Starting phenix.real_space_refine on Wed Sep 17 18:42:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gh5_51347/09_2025/9gh5_51347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gh5_51347/09_2025/9gh5_51347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gh5_51347/09_2025/9gh5_51347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gh5_51347/09_2025/9gh5_51347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gh5_51347/09_2025/9gh5_51347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gh5_51347/09_2025/9gh5_51347.map" } resolution = 2.7 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= 0.001 sd= 0.018 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 15 5.16 5 C 6399 2.51 5 N 1791 2.21 5 O 2178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10383 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1813 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 1, 'TRANS': 247} Chain: "B" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1813 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 1, 'TRANS': 247} Chain: "C" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1813 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 1, 'TRANS': 247} Chain: "D" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1563 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 184} Chain: "E" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1563 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 184} Chain: "F" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1563 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 184} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.79, per 1000 atoms: 0.27 Number of scatterers: 10383 At special positions: 0 Unit cell: (185.92, 184.26, 135.29, 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 15 16.00 O 2178 8.00 N 1791 7.00 C 6399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 167 " - pdb=" SG CYS D 215 " distance=2.04 Simple disulfide: pdb=" SG CYS E 167 " - pdb=" SG CYS E 215 " distance=2.04 Simple disulfide: pdb=" SG CYS F 167 " - pdb=" SG CYS F 215 " distance=2.03 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 D 501 " - " ASN D 104 " " NAG D 502 " - " ASN D 111 " " NAG D 503 " - " ASN D 182 " " NAG D 504 " - " ASN D 197 " " NAG D 505 " - " ASN D 152 " " NAG D 506 " - " ASN D 224 " " NAG E 501 " - " ASN E 104 " " NAG E 502 " - " ASN E 111 " " NAG E 503 " - " ASN E 182 " " NAG E 504 " - " ASN E 197 " " NAG E 505 " - " ASN E 152 " " NAG E 506 " - " ASN E 224 " " NAG F 501 " - " ASN F 104 " " NAG F 502 " - " ASN F 111 " " NAG F 503 " - " ASN F 182 " " NAG F 504 " - " ASN F 197 " " NAG F 505 " - " ASN F 152 " " NAG F 506 " - " ASN F 224 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 438.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 21 sheets defined 9.2% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'B' and resid 231 through 238 Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 265 through 273 removed outlier: 3.552A pdb=" N TRP B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 238 Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 113 through 117 removed outlier: 3.645A pdb=" N THR D 117 " --> pdb=" O GLN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 113 through 117 removed outlier: 3.668A pdb=" N THR E 117 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 210 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 113 through 117 removed outlier: 3.623A pdb=" N THR F 117 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 210 removed outlier: 3.533A pdb=" N THR F 210 " --> pdb=" O ARG F 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.624A pdb=" N THR A 38 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY A 55 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA A 40 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER A 52 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLY A 69 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE A 54 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER A 94 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N GLY A 111 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE A 96 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS A 113 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N SER A 98 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THR A 115 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A 114 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN A 129 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 116 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ASN A 151 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLN A 129 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.709A pdb=" N VAL A 45 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS A 59 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG A 73 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A 87 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A 114 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN A 129 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 116 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 189 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 165 removed outlier: 6.549A pdb=" N LYS A 164 " --> pdb=" O ILE A 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 215 removed outlier: 6.138A pdb=" N LYS A 213 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 189 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR C 157 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C 114 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLN C 129 " --> pdb=" O ASN C 114 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 116 " --> pdb=" O GLN C 129 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 87 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG C 73 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LYS C 59 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 45 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.817A pdb=" N SER C 52 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLY C 69 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE C 54 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER C 66 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLY C 83 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE C 68 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER C 94 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLY C 111 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE C 96 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LYS C 113 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N