Starting phenix.real_space_refine on Tue Jun 10 23:41:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f5n_50194/06_2025/9f5n_50194_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f5n_50194/06_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_50194/06_2025/9f5n_50194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f5n_50194/06_2025/9f5n_50194.map" model { file = "/net/cci-nas-00/data/ceres_data/9f5n_50194/06_2025/9f5n_50194_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f5n_50194/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.28, per 1000 atoms: 0.51 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: 3.52 Conformation dependent library (CDL) restraints added in 1.8 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: 1.75 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: 4.03 Time building geometry restraints manager: 4.09 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.540 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.350 ------------------------------------------------------------------------------- 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 : 1.467 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: 1.4916 time to fit residues: 284.8680 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 : 1.306 ------------------------------------------------------------------------------- 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 = 73)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.109093 restraints weight = 12038.462| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.00 r_work: 0.2930 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 1.534 Fit side-chains REVERT: A 72 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7263 (mm110) REVERT: A 148 GLN cc_start: 0.7505 (mm110) cc_final: 0.7113 (mm110) REVERT: A 228 LEU cc_start: 0.6059 (tp) cc_final: 0.5821 (tt) REVERT: A 235 LEU cc_start: 0.6169 (mt) cc_final: 0.5582 (tt) REVERT: A 297 ILE cc_start: 0.6654 (mt) cc_final: 0.5868 (pp) REVERT: C 55 LYS cc_start: 0.6818 (mmtp) cc_final: 0.6509 (mptt) REVERT: C 72 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7216 (mm110) REVERT: C 148 GLN cc_start: 0.7527 (mm110) cc_final: 0.7242 (mm110) REVERT: C 228 LEU cc_start: 0.6127 (tp) cc_final: 0.5847 (tm) REVERT: C 235 LEU cc_start: 0.6281 (mt) cc_final: 0.5623 (tt) REVERT: C 297 ILE cc_start: 0.6703 (mt) cc_final: 0.5867 (pp) REVERT: B 55 LYS cc_start: 0.6768 (mmtp) cc_final: 0.6501 (mptt) REVERT: B 72 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7191 (mm110) REVERT: B 228 LEU cc_start: 0.6025 (tp) cc_final: 0.5822 (tt) REVERT: B 235 LEU cc_start: 0.6330 (mt) cc_final: 0.5668 (tt) REVERT: B 297 ILE cc_start: 0.6566 (mt) cc_final: 0.6299 (mm) REVERT: D 68 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7886 (mp) REVERT: D 228 LEU cc_start: 0.5907 (tp) cc_final: 0.5671 (tt) REVERT: D 235 LEU cc_start: 0.6160 (mt) cc_final: 0.5571 (tt) REVERT: D 297 ILE cc_start: 0.6584 (mt) cc_final: 0.5810 (pp) REVERT: E 55 LYS cc_start: 0.6685 (mmtp) cc_final: 0.6477 (mptt) REVERT: E 72 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7299 (mm110) REVERT: E 228 LEU cc_start: 0.5953 (tp) cc_final: 0.5650 (tm) REVERT: E 235 LEU cc_start: 0.6139 (mt) cc_final: 0.5500 (tt) REVERT: E 297 ILE cc_start: 0.6572 (mt) cc_final: 0.6309 (mm) REVERT: E 299 SER cc_start: 0.5375 (m) cc_final: 0.5121 (p) outliers start: 15 outliers final: 5 residues processed: 155 average time/residue: 1.4198 time to fit residues: 237.5486 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 : 1.286 ------------------------------------------------------------------------------- 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: 6.9990 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: 6.9990 chunk 125 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.140292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.106277 restraints weight = 12116.755| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.06 r_work: 0.2895 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12585 Z= 0.244 Angle : 0.706 6.315 17140 Z= 0.368 Chirality : 0.048 0.161 1980 Planarity : 0.006 0.039 2170 Dihedral : 7.661 59.690 1965 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.66 % Allowed : 6.06 % 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: 0.71 (0.20), residues: 1540 helix: 1.72 (0.21), residues: 610 sheet: 0.09 (0.23), residues: 455 loop : -0.69 (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 0.003 PHE D 117 TYR 0.017 0.002 TYR E 198 ARG 0.006 0.001 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.05326 ( 710) hydrogen bonds : angle 5.15577 ( 2475) covalent geometry : bond 0.00536 (12585) covalent geometry : angle 0.70565 (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 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.316 Fit side-chains REVERT: A 72 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7304 (mm110) REVERT: A 117 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: A 148 GLN cc_start: 0.7484 (mm110) cc_final: 0.7111 (mm110) REVERT: A 228 LEU cc_start: 0.6000 (tp) cc_final: 0.5760 (tt) REVERT: A 235 LEU cc_start: 0.6196 (mt) cc_final: 0.5575 (tt) REVERT: A 297 ILE cc_start: 0.6624 (mt) cc_final: 0.5873 (pp) REVERT: C 55 LYS cc_start: 0.6745 (mmtp) cc_final: 0.6447 (mptt) REVERT: C 72 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7186 (mm110) REVERT: C 148 GLN cc_start: 0.7504 (mm110) cc_final: 0.7224 (mm110) REVERT: C 228 LEU cc_start: 0.6041 (tp) cc_final: 0.5702 (tm) REVERT: C 235 LEU cc_start: 0.6254 (mt) cc_final: 0.5490 (tt) REVERT: C 297 ILE cc_start: 0.6665 (mt) cc_final: 0.5905 (pp) REVERT: B 55 LYS cc_start: 0.6717 (mmtp) cc_final: 0.6513 (mptt) REVERT: B 72 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7210 (mm110) REVERT: B 228 LEU cc_start: 0.6122 (tp) cc_final: 0.5811 (tm) REVERT: B 235 LEU cc_start: 0.6294 (mt) cc_final: 0.5613 (tt) REVERT: D 68 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7928 (mp) REVERT: D 117 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: D 228 LEU cc_start: 0.5895 (tp) cc_final: 0.5660 (tt) REVERT: D 235 LEU cc_start: 0.6232 (mt) cc_final: 0.5573 (tt) REVERT: E 55 LYS cc_start: 0.6603 (mmtp) cc_final: 0.6381 (mptt) REVERT: E 72 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7324 (mm110) REVERT: E 228 LEU cc_start: 0.6011 (tp) cc_final: 0.5705 (tm) REVERT: E 235 LEU cc_start: 0.6111 (mt) cc_final: 0.5433 (tt) REVERT: E 299 SER cc_start: 0.5381 (m) cc_final: 0.5072 (p) outliers start: 32 outliers final: 18 residues processed: 164 average time/residue: 1.4932 time to fit residues: 265.3856 Evaluate side-chains 159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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: 0.0030 chunk 143 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 240 ASN C 232 ASN C 240 ASN B 240 ASN D 240 ASN E 232 ASN E 240 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.141035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.106713 restraints weight = 12011.573| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.07 r_work: 0.2909 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12585 Z= 0.174 Angle : 0.607 6.063 17140 Z= 0.318 Chirality : 0.044 0.135 1980 Planarity : 0.005 0.036 2170 Dihedral : 7.290 58.574 1965 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.41 % Allowed : 7.47 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.08 (0.21), residues: 1540 helix: 2.14 (0.21), residues: 610 sheet: 0.14 (0.23), residues: 460 loop : -0.50 (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 B 170 PHE 0.017 0.002 PHE C 117 TYR 0.015 0.002 TYR E 198 ARG 0.004 0.001 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 710) hydrogen bonds : angle 4.82766 ( 2475) covalent geometry : bond 0.00375 (12585) covalent geometry : angle 0.60743 (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 163 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.286 Fit side-chains REVERT: A 72 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7266 (mm110) REVERT: A 117 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7556 (m-80) REVERT: A 148 GLN cc_start: 0.7476 (mm110) cc_final: 0.7090 (mm110) REVERT: A 228 LEU cc_start: 0.5905 (tp) cc_final: 0.5664 (tt) REVERT: A 235 LEU cc_start: 0.6144 (mt) cc_final: 0.5463 (tt) REVERT: C 72 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7173 (mm110) REVERT: C 117 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.6793 (m-10) REVERT: C 148 GLN cc_start: 0.7477 (mm110) cc_final: 0.7195 (mm110) REVERT: C 228 LEU cc_start: 0.5979 (tp) cc_final: 0.5713 (tt) REVERT: C 235 LEU cc_start: 0.6265 (mt) cc_final: 0.5484 (tt) REVERT: C 297 ILE cc_start: 0.6673 (mt) cc_final: 0.5866 (pp) REVERT: B 72 GLN cc_start: 0.7397 (mm-40) cc_final: 0.7145 (mm110) REVERT: B 228 LEU cc_start: 0.6006 (tp) cc_final: 0.5781 (tt) REVERT: B 