 (m) cc_final: 0.4950 (p) REVERT: C 28 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8195 (mt-10) REVERT: C 55 LYS cc_start: 0.6828 (mmtp) cc_final: 0.6521 (mptt) REVERT: C 72 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7250 (mm110) REVERT: C 98 GLU cc_start: 0.7909 (tt0) cc_final: 0.7635 (mt-10) REVERT: C 148 GLN cc_start: 0.7465 (mm110) cc_final: 0.7204 (mm110) REVERT: C 169 THR cc_start: 0.8341 (m) cc_final: 0.7887 (p) REVERT: C 228 LEU cc_start: 0.6001 (tp) cc_final: 0.5682 (tm) REVERT: C 235 LEU cc_start: 0.6238 (mt) cc_final: 0.5552 (tt) REVERT: C 297 ILE cc_start: 0.6589 (mt) cc_final: 0.5808 (pp) REVERT: B 55 LYS cc_start: 0.6790 (mmtp) cc_final: 0.6554 (mptt) REVERT: B 72 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7312 (mm-40) REVERT: B 228 LEU cc_start: 0.5997 (tp) cc_final: 0.5761 (tt) REVERT: B 235 LEU cc_start: 0.6255 (mt) cc_final: 0.5610 (tt) REVERT: B 299 SER cc_start: 0.5271 (m) cc_final: 0.4901 (p) REVERT: D 72 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7275 (mm110) REVERT: D 228 LEU cc_start: 0.5906 (tp) cc_final: 0.5684 (tt) REVERT: D 235 LEU cc_start: 0.6034 (mt) cc_final: 0.5454 (tt) REVERT: D 299 SER cc_start: 0.5345 (m) cc_final: 0.4977 (p) REVERT: E 55 LYS cc_start: 0.6727 (mmtp) cc_final: 0.6521 (mptt) REVERT: E 72 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7294 (mm110) REVERT: E 228 LEU cc_start: 0.5851 (tp) cc_final: 0.5581 (tm) REVERT: E 235 LEU cc_start: 0.6203 (mt) cc_final: 0.5579 (tt) REVERT: E 299 SER cc_start: 0.5296 (m) cc_final: 0.4937 (p) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.7635 time to fit residues: 145.5311 Evaluate side-chains 155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.0770 chunk 149 optimal weight: 0.7980 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 113 GLN A 196 ASN A 240 ASN C 42 GLN C 84 GLN C 196 ASN C 240 ASN B 84 GLN B 113 GLN B 196 ASN B 240 ASN D 84 GLN D 196 ASN D 240 ASN E 84 GLN E 113 GLN E 196 ASN E 240 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.143176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.110588 restraints weight = 12071.384| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.01 r_work: 0.2935 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12585 Z= 0.120 Angle : 0.512 4.924 17140 Z= 0.275 Chirality : 0.042 0.135 1980 Planarity : 0.004 0.034 2170 Dihedral : 7.596 55.831 1965 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.83 % Allowed : 7.05 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 1.36 (0.21), residues: 1540 helix: 2.60 (0.21), residues: 610 sheet: 0.21 (0.24), residues: 455 loop : -0.61 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.008 0.001 TYR C 59 PHE 0.014 0.001 PHE D 117 TRP 0.011 0.002 TRP C 40 HIS 0.004 0.001 HIS D 194 Details of bonding type rmsd covalent geometry : bond 0.00246 (12585) covalent geometry : angle 0.51230 (17140) hydrogen bonds : bond 0.03974 ( 710) hydrogen bonds : angle 4.59819 ( 2475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.494 Fit side-chains REVERT: A 72 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7267 (mm110) REVERT: A 148 GLN cc_start: 0.7486 (mm110) cc_final: 0.7084 (mm110) REVERT: A 228 LEU cc_start: 0.5994 (tp) cc_final: 0.5742 (tt) REVERT: A 235 LEU cc_start: 0.6160 (mt) cc_final: 0.5557 (tt) REVERT: A 297 ILE cc_start: 0.6634 (mt) cc_final: 0.5826 (pp) REVERT: C 55 LYS cc_start: 0.6769 (mmtp) cc_final: 0.6439 (mptt) REVERT: C 72 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7268 (mm110) REVERT: C 148 GLN cc_start: 0.7502 (mm110) cc_final: 0.7200 (mm110) REVERT: C 228 LEU cc_start: 0.6095 (tp) cc_final: 0.5805 (tm) REVERT: C 235 LEU cc_start: 0.6228 (mt) cc_final: 0.5580 (tt) REVERT: C 297 ILE cc_start: 0.6646 (mt) cc_final: 0.5800 (pp) REVERT: B 55 LYS cc_start: 0.6800 (mmtp) cc_final: 0.6537 (mptt) REVERT: B 72 