SER C 98 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR C 115 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C 114 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLN C 129 " --> pdb=" O ASN C 114 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 116 " --> pdb=" O GLN C 129 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ASN C 151 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLN C 129 " --> pdb=" O ASN C 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.811A pdb=" N SER B 52 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLY B 69 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE B 54 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER B 94 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLY B 111 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE B 96 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LYS B 113 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N SER B 98 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N THR B 115 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN B 114 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLN B 129 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 116 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ASN B 151 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLN B 129 " --> pdb=" O ASN B 151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 46 removed outlier: 6.692A pdb=" N VAL B 45 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS B 59 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG B 73 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 87 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN B 114 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLN B 129 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 116 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR B 157 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 189 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 165 removed outlier: 6.560A pdb=" N LYS B 164 " --> pdb=" O ILE B 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 165 removed outlier: 6.535A pdb=" N LYS C 164 " --> pdb=" O ILE C 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.666A pdb=" N THR D 37 " --> pdb=" O HIS D 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 44 through 46 removed outlier: 3.737A pdb=" N PHE D 138 " --> pdb=" O GLY D 118 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY D 118 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE D 119 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS D 69 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR D 121 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP D 67 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN D 123 " --> pdb=" O TYR D 65 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR D 65 " --> pdb=" O GLN D 123 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 125 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N PHE D 63 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA D 83 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR D 65 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY D 81 " --> pdb=" O TYR D 65 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP D 67 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 149 through 151 Processing sheet with id=AB4, first strand: chain 'D' and resid 183 through 184 removed outlier: 3.558A pdb=" N LEU D 177 " --> pdb=" O GLU D 216 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 37 through 41 removed outlier: 3.724A pdb=" N THR E 37 " --> pdb=" O HIS E 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 44 through 46 removed outlier: 3.754A pdb=" N PHE E 138 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY E 118 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N PHE E 119 " --> pdb=" O LYS E 69 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS E 69 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR E 121 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TRP E 67 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLN E 123 " --> pdb=" O TYR E 65 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR E 65 " --> pdb=" O GLN E 123 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE E 125 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N PHE E 63 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA E 83 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR E 65 " --> pdb=" O GLY E 81 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY E 81 " --> pdb=" O TYR E 65 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP E 67 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 149 through 151 Processing sheet with id=AB8, first strand: chain 'E' and resid 183 through 184 removed outlier: 4.552A pdb=" N ILE E 217 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN E 224 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 37 through 41 removed outlier: 3.694A pdb=" N THR F 37 " --> pdb=" O HIS F 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 44 through 46 removed outlier: 3.723A pdb=" N PHE F 138 " --> pdb=" O GLY F 118 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY F 118 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE F 119 " --> pdb=" O LYS F 69 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS F 69 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR F 121 " --> pdb=" O TRP F 67 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP F 67 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN F 123 " --> pdb=" O TYR F 65 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR F 65 " --> pdb=" O GLN F 123 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE F 125 " --> pdb=" O PHE F 63 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N PHE F 63 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA F 83 " --> pdb=" O PHE F 63 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR F 65 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLY F 81 " --> pdb=" O TYR F 65 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP F 67 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 149 through 151 Processing sheet with id=AC3, first strand: chain 'F' and resid 183 through 184 removed outlier: 4.382A pdb=" N ILE F 217 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN F 224 " --> pdb=" O ILE F 217 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 738 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: 1.84 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1843 1.32 - 1.44: 2805 1.44 - 1.57: 5896 1.57 - 1.69: 1 1.69 - 1.81: 24 Bond restraints: 