235 LEU cc_start: 0.6319 (mt) cc_final: 0.5614 (tt) REVERT: D 68 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7839 (mp) REVERT: D 228 LEU cc_start: 0.5849 (tp) cc_final: 0.5609 (tt) REVERT: D 235 LEU cc_start: 0.6183 (mt) cc_final: 0.5534 (tt) REVERT: E 55 LYS cc_start: 0.6589 (mmtp) cc_final: 0.6345 (mptt) REVERT: E 72 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7287 (mm110) REVERT: E 228 LEU cc_start: 0.5987 (tp) cc_final: 0.5767 (tt) REVERT: E 235 LEU cc_start: 0.6082 (mt) cc_final: 0.5398 (tt) REVERT: E 299 SER cc_start: 0.5368 (m) cc_final: 0.5090 (p) outliers start: 29 outliers final: 19 residues processed: 156 average time/residue: 1.2725 time to fit residues: 215.0772 Evaluate side-chains 155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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: 8.9990 chunk 102 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 232 ASN 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 = 0.3523 r_free = 0.3523 target = 0.142115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.107993 restraints weight = 12062.861| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.07 r_work: 0.2925 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12585 Z= 0.138 Angle : 0.554 5.871 17140 Z= 0.290 Chirality : 0.042 0.132 1980 Planarity : 0.004 0.034 2170 Dihedral : 7.046 59.116 1965 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.57 % Allowed : 7.88 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.41 (0.21), residues: 1540 helix: 2.55 (0.21), residues: 610 sheet: 0.16 (0.23), residues: 460 loop : -0.36 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 75 HIS 0.004 0.001 HIS B 170 PHE 0.014 0.002 PHE E 117 TYR 0.012 0.002 TYR E 198 ARG 0.003 0.000 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 710) hydrogen bonds : angle 4.57406 ( 2475) covalent geometry : bond 0.00292 (12585) covalent geometry : angle 0.55437 (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 167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.430 Fit side-chains REVERT: A 72 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7236 (mm110) REVERT: A 148 GLN cc_start: 0.7456 (mm110) cc_final: 0.7068 (mm110) REVERT: A 228 LEU cc_start: 0.5860 (tp) cc_final: 0.5612 (tt) REVERT: A 235 LEU cc_start: 0.6202 (mt) cc_final: 0.5518 (tt) REVERT: C 72 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7122 (mm110) REVERT: C 117 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.6736 (m-10) REVERT: C 148 GLN cc_start: 0.7473 (mm110) cc_final: 0.7200 (mm110) REVERT: C 228 LEU cc_start: 0.5994 (tp) cc_final: 0.5729 (tt) REVERT: C 235 LEU cc_start: 0.6251 (mt) cc_final: 0.5462 (tt) REVERT: C 297 ILE cc_start: 0.6681 (mt) cc_final: 0.5858 (pp) REVERT: B 72 GLN cc_start: 0.7424 (mm-40) cc_final: 0.7190 (mm-40) REVERT: B 228 LEU cc_start: 0.5918 (tp) cc_final: 0.5706 (tt) REVERT: B 235 LEU cc_start: 0.6358 (mt) cc_final: 0.5568 (tt) REVERT: D 68 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7851 (mp) REVERT: D 228 LEU cc_start: 0.5820 (tp) cc_final: 0.5576 (tt) REVERT: D 235 LEU cc_start: 0.6117 (mt) cc_final: 0.5472 (tt) REVERT: D 297 ILE cc_start: 0.6572 (mt) cc_final: 0.6354 (mm) REVERT: D 299 SER cc_start: 0.5379 (m) cc_final: 0.5121 (p) REVERT: E 55 LYS cc_start: 0.6626 (mmtp) cc_final: 0.6357 (mptt) REVERT: E 72 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7304 (mm110) REVERT: E 228 LEU cc_start: 0.5900 (tp) cc_final: 0.5686 (tt) REVERT: E 235 LEU cc_start: 0.6108 (mt) cc_final: 0.5416 (tt) REVERT: E 299 SER cc_start: 0.5294 (m) cc_final: 0.5064 (p) outliers start: 31 outliers final: 23 residues processed: 159 average time/residue: 1.5903 time to fit residues: 273.8692 Evaluate side-chains 159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 A residue 243 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 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: 0.8980 chunk 53 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.142737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.109013 restraints weight = 12196.037| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.04 r_work: 0.2932 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12585 Z= 0.133 Angle : 0.545 5.754 17140 Z= 0.285 Chirality : 0.042 0.131 1980 Planarity : 0.004 0.033 2170 Dihedral : 6.993 58.527 1965 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.74 % Allowed : 7.97 % Favored : 89.29 % 