Starting phenix.real_space_refine on Wed May 14 19:22:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f5n_50194/05_2025/9f5n_50194_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f5n_50194/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9f5n_50194/05_2025/9f5n_50194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f5n_50194/05_2025/9f5n_50194.map" model { file = "/net/cci-nas-00/data/ceres_data/9f5n_50194/05_2025/9f5n_50194_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f5n_50194/05_2025/9f5n_50194_trim.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 4, 'HIS:plan': 1} 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: 5.66, per 1000 atoms: 0.46 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: 2.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.70 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: 4.07 Time building geometry restraints manager: 3.21 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.490 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.003 TRP D 40 HIS 0.009 0.003 HIS E 194 PHE 0.030 0.003 PHE A 117 TYR 0.017 0.002 TYR E 198 ARG 0.006 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.09968 ( 710) hydrogen bonds : angle 6.64338 ( 2475) covalent geometry : bond 0.00888 (12585) covalent geometry : angle 0.73640 (17140) *********************** 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 : 1.415 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: 1.4683 time to fit residues: 280.5971 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 : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 232 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.141862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.109094 restraints weight = 12038.460| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.00 r_work: 0.2931 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1099 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= 0.143 Angle : 0.553 5.402 17140 Z= 0.295 Chirality : 0.043 0.137 1980 Planarity : 0.004 0.034 2170 Dihedral : 7.815 59.763 1965 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.24 % Allowed : 6.89 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1540 helix: 2.35 (0.21), residues: 610 sheet: 0.19 (0.23), residues: 455 loop : -0.67 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 40 HIS 0.004 0.001 HIS D 194 PHE 0.017 0.002 PHE D 117 TYR 0.011 0.002 TYR E 198 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 710) hydrogen bonds : angle 4.73320 ( 2475) covalent geometry : bond 0.00300 (12585) covalent geometry : angle 0.55347 (17140) *********************** 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: 15 poor density : 147 time to evaluate : 1.382 Fit side-chains REVERT: A 72 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7260 (mm110) REVERT: A 148 GLN cc_start: 0.7504 (mm110) cc_final: 0.7112 (mm110) REVERT: A 228 LEU cc_start: 0.6043 (tp) cc_final: 0.5803 (tt) REVERT: A 235 LEU cc_start: 0.6156 (mt) cc_final: 0.5567 (tt) REVERT: A 297 ILE cc_start: 0.6648 (mt) cc_final: 0.5856 (pp) REVERT: C 55 LYS cc_start: 0.6796 (mmtp) cc_final: 0.6474 (mptt) REVERT: C 72 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7215 (mm110) REVERT: C 148 GLN cc_start: 0.7529 (mm110) cc_final: 0.7243 (mm110) REVERT: C 228 LEU cc_start: 0.6113 (tp) cc_final: 0.5832 (tm) REVERT: C 235 LEU cc_start: 0.6270 (mt) cc_final: 0.5609 (tt) REVERT: C 297 ILE cc_start: 0.6691 (mt) cc_final: 0.5854 (pp) REVERT: B 55 LYS cc_start: 0.6756 (mmtp) cc_final: 0.6475 (mptt) REVERT: B 72 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7190 (mm110) REVERT: B 228 LEU cc_start: 0.6008 (tp) cc_final: 0.5803 (tt) REVERT: B 235 LEU cc_start: 0.6315 (mt) cc_final: 0.5650 (tt) REVERT: B 297 ILE cc_start: 0.6546 (mt) cc_final: 0.6278 (mm) REVERT: D 68 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7885 (mp) REVERT: D 228 LEU cc_start: 0.5893 (tp) cc_final: 0.5656 (tt) REVERT: D 235 LEU cc_start: 0.6146 (mt) cc_final: 0.5555 (tt) REVERT: D 297 ILE cc_start: 0.6573 (mt) cc_final: 0.5794 (pp) REVERT: E 55 LYS cc_start: 0.6669 (mmtp) cc_final: 0.6447 (mptt) REVERT: E 72 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7292 (mm110) REVERT: E 228 LEU cc_start: 0.5939 (tp) cc_final: 0.5635 (tm) REVERT: E 235 LEU cc_start: 0.6129 (mt) cc_final: 0.5487 (tt) REVERT: E 297 ILE cc_start: 0.6551 (mt) cc_final: 0.6288 (mm) REVERT: E 299 SER cc_start: 0.5357 (m) cc_final: 0.5098 (p) outliers start: 15 outliers final: 5 residues processed: 155 average time/residue: 1.3599 time to fit residues: 227.8319 Evaluate side-chains 146 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 68 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 B 240 ASN D 72 GLN D 240 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 = 0.3497 r_free = 0.3497 target = 0.140225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.106122 restraints weight = 12125.789| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.06 r_work: 0.2898 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12585 Z= 0.237 Angle : 0.699 6.348 17140 Z= 0.364 Chirality : 0.047 0.160 1980 Planarity : 0.006 0.038 2170 Dihedral : 7.637 58.264 1965 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.74 % Allowed : 5.98 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1540 helix: 1.75 (0.21), residues: 610 sheet: 0.09 (0.23), residues: 455 loop : -0.68 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 75 HIS 0.006 0.002 HIS E 190 PHE 0.021 0.002 PHE D 117 TYR 0.018 0.002 TYR E 198 ARG 0.005 0.001 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.05308 ( 710) hydrogen bonds : angle 5.14087 ( 2475) covalent geometry : bond 0.00521 (12585) covalent geometry : angle 0.69942 (17140) *********************** 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 176 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.338 Fit side-chains REVERT: A 72 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7304 (mm110) REVERT: A 117 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: A 148 GLN cc_start: 0.7482 (mm110) cc_final: 0.7111 (mm110) REVERT: A 228 LEU cc_start: 0.5990 (tp) cc_final: 0.5750 (tt) REVERT: A 235 LEU cc_start: 0.6196 (mt) cc_final: 0.5578 (tt) REVERT: A 297 ILE cc_start: 0.6624 (mt) cc_final: 0.5874 (pp) REVERT: C 55 LYS cc_start: 0.6729 (mmtp) cc_final: 0.6429 (mptt) REVERT: C 72 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7185 (mm110) REVERT: C 148 GLN cc_start: 0.7506 (mm110) cc_final: 0.7231 (mm110) REVERT: C 228 LEU cc_start: 0.6051 (tp) cc_final: 0.5716 (tm) REVERT: C 235 LEU cc_start: 0.6249 (mt) cc_final: 0.5482 (tt) REVERT: C 297 ILE cc_start: 0.6667 (mt) cc_final: 0.5907 (pp) REVERT: B 55 LYS cc_start: 0.6715 (mmtp) cc_final: 0.6508 (mptt) REVERT: B 72 GLN cc_start: 0.7444 (mm-40) cc_final: 0.7209 (mm110) REVERT: B 228 LEU cc_start: 0.6108 (tp) cc_final: 0.5797 (tm) REVERT: B 235 LEU cc_start: 0.6272 (mt) cc_final: 0.5587 (tt) REVERT: D 68 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7921 (mp) REVERT: D 117 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: D 228 LEU cc_start: 0.5894 (tp) cc_final: 0.5658 (tt) REVERT: D 235 LEU cc_start: 0.6229 (mt) cc_final: 0.5569 (tt) REVERT: E 55 LYS cc_start: 0.6595 (mmtp) cc_final: 0.6370 (mptt) REVERT: E 72 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7320 (mm110) REVERT: E 228 LEU cc_start: 0.6048 (tp) cc_final: 0.5722 (tm) REVERT: E 235 LEU cc_start: 0.6096 (mt) cc_final: 0.5420 (tt) REVERT: E 299 SER cc_start: 0.5387 (m) cc_final: 0.5079 (p) outliers start: 33 outliers final: 18 residues processed: 166 average time/residue: 1.2832 time to fit residues: 230.8280 Evaluate side-chains 161 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 275 VAL 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 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 169 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 68 LEU Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 275 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 37 optimal weight: 0.0370 chunk 143 