Starting phenix.real_space_refine on Thu Feb 5 12:17:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dbx_46727/02_2026/9dbx_46727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dbx_46727/02_2026/9dbx_46727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dbx_46727/02_2026/9dbx_46727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dbx_46727/02_2026/9dbx_46727.map" model { file = "/net/cci-nas-00/data/ceres_data/9dbx_46727/02_2026/9dbx_46727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dbx_46727/02_2026/9dbx_46727.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.056 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 81 5.16 5 C 10737 2.51 5 N 2913 2.21 5 O 3324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17055 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2520 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "B" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "C" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2520 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "D" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "E" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2520 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "F" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "X" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "Y" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "Z" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.74, per 1000 atoms: 0.22 Number of scatterers: 17055 At special positions: 0 Unit cell: (128.7, 130.68, 147.84, 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 81 16.00 O 3324 8.00 N 2913 7.00 C 10737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.04 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 129 " " NAG B 501 " - " ASN B 154 " " NAG C 401 " - " ASN C 129 " " NAG D 501 " - " ASN D 154 " " NAG E 401 " - " ASN E 129 " " NAG F 501 " - " ASN F 154 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 946.3 milliseconds 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3978 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 51 sheets defined 20.7% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.081A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 125 through 127 removed outlier: 4.318A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.680A pdb=" N GLN B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 173 removed outlier: 3.978A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 4.070A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 79 " --> pdb=" O CYS C 76 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 80 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 126 removed outlier: 3.684A pdb=" N GLN D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 173 removed outlier: 3.976A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 4.082A pdb=" N GLU E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU E 78 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU E 79 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE E 80 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.512A pdb=" N GLU E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 126 removed outlier: 3.661A pdb=" N GLN F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 173 removed outlier: 3.980A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 173 " --> pdb=" O ASN F 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.063A pdb=" N SER L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'X' and resid 79 through 83 removed outlier: 4.080A pdb=" N SER X 83 " --> pdb=" O PRO X 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 87 Processing helix chain 'Z' and resid 79 through 83 removed outlier: 4.088A pdb=" N SER Z 83 " --> pdb=" O PRO Z 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 27 removed outlier: 3.599A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.274A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53 removed outlier: 5.940A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.365A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.242A pdb=" N SER A 261 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 118 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 259 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 120 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 257 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.242A pdb=" N SER A 261 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 118 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 259 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 120 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 257 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.455A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.746A pdb=" N ALA A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AB3, first strand: chain 'D' and resid 22 through 27 removed outlier: 3.607A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.265A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 53 removed outlier: 5.810A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.539A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.201A pdb=" N SER C 261 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE C 118 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA C 259 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG C 120 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA C 257 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.201A pdb=" N SER C 261 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE C 118 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA C 259 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG C 120 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA C 257 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.454A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.767A pdb=" N ALA C 247 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AC5, first strand: chain 'F' and resid 