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7210 (mm110) REVERT: B 235 LEU cc_start: 0.6265 (mt) cc_final: 0.5610 (tt) REVERT: B 297 ILE cc_start: 0.6529 (mt) cc_final: 0.6270 (mm) REVERT: D 228 LEU cc_start: 0.5907 (tp) cc_final: 0.5667 (tt) REVERT: D 235 LEU cc_start: 0.6096 (mt) cc_final: 0.5501 (tt) REVERT: D 297 ILE cc_start: 0.6542 (mt) cc_final: 0.5728 (pp) REVERT: E 55 LYS cc_start: 0.6660 (mmtp) cc_final: 0.6435 (mptt) REVERT: E 72 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7283 (mm110) REVERT: E 228 LEU cc_start: 0.5880 (tp) cc_final: 0.5669 (tt) REVERT: E 235 LEU cc_start: 0.6119 (mt) cc_final: 0.5466 (tt) REVERT: E 297 ILE cc_start: 0.6533 (mt) cc_final: 0.6269 (mm) REVERT: E 299 SER cc_start: 0.5333 (m) cc_final: 0.5085 (p) outliers start: 10 outliers final: 3 residues processed: 155 average time/residue: 0.7323 time to fit residues: 121.9156 Evaluate side-chains 149 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 169 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 240 ASN C 240 ASN B 232 ASN B 240 ASN D 72 GLN D 240 ASN E 232 ASN E 240 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.140860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.106751 restraints weight = 12123.833| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.06 r_work: 0.2903 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12585 Z= 0.195 Angle : 0.632 5.723 17140 Z= 0.331 Chirality : 0.045 0.144 1980 Planarity : 0.005 0.035 2170 Dihedral : 7.535 57.146 1965 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.83 % Allowed : 7.63 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 1.08 (0.21), residues: 1540 helix: 2.19 (0.21), residues: 610 sheet: 0.15 (0.23), residues: 455 loop : -0.59 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 57 TYR 0.016 0.002 TYR E 198 PHE 0.018 0.002 PHE A 117 TRP 0.007 0.002 TRP B 75 HIS 0.005 0.002 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00422 (12585) covalent geometry : angle 0.63175 (17140) hydrogen bonds : bond 0.04830 ( 710) hydrogen bonds : angle 4.90649 ( 2475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.496 Fit side-chains REVERT: A 72 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7242 (mm110) REVERT: A 148 GLN cc_start: 0.7488 (mm110) cc_final: 0.7114 (mm110) REVERT: A 228 LEU cc_start: 0.5939 (tp) cc_final: 0.5702 (tt) REVERT: A 235 LEU cc_start: 0.6208 (mt) cc_final: 0.5548 (tt) REVERT: A 297 ILE cc_start: 0.6627 (mt) cc_final: 0.5858 (pp) REVERT: C 55 LYS cc_start: 0.6758 (mmtp) cc_final: 0.6454 (mptt) REVERT: C 72 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7150 (mm110) REVERT: C 148 GLN cc_start: 0.7496 (mm110) cc_final: 0.7200 (mm110) REVERT: C 228 LEU cc_start: 0.5998 (tp) cc_final: 0.5676 (tm) REVERT: C 235 LEU cc_start: 0.6259 (mt) cc_final: 0.5512 (tt) REVERT: C 297 ILE cc_start: 0.6669 (mt) cc_final: 0.5864 (pp) REVERT: B 55 LYS cc_start: 0.6733 (mmtp) cc_final: 0.6478 (mptt) REVERT: B 72 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7150 (mm110) REVERT: B 235 LEU cc_start: 0.6284 (mt) cc_final: 0.5593 (tt) REVERT: D 68 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7914 (mp) REVERT: D 228 LEU cc_start: 0.5857 (tp) cc_final: 0.5617 (tt) REVERT: D 235 LEU cc_start: 0.6252 (mt) cc_final: 0.5589 (tt) REVERT: E 55 LYS cc_start: 0.6616 (mmtp) cc_final: 0.6392 (mptt) REVERT: E 72 GLN cc_start: 0.7533 (mm-40) cc_final: 0.7286 (mm110) REVERT: E 201 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.6479 (mpp-170) REVERT: E 228 LEU cc_start: 0.5951 (tp) cc_final: 0.5624 (tm) REVERT: E 235 LEU cc_start: 0.6048 (mt) cc_final: 0.5409 (tt) REVERT: E 299 SER cc_start: 0.5408 (m) cc_final: 0.5120 (p) outliers start: 22 outliers final: 13 residues processed: 157 average time/residue: 0.7032 time to fit residues: 118.8951 Evaluate side-chains 153 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 