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 overall best weight: 2.8064 ------------------------------------------------------------------------------- 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 232 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 = 0.3508 r_free = 0.3508 target = 0.141059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.106702 restraints weight = 12030.991| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.07 r_work: 0.2911 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1222 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= 0.167 Angle : 0.597 6.008 17140 Z= 0.312 Chirality : 0.044 0.133 1980 Planarity : 0.005 0.036 2170 Dihedral : 7.251 59.064 1965 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.41 % Allowed : 7.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1540 helix: 2.21 (0.21), residues: 610 sheet: 0.15 (0.23), residues: 460 loop : -0.49 (0.24), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 75 HIS 0.004 0.001 HIS D 194 PHE 0.016 0.002 PHE C 117 TYR 0.014 0.002 TYR E 198 ARG 0.004 0.001 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 710) hydrogen bonds : angle 4.78600 ( 2475) covalent geometry : bond 0.00358 (12585) covalent geometry : angle 0.59662 (17140) *********************** 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 164 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.513 Fit side-chains REVERT: A 72 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7268 (mm110) REVERT: A 117 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: A 148 GLN cc_start: 0.7463 (mm110) cc_final: 0.7078 (mm110) REVERT: A 228 LEU cc_start: 0.5895 (tp) cc_final: 0.5653 (tt) REVERT: A 235 LEU cc_start: 0.6169 (mt) cc_final: 0.5480 (tt) REVERT: A 297 ILE cc_start: 0.6646 (mt) cc_final: 0.5865 (pp) REVERT: C 72 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7160 (mm110) REVERT: C 117 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.6779 (m-10) REVERT: C 148 GLN cc_start: 0.7477 (mm110) cc_final: 0.7185 (mm110) REVERT: C 228 LEU cc_start: 0.5992 (tp) cc_final: 0.5728 (tt) REVERT: C 235 LEU cc_start: 0.6275 (mt) cc_final: 0.5466 (tt) REVERT: C 297 ILE cc_start: 0.6660 (mt) cc_final: 0.5854 (pp) REVERT: B 72 GLN cc_start: 0.7401 (mm-40) cc_final: 0.7148 (mm110) REVERT: B 228 LEU cc_start: 0.5986 (tp) cc_final: 0.5763 (tt) REVERT: B 235 LEU cc_start: 0.6317 (mt) cc_final: 0.5608 (tt) REVERT: D 68 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7878 (mp) REVERT: D 228 LEU cc_start: 0.5837 (tp) cc_final: 0.5596 (tt) REVERT: D 235 LEU cc_start: 0.6176 (mt) cc_final: 0.5524 (tt) REVERT: E 55 LYS cc_start: 0.6591 (mmtp) cc_final: 0.6341 (mptt) REVERT: E 72 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7290 (mm110) REVERT: E 228 LEU cc_start: 0.5957 (tp) cc_final: 0.5735 (tt) REVERT: E 235 LEU cc_start: 0.6085 (mt) cc_final: 0.5404 (tt) REVERT: E 299 SER cc_start: 0.5364 (m) cc_final: 0.5091 (p) outliers start: 29 outliers final: 19 residues processed: 157 average time/residue: 1.3679 time to fit residues: 232.4807 Evaluate side-chains 156 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 178 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain D residue 68 LEU 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 68 LEU 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 21 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 48 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.143060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.110774 restraints weight = 12064.311| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.04 r_work: 0.2913 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12585 Z= 0.125 Angle : 0.531 5.698 17140 Z= 0.278 Chirality : 0.042 0.132 1980 Planarity : 0.004 0.033 2170 Dihedral : 6.913 59.102 1965 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.49 % Allowed : 7.