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: 1.55 (0.21), residues: 1540 helix: 2.71 (0.21), residues: 610 sheet: 0.17 (0.24), residues: 460 loop : -0.28 (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 B 170 PHE 0.015 0.002 PHE E 117 TYR 0.012 0.002 TYR E 198 ARG 0.003 0.000 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 710) hydrogen bonds : angle 4.49575 ( 2475) covalent geometry : bond 0.00280 (12585) covalent geometry : angle 0.54511 (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 175 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 2.029 Fit side-chains REVERT: A 72 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7266 (mm110) REVERT: A 117 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: A 148 GLN cc_start: 0.7469 (mm110) cc_final: 0.7071 (mm110) REVERT: A 228 LEU cc_start: 0.5874 (tp) cc_final: 0.5615 (tt) REVERT: A 235 LEU cc_start: 0.6251 (mt) cc_final: 0.5558 (tt) REVERT: A 297 ILE cc_start: 0.6679 (mt) cc_final: 0.5891 (pp) REVERT: C 72 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7185 (mm110) REVERT: C 117 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.6761 (m-10) REVERT: C 148 GLN cc_start: 0.7458 (mm110) cc_final: 0.7166 (mm110) REVERT: C 228 LEU cc_start: 0.5997 (tp) cc_final: 0.5736 (tt) REVERT: C 235 LEU cc_start: 0.6269 (mt) cc_final: 0.5461 (tt) REVERT: C 297 ILE cc_start: 0.6701 (mt) cc_final: 0.5885 (pp) REVERT: B 72 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7231 (mm-40) REVERT: B 228 LEU cc_start: 0.5975 (tp) cc_final: 0.5766 (tt) REVERT: B 235 LEU cc_start: 0.6366 (mt) cc_final: 0.5585 (tt) REVERT: D 68 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7861 (mp) REVERT: D 228 LEU cc_start: 0.5776 (tp) cc_final: 0.5538 (tt) REVERT: D 235 LEU cc_start: 0.6147 (mt) cc_final: 0.5718 (mt) REVERT: D 297 ILE cc_start: 0.6574 (mt) cc_final: 0.6353 (mm) REVERT: D 299 SER cc_start: 0.5401 (m) cc_final: 0.5174 (p) REVERT: E 16 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7344 (tmtm) REVERT: E 55 LYS cc_start: 0.6684 (mmtp) cc_final: 0.6459 (mptt) REVERT: E 72 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7296 (mm110) REVERT: E 228 LEU cc_start: 0.5925 (tp) cc_final: 0.5711 (tt) REVERT: E 235 LEU cc_start: 0.6114 (mt) cc_final: 0.5423 (tt) outliers start: 33 outliers final: 26 residues processed: 165 average time/residue: 1.4326 time to fit residues: 256.2609 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 : 1.335 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 104 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.142406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.110023 restraints weight = 12122.768| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.05 r_work: 0.2927 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1383 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= 0.149 Angle : 0.570 5.924 17140 Z= 0.297 Chirality : 0.043 0.132 1980 Planarity : 0.004 0.033 2170 Dihedral : 7.128 56.956 1965 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.90 % Allowed : 7.97 % 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: 1.45 (0.21), residues: 1540 helix: 2.58 (0.21), residues: 610 sheet: 0.13 (0.24), residues: 460 loop : -0.27 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 75 HIS 0.004 0.001 HIS B 170 PHE 0.015 0.002 PHE E 117 TYR 0.014 0.002 TYR E 198 ARG 0.005 0.001 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 710) hydrogen bonds : angle 4.59099 ( 2475) covalent geometry : bond 0.00318 (12585) covalent geometry : angle 0.56992 (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 177 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 2.656 Fit side-chains REVERT: A 16 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7333 (tmtm) REVERT: A 72 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7295 (mm110) REVERT: A 117 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: A 148 GLN cc_start: 0.7500 (mm110) cc_final: 0.7116 (mm110) REVERT: A 228 LEU cc_start: 0.5966 (tp) cc_final: 0.5709 (tt) REVERT: A 235 LEU cc_start: 0.6318 (mt) cc_final: 0.5638 (tt) REVERT: A 297 ILE cc_start: 0.6708 (mt) cc_final: 0.5930 (pp) REVERT: C 72 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7226 (mm110) REVERT: C 117 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.6786 (m-10) REVERT: C 148 GLN cc_start: 0.7467 (mm110) cc_final: 0.7176 (mm110) REVERT: C 228 LEU cc_start: 0.6037 (tp) cc_final: 0.5776 (tt) REVERT: C 