201 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 36 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN C 232 ASN C 240 ASN B 240 ASN D 240 ASN E 232 ASN E 240 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.141966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.107786 restraints weight = 12115.794| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.08 r_work: 0.2918 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12585 Z= 0.148 Angle : 0.564 5.671 17140 Z= 0.296 Chirality : 0.043 0.133 1980 Planarity : 0.004 0.033 2170 Dihedral : 7.090 55.978 1965 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.24 % Allowed : 7.80 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 1.31 (0.21), residues: 1540 helix: 2.48 (0.21), residues: 610 sheet: 0.16 (0.24), residues: 455 loop : -0.49 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 57 TYR 0.012 0.002 TYR A 198 PHE 0.012 0.002 PHE A 117 TRP 0.007 0.001 TRP B 75 HIS 0.004 0.001 HIS D 194 Details of bonding type rmsd covalent geometry : bond 0.00315 (12585) covalent geometry : angle 0.56407 (17140) hydrogen bonds : bond 0.04266 ( 710) hydrogen bonds : angle 4.63314 ( 2475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7420 (tmtm) REVERT: A 72 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7221 (mm110) REVERT: A 117 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: A 148 GLN cc_start: 0.7440 (mm110) cc_final: 0.7058 (mm110) REVERT: A 228 LEU cc_start: 0.5886 (tp) cc_final: 0.5632 (tt) REVERT: A 235 LEU cc_start: 0.6171 (mt) cc_final: 0.5478 (tt) REVERT: A 297 ILE cc_start: 0.6623 (mt) cc_final: 0.5827 (pp) REVERT: C 55 LYS cc_start: 0.6757 (mmtp) cc_final: 0.6476 (mptt) REVERT: C 72 GLN cc_start: 0.7446 (mm-40) cc_final: 0.7160 (mm110) REVERT: C 117 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.6821 (m-10) REVERT: C 148 GLN cc_start: 0.7448 (mm110) cc_final: 0.7141 (mm110) REVERT: C 228 LEU cc_start: 0.5921 (tp) cc_final: 0.5642 (tt) REVERT: C 235 LEU cc_start: 0.6289 (mt) cc_final: 0.5524 (tt) REVERT: C 297 ILE cc_start: 0.6680 (mt) cc_final: 0.5846 (pp) REVERT: B 55 LYS cc_start: 0.6726 (mmtp) cc_final: 0.6451 (mptt) REVERT: B 72 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7162 (mm-40) REVERT: B 235 LEU cc_start: 0.6345 (mt) cc_final: 0.5622 (tt) REVERT: D 68 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7874 (mp) REVERT: D 228 LEU cc_start: 0.5857 (tp) cc_final: 0.5609 (tt) REVERT: D 235 LEU cc_start: 0.6184 (mt) cc_final: 0.5551 (tt) REVERT: E 55 LYS cc_start: 0.6621 (mmtp) cc_final: 0.6360 (mptt) REVERT: E 72 GLN cc_start: 0.7533 (mm-40) cc_final: 0.7253 (mm110) REVERT: E 228 LEU cc_start: 0.5871 (tp) cc_final: 0.5650 (tt) REVERT: E 235 LEU cc_start: 0.6053 (mt) cc_final: 0.5382 (tt) REVERT: E 299 SER cc_start: 0.5373 (m) cc_final: 0.5133 (p) outliers start: 27 outliers final: 15 residues processed: 158 average time/residue: 0.7147 time to fit residues: 121.6529 Evaluate side-chains 155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 242 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 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 232 ASN A 240 ASN C 232 ASN C 240 ASN D 232 ASN D 240 ASN E 240 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.140277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.105893 restraints weight = 12088.887| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.08 r_work: 0.2891 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12585 Z= 0.274 Angle : 0.745 6.659 17140 Z= 0.387 Chirality : 0.049 0.165 1980 Planarity : 0.006 0.039 2170 Dihedral : 7.761 59.325 1965 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.73 % Allowed : 6.64 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 0.61 (0.20), residues: 1540 helix: 1.55 (0.21), residues: 610 sheet: 0.02 (0.23), residues: 455 loop : -0.59 