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.21), residues: 1540 helix: 2.72 (0.21), residues: 610 sheet: 0.17 (0.23), residues: 460 loop : -0.32 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 75 HIS 0.003 0.001 HIS A 170 PHE 0.013 0.001 PHE E 117 TYR 0.011 0.001 TYR E 198 ARG 0.002 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 710) hydrogen bonds : angle 4.45474 ( 2475) covalent geometry : bond 0.00261 (12585) covalent geometry : angle 0.53079 (17140) *********************** 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 171 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.249 Fit side-chains REVERT: A 72 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7354 (mm110) REVERT: A 148 GLN cc_start: 0.7475 (mm110) cc_final: 0.7108 (mm110) REVERT: A 228 LEU cc_start: 0.5918 (tp) cc_final: 0.5674 (tt) REVERT: A 235 LEU cc_start: 0.6289 (mt) cc_final: 0.5600 (tt) REVERT: A 297 ILE cc_start: 0.6702 (mt) cc_final: 0.5913 (pp) REVERT: C 72 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7222 (mm110) REVERT: C 117 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.6764 (m-10) REVERT: C 148 GLN cc_start: 0.7493 (mm110) cc_final: 0.7225 (mm110) REVERT: C 228 LEU cc_start: 0.6043 (tp) cc_final: 0.5787 (tt) REVERT: C 235 LEU cc_start: 0.6324 (mt) cc_final: 0.5544 (tt) REVERT: C 297 ILE cc_start: 0.6723 (mt) cc_final: 0.5900 (pp) REVERT: B 72 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7271 (mm-40) REVERT: B 228 LEU cc_start: 0.5998 (tp) cc_final: 0.5793 (tt) REVERT: B 235 LEU cc_start: 0.6394 (mt) cc_final: 0.5610 (tt) REVERT: D 68 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7923 (mp) REVERT: D 228 LEU cc_start: 0.5810 (tp) cc_final: 0.5566 (tt) REVERT: D 235 LEU cc_start: 0.6172 (mt) cc_final: 0.5763 (mt) REVERT: D 297 ILE cc_start: 0.6609 (mt) cc_final: 0.6394 (mm) REVERT: D 299 SER cc_start: 0.5451 (m) cc_final: 0.5230 (p) REVERT: E 55 LYS cc_start: 0.6683 (mmtp) cc_final: 0.6408 (mptt) REVERT: E 72 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7396 (mm110) REVERT: E 228 LEU cc_start: 0.5950 (tp) cc_final: 0.5736 (tt) REVERT: E 235 LEU cc_start: 0.6154 (mt) cc_final: 0.5463 (tt) REVERT: E 299 SER cc_start: 0.5302 (m) cc_final: 0.5097 (p) outliers start: 30 outliers final: 22 residues processed: 163 average time/residue: 1.3213 time to fit residues: 232.9177 Evaluate side-chains 163 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 178 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 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 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 E residue 68 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 178 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.141750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.109735 restraints weight = 12175.739| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.03 r_work: 0.2905 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12585 Z= 0.188 Angle : 0.625 6.014 17140 Z= 0.325 Chirality : 0.045 0.140 1980 Planarity : 0.005 0.035 2170 Dihedral : 7.339 58.432 1965 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.82 % Allowed : 8.13 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.21), residues: 1540 helix: 2.27 (0.21), residues: 610 sheet: 0.08 (0.24), residues: 455 loop : -0.44 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 75 HIS 0.004 0.002 HIS D 194 PHE 0.020 0.002 PHE E 117 TYR 0.016 0.002 TYR E 198 ARG 0.005 0.001 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.04687 ( 710) hydrogen bonds : angle 4.81754 ( 2475) covalent geometry : bond 0.00408 (12585) covalent geometry : angle 0.62487 (17140) *********************** 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 174 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.266 Fit side-chains REVERT: A 72 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7329 (mm110) REVERT: A 117 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: A 148 GLN cc_start: 0.7501 (mm110) cc_final: 0.7126 (mm110) REVERT: A 228 LEU cc_start: 0.5945 (tp) cc_final: 0.5630 (tm) REVERT: A 235 LEU cc_start: 0.6265 (mt) cc_final: 0.5606 (tt) REVERT: A 297 ILE cc_start: 0.6702 (mt) cc_final: 0.5933 (pp) REVERT: C 