235 LEU cc_start: 0.6305 (mt) cc_final: 0.5510 (tt) REVERT: C 297 ILE cc_start: 0.6720 (mt) cc_final: 0.5909 (pp) REVERT: B 72 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7299 (mm110) REVERT: B 235 LEU cc_start: 0.6407 (mt) cc_final: 0.5641 (tt) REVERT: D 68 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7900 (mp) REVERT: D 228 LEU cc_start: 0.5865 (tp) cc_final: 0.5624 (tt) REVERT: D 235 LEU cc_start: 0.6177 (mt) cc_final: 0.5794 (mt) REVERT: D 299 SER cc_start: 0.5454 (m) cc_final: 0.5212 (p) REVERT: E 16 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7359 (tmtm) REVERT: E 55 LYS cc_start: 0.6715 (mmtp) cc_final: 0.6504 (mptt) REVERT: E 72 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7370 (mm110) REVERT: E 228 LEU cc_start: 0.5974 (tp) cc_final: 0.5764 (tt) REVERT: E 235 LEU cc_start: 0.6150 (mt) cc_final: 0.5467 (tt) outliers start: 35 outliers final: 26 residues processed: 166 average time/residue: 1.9456 time to fit residues: 353.7050 Evaluate side-chains 171 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 65 optimal weight: 0.0570 chunk 121 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 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: 10.0000 overall best weight: 3.3504 ------------------------------------------------------------------------------- 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 232 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 = 0.3517 r_free = 0.3517 target = 0.141660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.107872 restraints weight = 12135.762| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.04 r_work: 0.2912 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12585 Z= 0.187 Angle : 0.628 5.984 17140 Z= 0.326 Chirality : 0.045 0.141 1980 Planarity : 0.005 0.035 2170 Dihedral : 7.367 58.028 1965 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.32 % Allowed : 7.63 % 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: 2.25 (0.21), residues: 610 sheet: 0.06 (0.24), residues: 455 loop : -0.37 (0.24), residues: 475 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 0.022 0.002 PHE E 117 TYR 0.017 0.002 TYR E 198 ARG 0.007 0.001 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 710) hydrogen bonds : angle 4.82306 ( 2475) covalent geometry : bond 0.00407 (12585) covalent geometry : angle 0.62799 (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 179 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 1.462 Fit side-chains REVERT: A 16 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7326 (tmtm) REVERT: A 72 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7308 (mm110) REVERT: A 117 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: A 148 GLN cc_start: 0.7486 (mm110) cc_final: 0.7118 (mm110) REVERT: A 228 LEU cc_start: 0.5974 (tp) cc_final: 0.5665 (tm) REVERT: A 235 LEU cc_start: 0.6304 (mt) cc_final: 0.5630 (tt) REVERT: A 297 ILE cc_start: 0.6688 (mt) cc_final: 0.5915 (pp) REVERT: C 72 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7204 (mm110) REVERT: C 117 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.6818 (m-10) REVERT: C 148 GLN cc_start: 0.7458 (mm110) cc_final: 0.7172 (mm110) REVERT: C 228 LEU cc_start: 0.5999 (tp) cc_final: 0.5670 (tm) REVERT: C 235 LEU cc_start: 0.6268 (mt) cc_final: 0.5474 (tt) REVERT: C 297 ILE cc_start: 0.6742 (mt) cc_final: 0.5962 (pp) REVERT: B 16 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7236 (tmtm) REVERT: B 72 GLN cc_start: 0.7465 (mm-40) cc_final: 0.7238 (mm110) REVERT: B 228 LEU cc_start: 0.6314 (tt) cc_final: 0.6049 (tm) REVERT: B 235 LEU cc_start: 0.6314 (mt) cc_final: 0.5581 (tt) REVERT: D 16 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7265 (tmtm) REVERT: D 68 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7872 (mp) REVERT: D 228 LEU cc_start: 0.5884 (tp) cc_final: 0.5635 (tt) REVERT: D 235 LEU cc_start: 0.6178 (mt) cc_final: 0.5510 (tt) REVERT: E 16 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7364 (tmtm) REVERT: E 55 LYS cc_start: 0.6662 (mmtp) cc_final: 0.6424 (mptt) REVERT: E 72 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7354 (mm110) REVERT: E 228 LEU cc_start: 0.6073 (tp) cc_final: 0.5817 (tt) REVERT: E 235 LEU cc_start: 0.6085 (mt) cc_final: 0.5381 (tt) outliers start: 40 outliers final: 28 residues processed: 165 average time/residue: 1.3496 time to fit residues: 241.5684 Evaluate side-chains 172 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 