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 107 TYR 0.018 0.003 TYR B 198 PHE 0.024 0.003 PHE E 117 TRP 0.008 0.002 TRP B 75 HIS 0.006 0.002 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00606 (12585) covalent geometry : angle 0.74491 (17140) hydrogen bonds : bond 0.05573 ( 710) hydrogen bonds : angle 5.23656 ( 2475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.539 Fit side-chains REVERT: A 16 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7450 (tmtm) REVERT: A 72 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7315 (mm110) REVERT: A 117 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: A 148 GLN cc_start: 0.7475 (mm110) cc_final: 0.7116 (mm110) REVERT: A 228 LEU cc_start: 0.6003 (tp) cc_final: 0.5713 (tm) REVERT: A 235 LEU cc_start: 0.6245 (mt) cc_final: 0.5606 (tt) REVERT: A 297 ILE cc_start: 0.6639 (mt) cc_final: 0.5891 (pp) REVERT: C 55 LYS cc_start: 0.6750 (mmtp) cc_final: 0.6425 (mptt) REVERT: C 72 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7201 (mm110) REVERT: C 117 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.6804 (m-10) REVERT: C 148 GLN cc_start: 0.7455 (mm110) cc_final: 0.7153 (mm110) REVERT: C 228 LEU cc_start: 0.5984 (tp) cc_final: 0.5692 (tm) REVERT: C 235 LEU cc_start: 0.6195 (mt) cc_final: 0.5491 (tt) REVERT: C 313 LEU cc_start: 0.7022 (mt) cc_final: 0.6806 (mt) REVERT: B 72 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7185 (mm110) REVERT: B 117 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: B 235 LEU cc_start: 0.6304 (mt) cc_final: 0.5627 (tt) REVERT: D 68 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7965 (mp) REVERT: D 117 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: D 228 LEU cc_start: 0.5887 (tp) cc_final: 0.5618 (tm) REVERT: D 235 LEU cc_start: 0.6217 (mt) cc_final: 0.5568 (tt) REVERT: E 16 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7316 (tmtm) REVERT: E 72 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7309 (mm110) REVERT: E 201 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.6482 (mpp-170) REVERT: E 228 LEU cc_start: 0.6118 (tp) cc_final: 0.5751 (tm) REVERT: E 235 LEU cc_start: 0.6153 (mt) cc_final: 0.5483 (tt) REVERT: E 299 SER cc_start: 0.5401 (m) cc_final: 0.5081 (p) outliers start: 45 outliers final: 27 residues processed: 176 average time/residue: 0.6636 time to fit residues: 126.3211 Evaluate side-chains 178 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 117 PHE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 275 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 66 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 240 ASN C 113 GLN C 232 ASN C 240 ASN B 240 ASN D 72 GLN D 240 ASN E 232 ASN E 240 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.143009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.109377 restraints weight = 12090.509| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.05 r_work: 0.2938 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12585 Z= 0.117 Angle : 0.523 5.857 17140 Z= 0.275 Chirality : 0.042 0.132 1980 Planarity : 0.004 0.033 2170 Dihedral : 6.884 59.700 1965 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.41 % Allowed : 8.71 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 1.47 (0.21), residues: 1540 helix: 2.61 (0.21), residues: 610 sheet: 0.16 (0.24), residues: 460 loop : -0.31 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 86 TYR 0.010 0.001 TYR C 198 PHE 0.012 0.001 PHE E 117 TRP 0.007 0.001 TRP B 75 HIS 0.003 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00244 (12585) covalent geometry : angle 0.52316 (17140) hydrogen bonds : bond 0.03885 ( 710) hydrogen bonds : angle 4.44875 ( 2475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.491 Fit side-chains REVERT: A 16 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7330 (tmtm) REVERT: A 72 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7256 (mm110) REVERT: A 117 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: A 148 GLN cc_start: 0.7459 (mm110) cc_final: 0.7070 (mm110) REVERT: A 228 LEU cc_start: 0.5885 (tp) cc_final: 0.5635 (tt) REVERT: A 235 LEU cc_start: 0.6237 (mt) cc_final: 0.5540 (tt) REVERT: A 277 LEU cc_start: 0.6425 (mt) cc_final: 0.6159 (tp) REVERT: A 297 ILE cc_start: 0.6667 (mt) cc_final: 0.5871 (pp) REVERT: C 55 LYS cc_start: 0.6797 (mmtp) cc_final: 0.6453 (mptt) REVERT: C 72 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7156 (mm110) REVERT: C 117 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.6757 (m-10) REVERT: C 148 GLN cc_start: 0.7452 (mm110) cc_final: 0.7155 (mm110) REVERT: C 228 LEU cc_start: 0.6040 (tp) cc_final: 0.5782 (tt) REVERT: C 235 LEU cc_start: 0.6278 (mt) cc_final: 0.5465 (tt) REVERT: C 297 ILE cc_start: 0.6726 (mt) cc_final: 0.5892 (pp) REVERT: B 72 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7185 (mm110) REVERT: B 235 LEU cc_start: 0.6342 (mt) cc_final: 0.5578 (tt) REVERT: B 277 LEU cc_start: 0.6479 (mt) cc_final: 0.6270 (tp) REVERT: B 297 ILE cc_start: 0.6603 (mt) cc_final: 0.6341 (mm) REVERT: D 68 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7848 (mp) REVERT: D 98 GLU cc_start: 0.7629 (tt0) cc_final: 0.7309 (mt-10) REVERT: D 228 LEU cc_start: 0.5719 (tp) cc_final: 0.5482 (tt) REVERT: D 235 LEU cc_start: 0.6148 (mt) cc_final: 0.5733 (mt) REVERT: D 297 ILE cc_start: 0.6627 (mt) cc_final: 0.6401 (mm) REVERT: E 16 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7339 (tmtm) REVERT: E 72 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7285 (mm110) REVERT: E 228 LEU cc_start: 0.5885 (tp) cc_final: 0.5665 (tt) REVERT: E 235 LEU cc_start: 0.6149 (mt) cc_final: 0.5455 (tt) REVERT: E 299 SER cc_start: 0.5326 (m) cc_final: 0.5095 (p) outliers start: 29 outliers final: 17 residues processed: 165 average time/residue: 0.7222 time to fit residues: 128.1715 Evaluate side-chains 165 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 242 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 74 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 99 optimal weight: 0.4980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN C 232 ASN C 240 ASN D 72 GLN D 240 ASN E 232 ASN E 240 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.141540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.107289 restraints weight = 12025.551| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.06 r_work: 0.2913 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12585 Z= 0.168 Angle : 0.601 6.022 17140 Z= 0.312 Chirality : 0.044 0.137 1980 Planarity : 0.004 0.035 2170 Dihedral : 7.244 59.565 1965 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.07 % Allowed : 8.05 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 1.27 (0.21), residues: 1540 helix: 2.38 (0.21), residues: 610 sheet: 0.10 (0.24), residues: 460 loop : -0.36 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 86 TYR 0.015 0.002 TYR C 198 PHE 0.019 0.002 PHE E 117 TRP 0.007 0.001 TRP B 75 HIS 0.004 0.001 HIS D 194 Details of bonding type rmsd covalent geometry : bond 0.00362 (12585) covalent geometry : angle 0.60083 (17140) hydrogen bonds : bond 0.04484 ( 710) hydrogen bonds : angle 4.72499 ( 2475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.478 Fit side-chains REVERT: A 16 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7346 (tmtm) REVERT: A 72 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7288 (mm110) REVERT: A 117 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: A 148 GLN cc_start: 0.7492 (mm110) cc_final: 0.7095 (mm110) REVERT: A 228 LEU cc_start: 0.5896 (tp) cc_final: 0.5599 (tm) REVERT: A 235 LEU cc_start: 0.6243 (mt) cc_final: 0.5561 (tt) REVERT: C 72 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7184 (mm110) REVERT: C 117 