22 through 27 removed outlier: 3.572A pdb=" N GLY F 23 " --> pdb=" O GLY E 16 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.262A pdb=" N ASP E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 53 removed outlier: 5.816A pdb=" N LEU E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.541A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 115 through 122 removed outlier: 6.203A pdb=" N SER E 261 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE E 118 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA E 259 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG E 120 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA E 257 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 175 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 115 through 122 removed outlier: 6.203A pdb=" N SER E 261 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE E 118 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA E 259 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG E 120 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA E 257 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 175 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.449A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 169 removed outlier: 3.643A pdb=" N ALA E 247 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 281 through 282 Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.263A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.437A pdb=" N TRP H 35 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 12 removed outlier: 9.690A pdb=" N TYR H 91 " --> pdb=" O HIS H 102 " (cutoff:3.500A) removed outlier: 10.744A pdb=" N HIS H 102 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ALA H 93 " --> pdb=" O PHE H 100H" (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE H 100H" --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ALA H 95 " --> pdb=" O ASN H 100F" (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN H 100F" --> pdb=" O ALA H 95 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.953A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.953A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 3 through 7 removed outlier: 4.263A pdb=" N GLN W 77 " --> pdb=" O ASP W 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 57 through 59 removed outlier: 6.595A pdb=" N TRP W 36 " --> pdb=" O VAL W 48 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR W 50 " --> pdb=" O TRP W 35 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP W 35 " --> pdb=" O THR W 50 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N TYR W 91 " --> pdb=" O HIS W 102 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N HIS W 102 " --> pdb=" O TYR W 91 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ALA W 93 " --> pdb=" O PHE W 100H" (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE W 100H" --> pdb=" O ALA W 93 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ALA W 95 " --> pdb=" O ASN W 100F" (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN W 100F" --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 57 through 59 removed outlier: 6.595A pdb=" N TRP W 36 " --> pdb=" O VAL W 48 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR W 50 " --> pdb=" O TRP W 35 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP W 35 " --> pdb=" O THR W 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'X' and resid 10 through 12 removed outlier: 6.822A pdb=" N LEU X 11 " --> pdb=" O GLU X 105 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 10 through 12 removed outlier: 6.822A pdb=" N LEU X 11 " --> pdb=" O GLU X 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 3 through 7 removed outlier: 4.263A pdb=" N GLN Y 77 " --> pdb=" O ASP Y 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 57 through 59 removed outlier: 6.588A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR Y 50 " --> pdb=" O TRP Y 35 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP Y 35 " --> pdb=" O THR Y 50 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N TYR Y 91 " --> pdb=" O HIS Y 102 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N HIS Y 102 " --> pdb=" O TYR Y 91 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ALA Y 93 " --> pdb=" O PHE Y 100H" (cutoff:3.500A) removed outlier: 7.676A pdb=" N PHE Y 100H" --> pdb=" O ALA Y 93 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ALA Y 95 " --> pdb=" O ASN Y 100F" (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN Y 100F" --> pdb=" O ALA Y 95 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 57 through 59 removed outlier: 6.588A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR Y 50 " --> pdb=" O TRP Y 35 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP Y 35 " --> pdb=" O THR Y 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'Z' and resid 10 through 12 removed outlier: 6.481A pdb=" N TRP Z 35 " --> pdb=" O LEU Z 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 10 through 12 711 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5547 1.34 - 1.47: 4329 1.47 - 1.59: 7482 1.59 - 1.72: 0 1.72 - 1.84: 114 Bond restraints: 17472 Sorted by residual: bond pdb=" N SER C 265 " pdb=" CA SER C 265 " ideal model delta sigma weight residual 1.457 1.485 -0.028 6.40e-03 2.44e+04 1.97e+01 bond pdb=" N SER E 265 " pdb=" CA SER E 265 " ideal model delta sigma weight residual 1.457 1.485 -0.028 6.40e-03 2.44e+04 1.93e+01 bond pdb=" N ASP A 278 " pdb=" CA ASP A 278 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 1.00e+01 bond pdb=" N ILE E 56 " pdb=" CA ILE E 56 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.18e-02 7.18e+03 9.99e+00 bond pdb=" N ARG Y 82A" pdb=" CA ARG Y 82A" ideal model delta sigma weight residual 1.453 1.491 -0.037 1.22e-02 6.72e+03 9.30e+00 ... (remaining 17467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 22975 1.73 - 3.45: 641 3.45 - 5.18: 82 5.18 - 6.91: 12 6.91 - 8.63: 5 Bond angle restraints: 23715 Sorted by residual: angle pdb=" N PRO A 128 " pdb=" CA PRO A 128 " pdb=" CB PRO A 128 " ideal model delta sigma weight residual 103.25 97.91 5.34 1.05e+00 9.07e-01 2.59e+01 angle pdb=" N LYS A 280 " pdb=" CA LYS A 280 " pdb=" C LYS A 280 " ideal model delta sigma weight residual 113.12 107.34 5.78 1.25e+00 6.40e-01 2.14e+01 angle pdb=" N ILE E 123 " pdb=" CA ILE E 123 " pdb=" C ILE E 123 " ideal model delta sigma weight residual 111.58 107.16 4.42 1.06e+00 8.90e-01 1.74e+01 angle pdb=" C SER C 265 " pdb=" CA SER C 265 " pdb=" CB SER C 265 " ideal model delta sigma weight residual 117.07 111.50 5.57 1.44e+00 4.82e-01 1.49e+01 angle pdb=" O SER C 265 " pdb=" C SER C 265 " pdb=" N GLY C 266 " ideal model delta sigma weight residual 121.47 124.35 -2.88 7.50e-01 1.78e+00 1.48e+01 ... (remaining 23710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9255 17.86 - 35.73: 907 35.73 - 53.59: 249 53.59 - 71.45: 56 71.45 - 89.31: 27 Dihedral angle restraints: 10494 sinusoidal: 4257 harmonic: 6237 Sorted by residual: dihedral pdb=" CA SER A 125C" pdb=" C SER A 125C" pdb=" N SER A 126 " pdb=" CA SER A 126 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 48.58 44.42 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CB CYS Y 22 " pdb=" SG CYS Y 22 " pdb=" SG CYS Y 92 " pdb=" CB CYS Y 92 " ideal model delta sinusoidal sigma weight residual 93.00 48.77 44.23 1 1.00e+01 1.00e-02 2.72e+01 ... (remaining 10491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1892 0.046 - 0.091: 474 0.091 - 0.137: 174 0.137 - 0.182: 18 0.182 - 0.228: 4 Chirality restraints: 2562 Sorted by residual: chirality pdb=" CA ILE A 56 " pdb=" N ILE A 56 " pdb=" C ILE A 56 " pdb=" CB ILE A 56 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE E 56 " pdb=" N ILE E 56 " pdb=" C ILE E 56 " pdb=" CB ILE E 56 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE C 56 " pdb=" N ILE C 56 " pdb=" C ILE C 56 " pdb=" CB ILE C 56 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2559 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG W 66 " -0.252 9.50e-02 1.11e+02 1.13e-01 7.84e+00 pdb=" NE ARG W 66 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG W 66 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG W 66 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG W 66 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 90 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO E 91 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 91 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 91 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 90 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 91 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.032 5.00e-02 4.00e+02 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1597 2.75 - 3.28: 15610 3.28 - 3.82: 28175 3.82 - 4.36: 34589 4.36 - 4.90: 60890 Nonbonded interactions: 140861 Sorted by model distance: nonbonded pdb=" NE2 GLN D 38 " pdb=" OE1 GLN D 42 " model vdw 2.206 3.120 nonbonded pdb=" NE2 GLN F 38 " pdb=" OE1 GLN F 42 " model vdw 2.219 3.120 nonbonded pdb=" O PRO Z 8 " pdb=" OG1 THR Z 102 " model vdw 2.230 3.040 nonbonded pdb=" NE2 GLN B 38 " pdb=" OE1 GLN B 42 " model vdw 2.233 3.120 nonbonded pdb=" NE2 HIS C 184 " pdb=" OD1 ASN C 231 " model vdw 2.233 3.120 ... (remaining 140856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'X' selection = chain 'Z' } 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: 12.620 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.210 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.004 0.043 17502 Z= 0.250 Angle : 0.656 8.635 23781 Z= 0.391 Chirality : 0.046 0.228 2562 Planarity : 0.005 0.113 3066 Dihedral : 15.737 89.313 6444 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.71 % Allowed : 14.77 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2133 helix: 2.20 (0.28), residues: 366 sheet: 0.28 (0.24), residues: 486 loop : -1.36 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 75 TYR 0.021 0.001 TYR A 105 PHE 0.013 0.001 PHE Y 78 TRP 0.011 0.001 TRP Y 35 HIS 0.002 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00406 (17472) covalent geometry : angle 0.65383 (23715) SS BOND : bond 0.00368 ( 24) SS BOND : angle 0.99145 ( 48) hydrogen bonds : bond 0.13742 ( 659) hydrogen bonds : angle 6.84380 ( 1884) link_NAG-ASN : bond 0.00271 ( 6) link_NAG-ASN : angle 1.63917 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6525 (pm20) REVERT: A 226 GLN cc_start: 0.7421 (mm110) cc_final: 0.6844 (mp10) REVERT: A 275 ASP cc_start: 0.7322 (m-30) cc_final: 0.6892 (m-30) REVERT: B 75 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7534 (ttm170) REVERT: B 133 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7962 (mp) REVERT: B 135 ASN cc_start: 0.7778 (t0) cc_final: 0.7475 (t160) REVERT: C 63 ASN cc_start: 0.7237 (m-40) cc_final: 0.6944 (t0) REVERT: C 75 GLU cc_start: 0.6793 (pt0) cc_final: 0.6566 (pm20) REVERT: C 79 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6662 (pp) REVERT: C 226 GLN cc_start: 0.7314 (mm110) cc_final: 0.6758 (mp10) REVERT: C 227 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6681 (pm20) REVERT: E 75 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: E 226 GLN cc_start: 0.7413 (mm110) cc_final: 0.6786 (mp10) REVERT: H 43 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7726 (mtp) REVERT: L 4 MET cc_start: 0.8701 (tpp) cc_final: 0.8175 (ttm) REVERT: Z 4 MET cc_start: 0.8568 (tpp) cc_final: 0.8046 (ttm) outliers start: 32 outliers final: 12 residues processed: 235 average time/residue: 0.4815 time to fit residues: 127.9014 Evaluate side-chains 213 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 264 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain Z residue 19 VAL Chi-restraints excluded: chain Z residue 29 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 overall best weight: 2.