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 C residue 275 VAL Chi-restraints excluded: chain B residue 16 LYS 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 16 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 275 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 150 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 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 168 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 = 0.3517 r_free = 0.3517 target = 0.141647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.107880 restraints weight = 12044.682| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.03 r_work: 0.2913 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1308 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= 0.189 Angle : 0.631 6.214 17140 Z= 0.327 Chirality : 0.045 0.141 1980 Planarity : 0.005 0.035 2170 Dihedral : 7.388 57.514 1965 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.40 % Allowed : 7.80 % Favored : 88.80 % 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: 2.16 (0.21), residues: 610 sheet: 0.07 (0.23), residues: 460 loop : -0.34 (0.24), residues: 470 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 0.024 0.002 PHE E 117 TYR 0.016 0.002 TYR E 198 ARG 0.007 0.001 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 710) hydrogen bonds : angle 4.84302 ( 2475) covalent geometry : bond 0.00412 (12585) covalent geometry : angle 0.63060 (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 176 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 1.632 Fit side-chains REVERT: A 16 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7343 (tmtm) REVERT: A 72 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7312 (mm110) REVERT: A 117 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: A 148 GLN cc_start: 0.7488 (mm110) cc_final: 0.7117 (mm110) REVERT: A 228 LEU cc_start: 0.5998 (tp) cc_final: 0.5691 (tm) REVERT: A 235 LEU cc_start: 0.6310 (mt) cc_final: 0.5635 (tt) REVERT: A 297 ILE cc_start: 0.6697 (mt) cc_final: 0.5929 (pp) REVERT: C 16 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7390 (tmtm) REVERT: C 72 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7204 (mm110) REVERT: C 117 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: C 148 GLN cc_start: 0.7462 (mm110) cc_final: 0.7170 (mm110) REVERT: C 228 LEU cc_start: 0.6032 (tp) cc_final: 0.5771 (tt) REVERT: C 235 LEU cc_start: 0.6252 (mt) cc_final: 0.5477 (tt) REVERT: C 297 ILE cc_start: 0.6758 (mt) cc_final: 0.5981 (pp) REVERT: B 16 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7237 (tmtm) REVERT: B 72 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7235 (mm110) REVERT: B 228 LEU cc_start: 0.6331 (tt) cc_final: 0.6057 (tm) REVERT: B 235 LEU cc_start: 0.6331 (mt) cc_final: 0.5582 (tt) REVERT: D 16 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7269 (tmtm) REVERT: D 68 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7871 (mp) REVERT: D 228 LEU cc_start: 0.5909 (tp) cc_final: 0.5629 (tm) REVERT: D 235 LEU cc_start: 0.6188 (mt) cc_final: 0.5477 (tt) REVERT: E 16 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7374 (tmtm) REVERT: E 55 LYS cc_start: 0.6669 (mmtp) cc_final: 0.6443 (mptt) REVERT: E 72 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7358 (mm110) REVERT: E 228 LEU cc_start: 0.6050 (tp) cc_final: 0.5824 (tt) REVERT: E 235 LEU cc_start: 0.6124 (mt) cc_final: 0.5408 (tt) outliers start: 41 outliers final: 31 residues processed: 161 average time/residue: 1.7066 time to fit residues: 297.4284 Evaluate side-chains 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 16 LYS 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 C residue 275 VAL Chi-restraints excluded: chain B residue 16 LYS 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 16 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 137 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 168 ASN D 240 ASN E 232 ASN E 240 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.143337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.110975 restraints weight = 11951.712| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.05 r_work: 0.2941 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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= 0.127 Angle : 0.541 6.082 17140 Z= 0.281 Chirality : 0.042 0.132 1980 Planarity : 0.004 0.033 2170 Dihedral : 7.032 58.888 1965 