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.6766 (m-10) REVERT: C 148 GLN cc_start: 0.7417 (mm110) cc_final: 0.7129 (mm110) REVERT: C 228 LEU cc_start: 0.5993 (tp) cc_final: 0.5728 (tt) REVERT: C 235 LEU cc_start: 0.6278 (mt) cc_final: 0.5477 (tt) REVERT: C 297 ILE cc_start: 0.6704 (mt) cc_final: 0.5900 (pp) REVERT: B 72 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7201 (mm110) REVERT: B 235 LEU cc_start: 0.6353 (mt) cc_final: 0.5578 (tt) REVERT: D 68 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7843 (mp) REVERT: D 228 LEU cc_start: 0.5841 (tp) cc_final: 0.5550 (tm) REVERT: D 235 LEU cc_start: 0.6126 (mt) cc_final: 0.5471 (tt) REVERT: E 16 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7292 (tmtm) REVERT: E 72 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7345 (mm110) REVERT: E 228 LEU cc_start: 0.5971 (tp) cc_final: 0.5741 (tt) REVERT: E 235 LEU cc_start: 0.6075 (mt) cc_final: 0.5358 (tt) REVERT: E 299 SER cc_start: 0.5314 (m) cc_final: 0.5091 (p) outliers start: 37 outliers final: 26 residues processed: 167 average time/residue: 0.6644 time to fit residues: 119.7669 Evaluate side-chains 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 0.4980 chunk 21 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN C 232 ASN C 240 ASN D 240 ASN E 232 ASN E 240 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.143925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.111942 restraints weight = 11996.031| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.12 r_work: 0.2942 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12585 Z= 0.117 Angle : 0.522 5.806 17140 Z= 0.272 Chirality : 0.041 0.131 1980 Planarity : 0.004 0.032 2170 Dihedral : 6.890 59.184 1965 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.82 % Allowed : 8.30 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 1.63 (0.21), residues: 1540 helix: 2.82 (0.21), residues: 610 sheet: 0.13 (0.24), residues: 460 loop : -0.21 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.010 0.001 TYR C 198 PHE 0.015 0.001 PHE E 117 TRP 0.007 0.001 TRP B 75 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00245 (12585) covalent geometry : angle 0.52231 (17140) hydrogen bonds : bond 0.03769 ( 710) hydrogen bonds : angle 4.37036 ( 2475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.414 Fit side-chains REVERT: A 16 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7337 (tmtm) REVERT: A 72 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7284 (mm110) REVERT: A 117 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: A 148 GLN cc_start: 0.7484 (mm110) cc_final: 0.7089 (mm110) REVERT: A 228 LEU cc_start: 0.5894 (tp) cc_final: 0.5618 (tt) REVERT: A 235 LEU cc_start: 0.6214 (mt) cc_final: 0.5513 (tt) REVERT: A 277 LEU cc_start: 0.6407 (mt) cc_final: 0.6150 (tp) REVERT: A 297 ILE cc_start: 0.6674 (mt) cc_final: 0.5878 (pp) REVERT: C 72 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7182 (mm110) REVERT: C 117 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.6794 (m-10) REVERT: C 148 GLN cc_start: 0.7437 (mm110) cc_final: 0.7131 (mm110) REVERT: C 228 LEU cc_start: 0.5947 (tp) cc_final: 0.5687 (tt) REVERT: C 235 LEU cc_start: 0.6282 (mt) cc_final: 0.5466 (tt) REVERT: C 297 ILE cc_start: 0.6684 (mt) cc_final: 0.5854 (pp) REVERT: B 72 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7264 (mm-40) REVERT: B 228 LEU cc_start: 0.6294 (tt) cc_final: 0.5984 (tm) REVERT: B 235 LEU cc_start: 0.6290 (mt) cc_final: 0.5487 (tt) REVERT: B 277 LEU cc_start: 0.6408 (mt) cc_final: 0.6198 (tp) REVERT: B 297 ILE cc_start: 0.6601 (mt) cc_final: 0.6334 (mm) REVERT: D 68 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7896 (mp) REVERT: D 98 GLU cc_start: 0.7688 (tt0) cc_final: 0.7374 (mt-10) REVERT: D 228 LEU cc_start: 0.5711 (tp) cc_final: 0.5456 (tt) REVERT: D 235 LEU cc_start: 0.6151 (mt) cc_final: 0.5718 (mt) REVERT: D 297 ILE cc_start: 0.6614 (mt) cc_final: 0.6393 (mm) REVERT: D 299 SER cc_start: 0.5329 (m) cc_final: 0.5117 (p) REVERT: E 16 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7348 (tmtm) REVERT: E 72 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7348 (mm110) REVERT: E 228 LEU cc_start: 0.5839 (tp) cc_final: 0.5625 (tt) REVERT: E 235 LEU cc_start: 0.6098 (mt) cc_final: 0.5409 (tt) REVERT: E 297 ILE cc_start: 0.6468 (mt) cc_final: 0.6222 (mm) outliers start: 34 outliers final: 25 residues processed: 168 average time/residue: 0.6737 time to fit residues: 122.3871 Evaluate side-chains 171 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 275 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN C 42 GLN C 232 ASN C 240 ASN D 240 ASN E 232 ASN E 240 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.140437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.106846 restraints weight = 11976.059| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.01 r_work: 0.2892 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 12585 Z= 0.321 Angle : 0.805 7.327 17140 Z= 0.416 Chirality : 0.052 0.180 1980 Planarity : 0.007 0.046 2170 Dihedral : 7.882 59.435 1965 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.99 % Allowed : 8.55 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 0.40 (0.20), residues: 1540 helix: 1.31 (0.20), residues: 610 sheet: -0.26 (0.23), residues: 480 loop : -0.38 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 86 TYR 0.018 0.003 TYR B 198 PHE 0.035 0.003 PHE E 117 TRP 0.009 0.003 TRP B 75 HIS 0.007 0.003 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00715 (12585) covalent geometry : angle 0.80509 (17140) hydrogen bonds : bond 0.05849 ( 710) hydrogen bonds : angle 5.34819 ( 2475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.492 Fit side-chains REVERT: A 16 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7503 (tmtm) REVERT: A 72 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7352 (mm110) REVERT: A 117 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: A 148 GLN cc_start: 0.7463 (mm110) cc_final: 0.7097 (mm110) REVERT: A 228 LEU cc_start: 0.6035 (tp) cc_final: 0.5731 (tm) REVERT: A 235 LEU cc_start: 0.6282 (mt) cc_final: 0.5674 (tt) REVERT: C 72 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7263 (mm110) REVERT: C 117 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.6843 (m-10) REVERT: C 148 GLN cc_start: 0.7468 (mm110) cc_final: 0.7178 (mm110) REVERT: C 228 LEU cc_start: 0.6082 (tp) cc_final: 0.5805 (tm) REVERT: C 235 LEU cc_start: 0.6241 (mt) cc_final: 0.5565 (tt) REVERT: B 72 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7222 (mm110) REVERT: B 235 LEU cc_start: 0.6404 (mt) cc_final: 0.5659 (tt) REVERT: B 277 LEU cc_start: 0.6322 (mt) cc_final: 0.6112 (tp) REVERT: D 68 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8039 (mp) REVERT: D 228 LEU cc_start: 0.5937 (tp) cc_final: 0.5676 (tm) REVERT: D 235 LEU cc_start: 0.6222 (mt) cc_final: 0.5607 (tt) REVERT: E 16 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7355 (tmtm) REVERT: E 235 LEU cc_start: 0.6231 (mt) cc_final: 0.5564 (tt) outliers start: 36 outliers final: 28 residues processed: 166 average time/residue: 0.7200 time to fit residues: 128.5427 Evaluate side-chains 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 81 optimal weight: 0.0000 chunk 37 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 240 ASN C 232 ASN C 240 ASN B 240 ASN D 240 ASN E 232 ASN E 240 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.142968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.108821 restraints weight = 12115.432| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.07 r_work: 0.2933 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12585 Z= 0.118 Angle : 0.531 5.973 17140 Z= 0.278 Chirality : 0.042 0.133 1980 Planarity : 0.004 0.034 2170 Dihedral : 6.938 58.091 1965 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.32 % Allowed : 9.63 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 1.39 (0.21), residues: 1540 helix: 2.50 (0.21), residues: 610 sheet: 0.11 (0.24), residues: 460 loop : -0.28 (0.24), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 86 TYR 0.010 0.001 TYR C 198 PHE 0.012 0.001 PHE E 117 TRP 0.008 0.001 TRP B 75 HIS 0.003 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00246 (12585) covalent geometry : angle 0.53128 (17140) hydrogen bonds : bond 0.03905 ( 710) hydrogen bonds : angle 4.47858 ( 2475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.514 Fit side-chains REVERT: A 16 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7262 (tmtm) REVERT: A 117 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: A 148 GLN cc_start: 0.7426 (mm110) cc_final: 0.7047 (mm110) REVERT: A 228 LEU cc_start: 0.5841 (tp) cc_final: 0.5580 (tt) REVERT: A 235 LEU cc_start: 0.6166 (mt) cc_final: 0.5466 (tt) REVERT: A 297 ILE cc_start: 0.6662 (mt) cc_final: 0.5854 (pp) REVERT: C 72 GLN cc_start: 0.7426 (mm-40) cc_final: 0.7166 (mm110) REVERT: C 117 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.6757 (m-10) REVERT: C 148 GLN cc_start: 0.7434 (mm110) cc_final: 0.7134 (mm110) REVERT: C 228 LEU cc_start: 0.5969 (tp) cc_final: 0.5700 (tt) REVERT: C 235 LEU cc_start: 0.6266 (mt) cc_final: 0.5449 (tt) REVERT: C 297 ILE cc_start: 0.6668 (mt) cc_final: 0.6401 (mm) REVERT: B 72 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7209 (mm110) REVERT: B 235 LEU cc_start: 0.6326 (mt) cc_final: 0.5531 (tt) REVERT: B 277 LEU cc_start: 0.6399 (mt) cc_final: 0.6175 (tp) REVERT: B 297 ILE cc_start: 0.6583 (mt) cc_final: 0.6324 (mm) REVERT: D 68 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7873 (mp) REVERT: D 98 GLU cc_start: 0.7641 (tt0) cc_final: 0.7312 (mt-10) REVERT: D 146 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8053 (mt-10) REVERT: D 228 LEU cc_start: 0.5698 (tp) cc_final: 0.5450 (tt) REVERT: D 235 LEU cc_start: 0.6138 (mt) cc_final: 0.5741 (mt) REVERT: D 245 SER cc_start: 0.7069 (p) cc_final: 0.6294 (m) REVERT: D 297 ILE cc_start: 0.6563 (mt) cc_final: 0.6336 (mm) REVERT: E 16 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7355 (tmtm) REVERT: E 228 LEU cc_start: 0.5855 (tp) cc_final: 0.5646 (tt) REVERT: E 235 LEU cc_start: 0.6092 (mt) cc_final: 0.5400 (tt) REVERT: E 297 ILE cc_start: 0.6470 (mt) cc_final: 0.6222 (mm) outliers start: 28 outliers final: 23 residues processed: 162 average time/residue: 0.6962 time to fit residues: 121.6375 Evaluate side-chains 170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 240 ASN C 232 ASN C 240 ASN D 72 GLN D 240 ASN E 232 ASN E 240 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.141673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.107349 restraints weight = 11977.634| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.06 r_work: 0.2913 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12585 Z= 0.159 Angle : 0.593 6.071 17140 Z= 0.307 Chirality : 0.043 0.133 1980 Planarity : 0.004 0.036 2170 Dihedral : 7.181 56.892 1965 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.90 % Allowed : 8.80 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 1.29 (0.21), residues: 1540 helix: 2.40 (0.21), residues: 610 sheet: 0.07 (0.24), residues: 460 loop : -0.31 (0.24), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 86 TYR 0.014 0.002 TYR A 198 PHE 0.018 0.002 PHE E 117 TRP 0.007 0.001 TRP B 75 HIS 0.004 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00341 (12585) covalent geometry : angle 0.59293 (17140) hydrogen bonds : bond 0.04359 ( 710) hydrogen bonds : angle 4.68002 ( 2475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4530.01 seconds wall clock time: 77 minutes 59.85 seconds (4679.85 seconds total)