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 289 ASN C 199 ASN C 289 ASN E 199 ASN E 289 ASN F 79 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.152187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128858 restraints weight = 21835.598| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.83 r_work: 0.3309 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17502 Z= 0.193 Angle : 0.629 15.712 23781 Z= 0.317 Chirality : 0.044 0.176 2562 Planarity : 0.004 0.058 3066 Dihedral : 6.294 61.972 2495 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.79 % Allowed : 14.24 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2133 helix: 2.18 (0.27), residues: 366 sheet: 0.26 (0.24), residues: 504 loop : -1.43 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 75 TYR 0.015 0.002 TYR A 105 PHE 0.015 0.002 PHE W 78 TRP 0.013 0.001 TRP Y 35 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00460 (17472) covalent geometry : angle 0.62448 (23715) SS BOND : bond 0.00502 ( 24) SS BOND : angle 1.41741 ( 48) hydrogen bonds : bond 0.04552 ( 659) hydrogen bonds : angle 5.49647 ( 1884) link_NAG-ASN : bond 0.00187 ( 6) link_NAG-ASN : angle 1.81182 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 200 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7231 (pt0) REVERT: A 226 GLN cc_start: 0.7376 (mm110) cc_final: 0.6837 (mp10) REVERT: A 275 ASP cc_start: 0.7526 (m-30) cc_final: 0.7290 (m-30) REVERT: B 164 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6613 (tp30) REVERT: C 75 GLU cc_start: 0.6839 (pt0) cc_final: 0.6638 (pm20) REVERT: C 79 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6674 (pp) REVERT: C 226 GLN cc_start: 0.7311 (mm110) cc_final: 0.6717 (mp10) REVERT: C 227 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6717 (mp0) REVERT: C 265 SER cc_start: 0.8464 (m) cc_final: 0.8251 (m) REVERT: D 164 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6632 (tp30) REVERT: E 216 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: E 226 GLN cc_start: 0.7359 (mm110) cc_final: 0.6771 (mp10) REVERT: F 164 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6629 (tp30) REVERT: H 99 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7103 (tt) REVERT: L 4 MET cc_start: 0.8712 (tpp) cc_final: 0.8196 (ttm) REVERT: W 99 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.6985 (tt) REVERT: Y 99 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7057 (tt) REVERT: Z 4 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7876 (ttm) outliers start: 71 outliers final: 33 residues processed: 244 average time/residue: 0.4733 time to fit residues: 131.4160 Evaluate side-chains 228 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 264 PHE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain Y residue 32 GLU Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 4 MET Chi-restraints excluded: chain Z residue 19 VAL Chi-restraints excluded: chain Z residue 29 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 197 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 289 ASN C 199 ASN C 289 ASN E 199 ASN E 289 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.153612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130571 restraints weight = 21805.755| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.91 r_work: 0.3325 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17502 Z= 0.156 Angle : 0.582 15.832 23781 Z= 0.292 Chirality : 0.043 0.158 2562 Planarity : 0.004 0.057 3066 Dihedral : 5.557 50.371 2481 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.57 % Allowed : 15.63 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2133 helix: 2.29 (0.27), residues: 366 sheet: 0.31 (0.24), residues: 501 loop : -1.35 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 75 TYR 0.013 0.001 TYR L 94 PHE 0.014 0.001 PHE W 78 TRP 0.012 0.001 TRP Y 35 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00369 (17472) covalent geometry : angle 0.57845 (23715) SS BOND : bond 0.00462 ( 24) SS BOND : angle 1.06139 ( 48) hydrogen bonds : bond 0.04262 ( 659) hydrogen bonds : angle 5.24839 ( 1884) link_NAG-ASN : bond 0.00252 ( 6) link_NAG-ASN : angle 1.88049 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 203 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: A 226 GLN cc_start: 0.7404 (mm110) cc_final: 0.6858 (mp10) REVERT: A 275 ASP cc_start: 0.7554 (m-30) cc_final: 0.7286 (m-30) REVERT: B 164 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6643 (tp30) REVERT: C 79 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6729 (pp) REVERT: C 227 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6732 (pm20) REVERT: C 265 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8238 (m) REVERT: D 164 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6621 (tp30) REVERT: E 216 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: E 226 GLN cc_start: 0.7296 (mm110) cc_final: 0.6686 (mp10) REVERT: F 164 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6628 (tp30) REVERT: H 99 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7085 (tt) REVERT: L 4 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8194 (ttm) REVERT: W 99 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.6970 (tt) REVERT: Y 99 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7040 (tt) REVERT: Z 4 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7860 (ttm) outliers start: 67 outliers final: 34 residues processed: 244 average time/residue: 0.4735 time to fit residues: 131.6767 Evaluate side-chains 228 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 264 PHE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain Y residue 32 GLU Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 4 MET Chi-restraints excluded: chain Z residue 19 VAL Chi-restraints excluded: chain Z residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 100 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 289 ASN C 199 ASN C 289 ASN E 199 ASN E 289 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129695 restraints weight = 21929.107| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.85 r_work: 