72 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7234 (mm110) REVERT: C 117 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.6832 (m-10) REVERT: C 148 GLN cc_start: 0.7509 (mm110) cc_final: 0.7216 (mm110) REVERT: C 228 LEU cc_start: 0.6050 (tp) cc_final: 0.5724 (tm) REVERT: C 235 LEU cc_start: 0.6293 (mt) cc_final: 0.5520 (tt) REVERT: C 297 ILE cc_start: 0.6739 (mt) cc_final: 0.5956 (pp) REVERT: B 72 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7253 (mm110) REVERT: B 235 LEU cc_start: 0.6358 (mt) cc_final: 0.5624 (tt) REVERT: D 68 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7882 (mp) REVERT: D 228 LEU cc_start: 0.5895 (tp) cc_final: 0.5615 (tm) REVERT: D 235 LEU cc_start: 0.6181 (mt) cc_final: 0.5555 (tt) REVERT: E 16 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7400 (tmtm) REVERT: E 55 LYS cc_start: 0.6703 (mmtp) cc_final: 0.6484 (mptt) REVERT: E 72 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7369 (mm110) REVERT: E 228 LEU cc_start: 0.6056 (tp) cc_final: 0.5826 (tt) REVERT: E 235 LEU cc_start: 0.6117 (mt) cc_final: 0.5414 (tt) REVERT: E 299 SER cc_start: 0.5326 (m) cc_final: 0.5075 (p) outliers start: 34 outliers final: 24 residues processed: 164 average time/residue: 1.3040 time to fit residues: 232.0858 Evaluate side-chains 167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 141 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 86 optimal weight: 8.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN C 113 GLN C 232 ASN C 240 ASN B 232 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 = 0.3551 r_free = 0.3551 target = 0.144415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.111243 restraints weight = 12129.178| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.02 r_work: 0.2961 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12585 Z= 0.103 Angle : 0.495 5.539 17140 Z= 0.259 Chirality : 0.041 0.131 1980 Planarity : 0.004 0.031 2170 Dihedral : 6.725 58.616 1965 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.49 % Allowed : 9.38 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.21), residues: 1540 helix: 2.97 (0.21), residues: 610 sheet: 0.18 (0.24), residues: 460 loop : -0.19 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 40 HIS 0.003 0.001 HIS B 170 PHE 0.011 0.001 PHE E 117 TYR 0.007 0.001 TYR C 198 ARG 0.002 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 710) hydrogen bonds : angle 4.23005 ( 2475) covalent geometry : bond 0.00213 (12585) covalent geometry : angle 0.49470 (17140) *********************** 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 169 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.388 Fit side-chains REVERT: A 16 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7332 (tmtm) REVERT: A 72 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7301 (mm110) REVERT: A 148 GLN cc_start: 0.7458 (mm110) cc_final: 0.7055 (mm110) REVERT: A 228 LEU cc_start: 0.5838 (tp) cc_final: 0.5582 (tt) REVERT: A 235 LEU cc_start: 0.6253 (mt) cc_final: 0.5539 (tt) REVERT: A 277 LEU cc_start: 0.6448 (mt) cc_final: 0.6177 (tp) REVERT: A 297 ILE cc_start: 0.6694 (mt) cc_final: 0.5887 (pp) REVERT: C 72 GLN cc_start: 0.7453 (mm-40) cc_final: 0.7202 (mm110) REVERT: C 117 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.6711 (m-10) REVERT: C 148 GLN cc_start: 0.7432 (mm110) cc_final: 0.7128 (mm110) REVERT: C 228 LEU cc_start: 0.5973 (tp) cc_final: 0.5715 (tt) REVERT: C 235 LEU cc_start: 0.6264 (mt) cc_final: 0.5466 (tt) REVERT: C 297 ILE cc_start: 0.6685 (mt) cc_final: 0.5834 (pp) REVERT: B 72 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7262 (mm-40) REVERT: B 228 LEU cc_start: 0.6295 (tt) cc_final: 0.5979 (tm) REVERT: B 235 LEU cc_start: 0.6280 (mt) cc_final: 0.5483 (tt) REVERT: B 297 ILE cc_start: 0.6588 (mt) cc_final: 0.6329 (mm) REVERT: D 98 GLU cc_start: 0.7604 (tt0) cc_final: 0.7330 (mt-10) REVERT: D 228 LEU cc_start: 0.5725 (tp) cc_final: 0.5467 (tt) REVERT: D 235 LEU cc_start: 0.6154 (mt) cc_final: 0.5717 (mt) REVERT: D 297 ILE cc_start: 0.6614 (mt) cc_final: 0.6401 (mm) REVERT: E 16 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7350 (tmtm) REVERT: E 55 LYS cc_start: 0.6680 (mmtp) cc_final: 0.6381 (mptt) REVERT: E 72 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7321 (mm110) REVERT: E 228 LEU cc_start: 0.5866 (tp) cc_final: 0.5659 (tt) REVERT: E 235 LEU cc_start: 0.6085 (mt) cc_final: 0.5364 (tt) REVERT: E 297 ILE cc_start: 0.6478 (mt) cc_final: 0.6225 (mm) outliers start: 18 outliers final: 13 residues processed: 159 average time/residue: 1.4179 time to fit residues: 243.2353 Evaluate side-chains 162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS 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 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 178 THR 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 E residue 16 LYS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 178 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 65 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 42 GLN D 72 GLN D 168 ASN D 240 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 = 0.3501 r_free = 0.3501 target = 0.140555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.106173 restraints weight = 12109.314| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.06 r_work: 0.2890 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12585 Z= 0.290 Angle : 0.765 6.961 17140 Z= 0.395 Chirality : 0.050 0.170 1980 Planarity : 0.006 0.043 2170 Dihedral : 7.760 59.751 1965 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.49 % Allowed : 7.47 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1540 helix: 1.62 (0.21), residues: 610 sheet: -0.21 (0.23), residues: 480 loop : -0.33 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 75 HIS 0.006 0.002 HIS D 194 PHE 0.030 0.003 PHE E 117 TYR 0.019 0.003 TYR E 198 ARG 0.007 0.001 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.05599 ( 710) hydrogen bonds : angle 5.21616 ( 2475) covalent geometry : bond 0.00644 (12585) covalent geometry : angle 0.76542 (17140) *********************** 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 187 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 1.338 Fit side-chains REVERT: A 16 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7435 (tmtm) REVERT: A 72 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7328 (mm110) REVERT: A 117 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: A 148 GLN cc_start: 0.7449 (mm110) cc_final: 0.7084 (mm110) REVERT: A 228 LEU cc_start: 0.5975 (tp) cc_final: 0.5690 (tm) REVERT: A 235 LEU cc_start: 0.6262 (mt) cc_final: 0.5640 (tt) REVERT: C 16 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7347 (tmtm) REVERT: C 72 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7239 (mm110) REVERT: C 117 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.6827 (m-10) REVERT: C 148 GLN cc_start: 0.7504 (mm110) cc_final: 0.7203 (mm110) REVERT: C 228 LEU cc_start: 0.6016 (tp) cc_final: 0.5726 (tm) REVERT: C 235 LEU cc_start: 0.6186 (mt) cc_final: 0.5503 (tt) REVERT: B 72 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7192 (mm110) REVERT: B 228 LEU cc_start: 0.6334 (tt) cc_final: 0.6058 (tm) REVERT: B 235 LEU cc_start: 0.6361 (mt) cc_final: 0.5649 (tt) REVERT: D 68 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7917 (mp) REVERT: D 117 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: D 228 LEU cc_start: 0.5911 (tp) cc_final: 0.5646 (tm) REVERT: D 235 LEU cc_start: 0.6217 (mt) cc_final: 0.5572 (tt) REVERT: E 16 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7369 (tmtm) REVERT: E 55 LYS cc_start: 0.6641 (mmtp) cc_final: 0.6402 (mptt) REVERT: E 235 LEU cc_start: 0.6196 (mt) cc_final: 0.5505 (tt) outliers start: 42 outliers final: 28 residues processed: 174 average time/residue: 1.3152 time to fit residues: 247.6752 Evaluate side-chains 174 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 16 LYS 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 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 150 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 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 = 0.3536 r_free = 0.3536 target = 0.143306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.109989 restraints weight = 12020.572| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.01 r_work: 0.2944 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1566 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= 0.114 Angle : 0.522 5.756 17140 Z= 0.273 Chirality : 0.042 0.133 1980 Planarity : 0.004 0.033 2170 Dihedral : 6.907 58.577 1965 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.32 % Allowed : 8.