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.90 % Allowed : 8.13 % Favored : 88.96 % 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: 1.53 (0.21), residues: 1540 helix: 2.69 (0.21), residues: 610 sheet: 0.12 (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 0.015 0.001 PHE E 117 TYR 0.011 0.001 TYR E 198 ARG 0.005 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 710) hydrogen bonds : angle 4.46391 ( 2475) covalent geometry : bond 0.00268 (12585) covalent geometry : angle 0.54068 (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 178 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.432 Fit side-chains REVERT: A 16 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7312 (tmtm) REVERT: A 72 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7291 (mm110) REVERT: A 117 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7441 (m-80) REVERT: A 148 GLN cc_start: 0.7485 (mm110) cc_final: 0.7098 (mm110) REVERT: A 228 LEU cc_start: 0.5952 (tp) cc_final: 0.5695 (tt) REVERT: A 235 LEU cc_start: 0.6325 (mt) cc_final: 0.5632 (tt) REVERT: A 277 LEU cc_start: 0.6483 (mt) cc_final: 0.6237 (tp) REVERT: A 297 ILE cc_start: 0.6716 (mt) cc_final: 0.5925 (pp) REVERT: C 72 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7239 (mm110) REVERT: C 117 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.6763 (m-10) REVERT: C 148 GLN cc_start: 0.7465 (mm110) cc_final: 0.7164 (mm110) REVERT: C 228 LEU cc_start: 0.5953 (tp) cc_final: 0.5695 (tt) REVERT: C 235 LEU cc_start: 0.6284 (mt) cc_final: 0.5474 (tt) REVERT: C 297 ILE cc_start: 0.6721 (mt) cc_final: 0.5899 (pp) REVERT: B 16 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7287 (tmtm) REVERT: B 72 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7308 (mm-40) REVERT: B 228 LEU cc_start: 0.6321 (tt) cc_final: 0.6032 (tm) REVERT: B 235 LEU cc_start: 0.6351 (mt) cc_final: 0.5551 (tt) REVERT: B 297 ILE cc_start: 0.6646 (mt) cc_final: 0.6384 (mm) REVERT: D 68 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7908 (mp) REVERT: D 228 LEU cc_start: 0.5770 (tp) cc_final: 0.5528 (tt) REVERT: D 235 LEU cc_start: 0.6169 (mt) cc_final: 0.5785 (mt) REVERT: D 297 ILE cc_start: 0.6589 (mt) cc_final: 0.6371 (mm) REVERT: D 299 SER cc_start: 0.5398 (m) cc_final: 0.5186 (p) REVERT: E 16 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7376 (tmtm) REVERT: E 55 LYS cc_start: 0.6705 (mmtp) cc_final: 0.6472 (mptt) REVERT: E 72 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7354 (mm110) REVERT: E 228 LEU cc_start: 0.5917 (tp) cc_final: 0.5705 (tt) REVERT: E 235 LEU cc_start: 0.6125 (mt) cc_final: 0.5417 (tt) REVERT: E 297 ILE cc_start: 0.6516 (mt) cc_final: 0.6270 (mm) outliers start: 35 outliers final: 28 residues processed: 166 average time/residue: 1.3535 time to fit residues: 243.2770 Evaluate side-chains 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 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 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 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: 6.9990 chunk 150 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 99 optimal weight: 0.0670 chunk 148 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- 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 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 = 0.3543 r_free = 0.3543 target = 0.143720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.109991 restraints weight = 12031.987| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.04 r_work: 0.2943 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1565 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= 0.121 Angle : 0.535 6.039 17140 Z= 0.277 Chirality : 0.042 0.130 1980 Planarity : 0.004 0.033 2170 Dihedral : 6.934 59.297 1965 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.90 % Allowed : 8.30 % Favored : 88.80 % 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: 1.65 (0.21), residues: 1540 helix: 2.86 (0.21), residues: 610 sheet: 0.11 (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 B 75 HIS 0.003 0.001 HIS A 170 PHE 0.014 0.001 PHE E 117 TYR 0.011 0.001 TYR E 198 ARG 0.004 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 710) hydrogen bonds : angle 4.38823 ( 2475) covalent geometry : bond 0.00256 (12585) covalent geometry : angle 0.53479 (17140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10052.37 seconds wall clock time: 178 minutes 18.40 seconds (10698.40 seconds total)