0.3338 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17502 Z= 0.184 Angle : 0.609 16.950 23781 Z= 0.304 Chirality : 0.044 0.201 2562 Planarity : 0.004 0.057 3066 Dihedral : 5.697 59.761 2480 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.75 % Allowed : 15.68 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2133 helix: 2.21 (0.27), residues: 366 sheet: 0.19 (0.23), residues: 510 loop : -1.35 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 75 TYR 0.014 0.002 TYR E 105 PHE 0.015 0.002 PHE W 78 TRP 0.013 0.001 TRP Y 35 HIS 0.004 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00441 (17472) covalent geometry : angle 0.60507 (23715) SS BOND : bond 0.00490 ( 24) SS BOND : angle 1.19522 ( 48) hydrogen bonds : bond 0.04379 ( 659) hydrogen bonds : angle 5.19343 ( 1884) link_NAG-ASN : bond 0.00169 ( 6) link_NAG-ASN : angle 1.91995 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 202 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6639 (pp) REVERT: A 216 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7213 (pt0) REVERT: B 133 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8093 (mp) REVERT: B 164 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6700 (tp30) REVERT: C 79 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6666 (pp) REVERT: D 164 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6676 (tp30) REVERT: E 216 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: F 164 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6668 (tp30) REVERT: H 99 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7122 (tt) REVERT: L 4 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8191 (ttm) REVERT: W 99 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.6979 (tt) REVERT: Y 99 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7035 (tt) REVERT: Z 4 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7872 (ttm) outliers start: 89 outliers final: 42 residues processed: 265 average time/residue: 0.4728 time to fit residues: 142.4443 Evaluate side-chains 250 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 264 PHE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain Y residue 32 GLU Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 4 MET Chi-restraints excluded: chain Z residue 19 VAL Chi-restraints excluded: chain Z residue 29 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 27 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 199 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 289 ASN C 199 ASN C 289 ASN E 199 ASN E 289 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.154708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130955 restraints weight = 21726.396| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.91 r_work: 0.3337 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17502 Z= 0.124 Angle : 0.552 16.607 23781 Z= 0.275 Chirality : 0.042 0.217 2562 Planarity : 0.004 0.056 3066 Dihedral : 5.378 53.695 2480 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.11 % Allowed : 16.37 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.18), residues: 2133 helix: 2.42 (0.27), residues: 366 sheet: 0.39 (0.24), residues: 501 loop : -1.27 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 120 TYR 0.012 0.001 TYR L 94 PHE 0.013 0.001 PHE W 78 TRP 0.011 0.001 TRP Y 35 HIS 0.002 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00289 (17472) covalent geometry : angle 0.54882 (23715) SS BOND : bond 0.00425 ( 24) SS BOND : angle 0.93066 ( 48) hydrogen bonds : bond 0.03912 ( 659) hydrogen bonds : angle 5.00219 ( 1884) link_NAG-ASN : bond 0.00161 ( 6) link_NAG-ASN : angle 1.81133 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 201 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6658 (pp) REVERT: A 216 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7187 (pt0) REVERT: A 226 GLN cc_start: 0.7442 (mm110) cc_final: 0.6905 (mp10) REVERT: A 275 ASP cc_start: 0.7829 (m-30) cc_final: 0.7624 (m-30) REVERT: B 75 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7828 (ttm-80) REVERT: B 133 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8023 (mp) REVERT: B 164 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6657 (tp30) REVERT: C 63 ASN cc_start: 0.7362 (m-40) cc_final: 0.7118 (t160) REVERT: C 227 GLU cc_start: 0.7618 (mm-30) cc_final: 0.6752 (pm20) REVERT: D 164 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6681 (tp30) REVERT: F 164 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6668 (tp30) REVERT: H 99 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7059 (tt) REVERT: L 4 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8205 (ttm) REVERT: W 99 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6998 (tt) REVERT: X 100 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6200 (pm20) REVERT: Y 99 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7045 (tt) REVERT: Z 4 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7890 (ttm) outliers start: 77 outliers final: 44 residues processed: 253 average time/residue: 0.4599 time to fit residues: 133.1717 Evaluate side-chains 249 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 264 PHE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 100 GLN Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 32 GLU Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 4 MET Chi-restraints excluded: chain Z residue 19 VAL Chi-restraints excluded: chain Z residue 29 ILE Chi-restraints excluded: chain Z residue 31 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 176 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 289 ASN C 199 ASN C 289 ASN E 199 ASN E 289 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131117 restraints weight = 21682.377| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.89 r_work: 0.3325 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17502 Z= 0.137 Angle : 0.560 16.623 23781 Z= 0.279 Chirality : 0.043 0.315 2562 Planarity : 0.004 0.055 3066 Dihedral : 5.275 