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.21), residues: 1540 helix: 2.66 (0.21), residues: 610 sheet: 0.13 (0.24), residues: 460 loop : -0.23 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 75 HIS 0.003 0.001 HIS A 170 PHE 0.014 0.001 PHE E 117 TYR 0.010 0.001 TYR E 198 ARG 0.005 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 710) hydrogen bonds : angle 4.40671 ( 2475) covalent geometry : bond 0.00236 (12585) covalent geometry : angle 0.52224 (17140) *********************** 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 174 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.409 Fit side-chains REVERT: A 16 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7266 (tmtm) REVERT: A 72 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7298 (mm110) REVERT: A 117 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: A 148 GLN cc_start: 0.7457 (mm110) cc_final: 0.7086 (mm110) REVERT: A 228 LEU cc_start: 0.5888 (tp) cc_final: 0.5619 (tt) REVERT: A 235 LEU cc_start: 0.6252 (mt) cc_final: 0.5564 (tt) REVERT: A 277 LEU cc_start: 0.6436 (mt) cc_final: 0.6169 (tp) REVERT: A 297 ILE cc_start: 0.6687 (mt) cc_final: 0.5883 (pp) REVERT: C 72 GLN cc_start: 0.7465 (mm-40) cc_final: 0.7215 (mm110) REVERT: C 117 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.6763 (m-10) REVERT: C 148 GLN cc_start: 0.7445 (mm110) cc_final: 0.7148 (mm110) REVERT: C 228 LEU cc_start: 0.6031 (tp) cc_final: 0.5764 (tt) REVERT: C 235 LEU cc_start: 0.6291 (mt) cc_final: 0.5482 (tt) REVERT: C 297 ILE cc_start: 0.6728 (mt) cc_final: 0.5895 (pp) REVERT: B 16 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7286 (tmtm) REVERT: B 72 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7287 (mm-40) REVERT: B 228 LEU cc_start: 0.6284 (tt) cc_final: 0.5992 (tm) REVERT: B 235 LEU cc_start: 0.6352 (mt) cc_final: 0.5541 (tt) REVERT: B 297 ILE cc_start: 0.6621 (mt) cc_final: 0.6362 (mm) REVERT: D 98 GLU cc_start: 0.7638 (tt0) cc_final: 0.7318 (mt-10) REVERT: D 228 LEU cc_start: 0.5737 (tp) cc_final: 0.5490 (tt) REVERT: D 235 LEU cc_start: 0.6178 (mt) cc_final: 0.5792 (mt) REVERT: D 297 ILE cc_start: 0.6604 (mt) cc_final: 0.6378 (mm) REVERT: E 16 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7397 (tmtm) REVERT: E 55 LYS cc_start: 0.6686 (mmtp) cc_final: 0.6444 (mptt) REVERT: E 228 LEU cc_start: 0.5860 (tp) cc_final: 0.5653 (tt) REVERT: E 235 LEU cc_start: 0.6104 (mt) cc_final: 0.5417 (tt) REVERT: E 297 ILE cc_start: 0.6490 (mt) cc_final: 0.6246 (mm) outliers start: 28 outliers final: 20 residues processed: 161 average time/residue: 1.4060 time to fit residues: 244.0306 Evaluate side-chains 168 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 C residue 13 ILE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 163 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 16 LYS 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 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 243 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 242 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 137 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 168 ASN D 240 ASN E 72 GLN 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 = 0.3501 r_free = 0.3501 target = 0.140620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.106904 restraints weight = 11902.215| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.01 r_work: 0.2895 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12585 Z= 0.306 Angle : 0.788 7.090 17140 Z= 0.407 Chirality : 0.051 0.174 1980 Planarity : 0.006 0.044 2170 Dihedral : 7.838 59.493 1965 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.74 % Allowed : 8.55 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1540 helix: 1.40 (0.20), residues: 610 sheet: -0.25 (0.23), residues: 480 loop : -0.37 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 75 HIS 0.007 0.002 HIS D 194 PHE 0.036 0.003 PHE E 117 TYR 0.022 0.003 TYR B 198 ARG 0.012 0.001 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.05716 ( 710) hydrogen bonds : angle 5.29750 ( 2475) covalent geometry : bond 0.00681 (12585) covalent geometry : angle 0.78760 (17140) ********************** 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 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.261 Fit side-chains REVERT: A 16 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7491 (tmtm) REVERT: A 117 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: A 148 GLN cc_start: 0.7464 (mm110) cc_final: 0.7086 (mm110) REVERT: A 228 LEU cc_start: 0.6004 (tp) cc_final: 0.5682 (tm) REVERT: A 235 LEU cc_start: 0.6315 (mt) cc_final: 0.5683 (tt) REVERT: C 72 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7268 (mm110) REVERT: C 117 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.6853 (m-10) REVERT: C 148 GLN cc_start: 0.7473 (mm110) cc_final: 0.7189 (mm110) REVERT: C 228 LEU cc_start: 0.6051 (tp) cc_final: 0.5763 (tm) REVERT: C 235 LEU cc_start: 0.6247 (mt) cc_final: 0.5534 (tt) REVERT: B 16 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7191 (tmtm) REVERT: B 72 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7220 (mm110) REVERT: B 228 LEU cc_start: 0.6363 (tt) cc_final: 0.6085 (tm) REVERT: B 235 LEU cc_start: 0.6402 (mt) cc_final: 0.5649 (tt) REVERT: D 68 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7924 (mp) REVERT: D 117 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: D 228 LEU cc_start: 0.5934 (tp) cc_final: 0.5670 (tm) REVERT: D 235 LEU cc_start: 0.6243 (mt) cc_final: 0.5601 (tt) REVERT: E 16 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7441 (tmtm) REVERT: E 55 LYS cc_start: 0.6665 (mmtp) cc_final: 0.6426 (mptt) REVERT: E 228 LEU cc_start: 0.6196 (tp) cc_final: 0.5842 (tm) REVERT: E 235 LEU cc_start: 0.6213 (mt) cc_final: 0.5554 (tt) outliers start: 33 outliers final: 23 residues processed: 159 average time/residue: 1.3760 time to fit residues: 235.7476 Evaluate side-chains 168 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 C residue 13 ILE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 163 ILE 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 B residue 16 LYS 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 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 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 132 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 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 = 0.3524 r_free = 0.3524 target = 0.142325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.110999 restraints weight = 12055.050| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.02 r_work: 0.2922 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12585 Z= 0.137 Angle : 0.560 6.075 17140 Z= 0.291 Chirality : 0.042 0.133 1980 Planarity : 0.004 0.034 2170 Dihedral : 7.091 57.711 1965 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.66 % Allowed : 8.80 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1540 helix: 2.39 (0.21), residues: 610 sheet: 0.09 (0.24), residues: 460 loop : -0.31 (0.24), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 75 HIS 0.003 0.001 HIS B 170 PHE 0.015 0.001 PHE E 117 TYR 0.012 0.002 TYR E 198 ARG 0.008 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 710) hydrogen bonds : angle 4.58076 ( 2475) covalent geometry : bond 0.00292 (12585) covalent geometry : angle 0.55970 (17140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8754.40 seconds wall clock time: 151 minutes 20.81 seconds (9080.81 seconds total)