47.232 2478 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.27 % Allowed : 17.07 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2133 helix: 2.43 (0.27), residues: 366 sheet: 0.63 (0.24), residues: 468 loop : -1.20 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 75 TYR 0.011 0.001 TYR L 94 PHE 0.014 0.001 PHE H 78 TRP 0.013 0.001 TRP Y 35 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00322 (17472) covalent geometry : angle 0.55671 (23715) SS BOND : bond 0.00377 ( 24) SS BOND : angle 0.99008 ( 48) hydrogen bonds : bond 0.03955 ( 659) hydrogen bonds : angle 4.94920 ( 1884) link_NAG-ASN : bond 0.00142 ( 6) link_NAG-ASN : angle 1.91002 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 203 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6658 (pp) REVERT: A 216 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7166 (pt0) REVERT: A 226 GLN cc_start: 0.7411 (mm110) cc_final: 0.6790 (mp10) REVERT: A 227 GLU cc_start: 0.7677 (mm-30) cc_final: 0.6749 (mp0) REVERT: A 275 ASP cc_start: 0.7784 (m-30) cc_final: 0.7532 (m-30) REVERT: B 75 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7829 (ttm-80) REVERT: B 133 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8007 (mp) REVERT: B 164 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6678 (tp30) REVERT: C 63 ASN cc_start: 0.7357 (m-40) cc_final: 0.7119 (t160) REVERT: C 226 GLN cc_start: 0.7431 (mm110) cc_final: 0.6907 (mp10) REVERT: C 227 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6798 (mp0) REVERT: D 164 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6682 (tp30) REVERT: E 226 GLN cc_start: 0.7423 (mm110) cc_final: 0.6822 (mp10) REVERT: F 164 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6696 (tp30) REVERT: H 99 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7064 (tt) REVERT: L 4 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8235 (ttm) REVERT: W 3 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7997 (mm110) REVERT: W 67 THR cc_start: 0.8767 (t) cc_final: 0.8552 (t) REVERT: W 99 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7001 (tt) REVERT: X 100 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6209 (pm20) REVERT: Y 99 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7036 (tt) REVERT: Z 4 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7888 (ttm) outliers start: 80 outliers final: 49 residues processed: 257 average time/residue: 0.4686 time to fit residues: 137.1284 Evaluate side-chains 254 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 192 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 264 PHE Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain W residue 3 GLN Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 100 GLN Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 32 GLU Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 4 MET Chi-restraints excluded: chain Z residue 19 VAL Chi-restraints excluded: chain Z residue 29 ILE Chi-restraints excluded: chain Z residue 31 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 116 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 128 optimal weight: 0.3980 chunk 5 optimal weight: 9.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 199 ASN A 289 ASN C 199 ASN C 289 ASN E 199 ASN E 289 ASN L 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 6 GLN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 6 GLN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129687 restraints weight = 22012.221| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.85 r_work: 0.3332 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 17502 Z= 0.303 Angle : 0.750 19.423 23781 Z= 0.370 Chirality : 0.050 0.488 2562 Planarity : 0.005 0.059 3066 Dihedral : 5.948 53.082 2478 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.48 % Allowed : 17.76 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.17), residues: 2133 helix: 1.91 (0.27), residues: 366 sheet: 0.13 (0.24), residues: 510 loop : -1.47 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 262 TYR 0.020 0.002 TYR L 96 PHE 0.017 0.002 PHE Y 78 TRP 0.015 0.002 TRP W 35 HIS 0.007 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00731 (17472) covalent geometry : angle 0.72832 (23715) SS BOND : bond 0.00685 ( 24) SS BOND : angle 1.57027 ( 48) hydrogen bonds : bond 0.05096 ( 659) hydrogen bonds : angle 5.34924 ( 1884) link_NAG-ASN : bond 0.00593 ( 6) link_NAG-ASN : angle 6.13128 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 206 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6641 (pp) REVERT: A 152 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7602 (pt) REVERT: A 216 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7201 (pt0) REVERT: A 275 ASP cc_start: 0.7772 (m-30) cc_final: 0.7519 (m-30) REVERT: B 75 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7860 (ttm110) REVERT: B 133 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8099 (mp) REVERT: B 164 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6738 (tp30) REVERT: C 75 GLU cc_start: 0.6938 (pt0) cc_final: 0.6608 (pm20) REVERT: C 152 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7666 (pt) REVERT: D 164 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6814 (tp30) REVERT: E 63 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.7002 (t0) REVERT: E 75 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6642 (pm20) REVERT: E 152 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7628 (pt) REVERT: F 164 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6741 (tp30) REVERT: H 66 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8243 (ptt90) REVERT: H 99 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7142 (tt) REVERT: L 4 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8228 (ttm) REVERT: W 3 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7969 (mm110) REVERT: W 99 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7018 (tt) REVERT: Z 4 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7867 (ttm) outliers start: 84 outliers final: 44 residues processed: 260 average time/residue: 0.4431 time to fit residues: 131.9837 Evaluate side-chains 253 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 264 PHE Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain W residue 3 GLN Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 32 GLU Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 4 MET Chi-restraints excluded: chain Z residue 19 VAL Chi-restraints excluded: chain Z residue 29 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 109 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 289 ASN C 199 ASN C 289 ASN E 199 ASN E 289 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 6 GLN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.156308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133075 restraints weight = 21704.274| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.83 r_work: 0.3380 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17502 Z= 0.115 Angle : 0.600 24.147 23781 Z= 0.292 Chirality : 0.042 0.247 2562 Planarity : 0.004 0.067 3066 Dihedral : 5.285 54.604 2472 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.09 % Allowed : 19.09 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2133 helix: 2.28 (0.27), residues: 366 sheet: 0.52 (0.25), residues: 471 loop : -1.22 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 75 TYR 0.013 0.001 TYR Y 91 PHE 0.012 0.001 PHE W 78 TRP 0.012 0.001 TRP Y 47 HIS 0.002 0.000 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00263 (17472) covalent geometry : angle 0.56402 (23715) SS BOND : bond 0.00275 ( 24) SS BOND : angle 0.94162 ( 48) hydrogen bonds : bond 0.03883 ( 659) hydrogen bonds : angle 5.01352 ( 1884) link_NAG-ASN : bond 0.00778 ( 6) link_NAG-ASN : angle 7.31829 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6822 (pt0) cc_final: 0.6468 (pm20) REVERT: A 79 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6580 (pp) REVERT: A 187 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.7065 (p0) REVERT: A 216 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7173 (pt0) REVERT: A 226 GLN cc_start: 0.7523 (mm110) cc_final: 0.7024 (mp10) REVERT: A 275 ASP cc_start: 0.7715 (m-30) cc_final: 0.7471 (m-30) REVERT: B 75 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7800 (ttm110) REVERT: B 133 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8037 (mp) REVERT: B 164 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6623 (tp30) REVERT: C 63 ASN cc_start: 0.7354 (m-40) cc_final: 0.7106 (t160) REVERT: C 75 GLU cc_start: 0.6905 (pt0) cc_final: 0.6645 (pm20) REVERT: C 226 GLN cc_start: 0.7510 (mm110) cc_final: 0.7034 (mp10) REVERT: C 227 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6887 (pm20) REVERT: D 164 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6699 (tp30) REVERT: E 75 GLU cc_start: 0.6936 (pt0) cc_final: 0.6596 (pm20) REVERT: E 226 GLN cc_start: 0.7552 (mm110) cc_final: 0.6972 (mp10) REVERT: E 227 GLU cc_start: 0.7731 (mm-30) cc_final: 0.6821 (mp0) REVERT: F 164 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6656 (tp30) REVERT: H 99 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7084 (tt) REVERT: L 4 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8211 (ttm) REVERT: W 99 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7048 (tt) REVERT: Y 99 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.6997 (tt) REVERT: Z 4 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8195 (ttm) REVERT: Z 31 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.6756 (t0) outliers start: 58 outliers final: 27 residues processed: 240 average time/residue: 0.4500 time to fit residues: 123.5007 Evaluate side-chains 230 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain Y residue 32 GLU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 4 MET Chi-restraints excluded: chain Z residue 19 VAL Chi-restraints excluded: chain Z residue 29 ILE Chi-restraints excluded: chain Z residue 31 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 107 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 119 optimal weight: 0.0010 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 289 ASN C 199 ASN C 289 ASN E 199 ASN E 289 ASN L 92 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN Z 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.154820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132000 restraints weight = 21807.698| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.80 r_work: 0.3385 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17502 Z= 0.160 Angle : 0.617 20.616 23781 Z= 0.303 Chirality : 0.044 0.191 2562 Planarity : 0.004 0.057 3066 Dihedral : 5.155 38.684 2468 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.83 % Allowed : 19.73 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.18), residues: 2133 helix: 2.29 (0.27), residues: 366 sheet: 0.52 (0.24), residues: 474 loop : -1.20 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 192 TYR 0.015 0.002 TYR L 94 PHE 0.014 0.001 PHE W 78 TRP 0.013 0.001 TRP Y 35 HIS 0.003 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00381 (17472) covalent geometry : angle 0.58979 (23715) SS BOND : bond 0.00415 ( 24) SS BOND : angle 1.12389 ( 48) hydrogen bonds : bond 0.04145 ( 659) hydrogen bonds : angle 5.01895 ( 1884) link_NAG-ASN : bond 0.00459 ( 6) link_NAG-ASN : angle 6.39906 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6809 (pt0) cc_final: 0.6446 (pm20) REVERT: A 79 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6521 (pp) REVERT: A 187 ASN cc_start: 0.7456 (OUTLIER) cc_final: 0.7154 (p0) REVERT: A 192 ARG cc_start: 0.7970 (tpp80) cc_final: 0.7206 (mtp85) REVERT: A 226 GLN cc_start: 0.7569 (mm110) cc_final: 0.7090 (mp10) REVERT: A 275 ASP cc_start: 0.7697 (m-30) cc_final: 0.7470 (m-30) REVERT: B 75 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7783 (ttm110) REVERT: B 133 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8046 (mp) REVERT: B 164 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6678 (tp30) REVERT: C 75 GLU cc_start: 0.6853 (pt0) cc_final: 0.6608 (pm20) REVERT: C 226 GLN cc_start: 0.7613 (mm110) cc_final: 0.7101 (mp10) REVERT: C 227 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6965 (mp0) REVERT: D 164 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6803 (tp30) REVERT: E 75 GLU cc_start: 0.6812 (pt0) cc_final: 0.6470 (pm20) REVERT: F 164 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: H 99 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7143 (tt) REVERT: L 4 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8205 (ttm) REVERT: W 99 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7038 (tt) REVERT: Y 99 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7034 (tt) REVERT: Z 4 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7847 (ttm) outliers start: 53 outliers final: 34 residues processed: 224 average time/residue: 0.4372 time to fit residues: 112.2351 Evaluate side-chains 231 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 32 GLU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 4 MET Chi-restraints excluded: chain Z residue 19 VAL Chi-restraints excluded: chain Z residue 29 ILE Chi-restraints excluded: chain Z residue 31 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 205 optimal weight: 0.0020 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 289 ASN C 63 ASN C 199 ASN C 289 ASN E 199 ASN E 289 ASN L 92 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.153794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130844 restraints weight = 21768.498| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.80 r_work: 0.3346 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17502 Z= 0.199 Angle : 0.646 18.488 23781 Z= 0.321 Chirality : 0.045 0.183 2562 Planarity : 0.004 0.057 3066 Dihedral : 5.368 40.051 2468 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.04 % Allowed : 19.68 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2133 helix: 2.17 (0.27), residues: 366 sheet: 0.26 (0.24), residues: 507 loop : -1.30 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 75 TYR 0.017 0.002 TYR L 94 PHE 0.015 0.002 PHE W 78 TRP 0.013 0.002 TRP Y 35 HIS 0.004 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00477 (17472) covalent geometry : angle 0.62507 (23715) SS BOND : bond 0.00506 ( 24) SS BOND : angle 1.26048 ( 48) hydrogen bonds : bond 0.04433 ( 659) hydrogen bonds : angle 5.11766 ( 1884) link_NAG-ASN : bond 0.00528 ( 6) link_NAG-ASN : angle 5.75693 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6807 (pt0) cc_final: 0.6474 (pm20) REVERT: A 79 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6562 (pp) REVERT: A 187 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7177 (p0) REVERT: A 226 GLN cc_start: 0.7573 (mm110) cc_final: 0.7054 (mp10) REVERT: A 275 ASP cc_start: 0.7711 (m-30) cc_final: 0.7466 (m-30) REVERT: B 133 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8052 (mp) REVERT: B 164 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6688 (tp30) REVERT: C 152 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7539 (pt) REVERT: C 226 GLN cc_start: 0.7568 (mm110) cc_final: 0.7010 (mp10) REVERT: C 227 GLU cc_start: 0.7614 (mm-30) cc_final: 0.6944 (mp0) REVERT: D 164 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6778 (tp30) REVERT: E 63 ASN cc_start: 0.7468 (OUTLIER) cc_final: 0.7009 (t0) REVERT: E 75 GLU cc_start: 0.6884 (pt0) cc_final: 0.6488 (pm20) REVERT: E 152 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7543 (pt) REVERT: E 226 GLN cc_start: 0.7663 (mm110) cc_final: 0.7167 (mp10) REVERT: F 164 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6719 (tp30) REVERT: H 99 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7186 (tt) REVERT: L 4 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8254 (ttm) REVERT: W 99 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7036 (tt) REVERT: X 100 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6257 (pm20) REVERT: Y 99 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7056 (tt) REVERT: Z 4 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7864 (ttm) outliers start: 57 outliers final: 33 residues processed: 221 average time/residue: 0.4592 time to fit residues: 115.7348 Evaluate side-chains 230 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 100 GLN Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 32 GLU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 4 MET Chi-restraints excluded: chain Z residue 19 VAL Chi-restraints excluded: chain Z residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 32 optimal weight: 0.0020 chunk 42 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 289 ASN C 199 ASN C 289 ASN E 199 ASN E 289 ASN L 92 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134207 restraints weight = 21660.350| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.85 r_work: 0.3376 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17502 Z= 0.111 Angle : 0.558 16.078 23781 Z= 0.277 Chirality : 0.042 0.162 2562 Planarity : 0.004 0.056 3066 Dihedral : 4.973 42.290 2468 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.24 % Allowed : 20.43 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.18), residues: 2133 helix: 2.41 (0.27), residues: 366 sheet: 0.63 (0.25), residues: 471 loop : -1.09 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 192 TYR 0.012 0.001 TYR H 91 PHE 0.012 0.001 PHE W 78 TRP 0.011 0.001 TRP Y 35 HIS 0.003 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00254 (17472) covalent geometry : angle 0.53986 (23715) SS BOND : bond 0.00298 ( 24) SS BOND : angle 0.88707 ( 48) hydrogen bonds : bond 0.03742 ( 659) hydrogen bonds : angle 4.87231 ( 1884) link_NAG-ASN : bond 0.00411 ( 6) link_NAG-ASN : angle 5.07944 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5515.64 seconds wall clock time: 94 minutes 50.76 seconds (5690.76 seconds total)