10569 Sorted by residual: bond pdb=" C7 NAG E 506 " pdb=" N2 NAG E 506 " ideal model delta sigma weight residual 1.346 1.468 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C7 NAG D 501 " pdb=" N2 NAG D 501 " ideal model delta sigma weight residual 1.346 1.468 -0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C7 NAG E 504 " pdb=" N2 NAG E 504 " ideal model delta sigma weight residual 1.346 1.466 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C7 NAG F 502 " pdb=" N2 NAG F 502 " ideal model delta sigma weight residual 1.346 1.465 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C7 NAG D 502 " pdb=" N2 NAG D 502 " ideal model delta sigma weight residual 1.346 1.465 -0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 10564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 13965 2.27 - 4.55: 298 4.55 - 6.82: 86 6.82 - 9.10: 6 9.10 - 11.37: 3 Bond angle restraints: 14358 Sorted by residual: angle pdb=" CA LYS E 146 " pdb=" CB LYS E 146 " pdb=" CG LYS E 146 " ideal model delta sigma weight residual 114.10 124.67 -10.57 2.00e+00 2.50e-01 2.79e+01 angle pdb=" CA LYS F 146 " pdb=" CB LYS F 146 " pdb=" CG LYS F 146 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 angle pdb=" C ASN E 224 " pdb=" CA ASN E 224 " pdb=" CB ASN E 224 " ideal model delta sigma weight residual 110.43 116.89 -6.46 1.68e+00 3.54e-01 1.48e+01 angle pdb=" C CYS D 167 " pdb=" N GLU D 168 " pdb=" CA GLU D 168 " ideal model delta sigma weight residual 120.09 124.87 -4.78 1.25e+00 6.40e-01 1.46e+01 angle pdb=" C CYS E 167 " pdb=" N GLU E 168 " pdb=" CA GLU E 168 " ideal model delta sigma weight residual 120.09 124.32 -4.23 1.25e+00 6.40e-01 1.15e+01 ... (remaining 14353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.39: 5640 18.39 - 36.77: 625 36.77 - 55.16: 149 55.16 - 73.54: 33 73.54 - 91.93: 21 Dihedral angle restraints: 6468 sinusoidal: 2658 harmonic: 3810 Sorted by residual: dihedral pdb=" CB CYS D 167 " pdb=" SG CYS D 167 " pdb=" SG CYS D 215 " pdb=" CB CYS D 215 " ideal model delta sinusoidal sigma weight residual -86.00 -176.27 90.27 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS E 167 " pdb=" SG CYS E 167 " pdb=" SG CYS E 215 " pdb=" CB CYS E 215 " ideal model delta sinusoidal sigma weight residual -86.00 -172.74 86.74 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CA ASN E 224 " pdb=" C ASN E 224 " pdb=" N ARG E 225 " pdb=" CA ARG E 225 " ideal model delta harmonic sigma weight residual 180.00 -144.08 -35.92 0 5.00e+00 4.00e-02 5.16e+01 ... (remaining 6465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1466 0.091 - 0.181: 150 0.181 - 0.272: 15 0.272 - 0.363: 1 0.363 - 0.453: 3 Chirality restraints: 1635 Sorted by residual: chirality pdb=" C1 NAG F 505 " pdb=" ND2 ASN F 152 " pdb=" C2 NAG F 505 " pdb=" O5 NAG F 505 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.14e+00 chirality pdb=" C1 NAG F 506 " pdb=" ND2 ASN F 224 " pdb=" C2 NAG F 506 " pdb=" O5 NAG F 506 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C1 NAG D 505 " pdb=" ND2 ASN D 152 " pdb=" C2 NAG D 505 " pdb=" O5 NAG D 505 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 1632 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 155 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO E 156 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 156 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 156 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 155 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO D 156 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 155 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO F 156 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO F 156 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 156 " -0.030 5.00e-02 4.00e+02 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 561 2.72 - 3.26: 10621 3.26 - 3.81: 17725 3.81 - 4.35: 22699 4.35 - 4.90: 38507 Nonbonded interactions: 90113 Sorted by model distance: nonbonded pdb=" O CYS F 167 " pdb=" NH1 ARG F 198 " model vdw 2.174 3.120 nonbonded pdb=" O LEU B 191 " pdb=" OG SER B 195 " model vdw 2.237 3.040 nonbonded pdb=" O LEU A 191 " pdb=" OG SER A 195 " model vdw 2.243 3.040 nonbonded pdb=" O LEU C 191 " pdb=" OG SER C 195 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR B 33 " pdb=" OD1 ASN B 47 " model vdw 2.262 3.040 ... (remaining 90108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 6.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.130 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 : 0.010 0.122 10590 Z= 0.478 Angle : 0.890 12.637 14418 Z= 0.421 Chirality : 0.056 0.453 1635 Planarity : 0.006 0.078 1908 Dihedral : 17.195 91.931 4035 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.54 % Allowed : 22.92 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.22), residues: 1335 helix: -2.42 (0.47), residues: 93 sheet: -0.40 (0.23), residues: 465 loop : -1.13 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 254 TYR 0.017 0.001 TYR F 176 PHE 0.009 0.001 PHE B 173 TRP 0.014 0.001 TRP D 179 HIS 0.001 0.000 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00956 (10569) covalent geometry : angle 0.82913 (14358) SS BOND : bond 0.00440 ( 3) SS BOND : angle 1.24172 ( 6) hydrogen bonds : bond 0.22840 ( 268) hydrogen bonds : angle 8.88851 ( 738) link_NAG-ASN : bond 0.00903 ( 18) link_NAG-ASN : angle 5.31966 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7937 (mt-10) REVERT: A 57 ASP cc_start: 0.7871 (t0) cc_final: 0.7288 (t0) REVERT: A 73 ARG cc_start: 0.8180 (mpt180) cc_final: 0.7868 (mpt90) REVERT: A 122 SER cc_start: 0.8777 (m) cc_final: 0.8515 (p) REVERT: A 198 SER cc_start: 0.8372 (t) cc_final: 0.8142 (m) REVERT: A 208 SER cc_start: 0.8148 (m) cc_final: 0.7941 (t) REVERT: A 211 LYS cc_start: 0.8075 (mttp) cc_final: 0.7807 (mttm) REVERT: A 219 ASP cc_start: 0.7928 (m-30) cc_final: 0.7697 (m-30) REVERT: A 251 ASN cc_start: 0.7072 (OUTLIER) cc_final: 0.6701 (t0) REVERT: B 30 LYS cc_start: 0.7686 (ptmm) cc_final: 0.7477 (ptmm) REVERT: B 39 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7831 (mt-10) REVERT: B 57 ASP cc_start: 0.7801 (t0) cc_final: 0.7461 (t70) REVERT: B 63 LYS cc_start: 0.7669 (ttmt) cc_final: 0.7354 (tttm) REVERT: B 122 SER cc_start: 0.8697 (m) cc_final: 0.8390 (p) REVERT: B 140 MET cc_start: 0.8313 (ttp) cc_final: 0.8086 (ttp) REVERT: B 198 SER cc_start: 0.8517 (t) cc_final: 0.8246 (p) REVERT: B 211 LYS cc_start: 0.7921 (mttp) cc_final: 0.7671 (mttm) REVERT: B 219 ASP cc_start: 0.7887 (m-30) cc_final: 0.7677 (m-30) REVERT: B 234 GLN cc_start: 0.6669 (mt0) cc_final: 0.6326 (mt0) REVERT: B 242 ASP cc_start: 0.7640 (t0) cc_final: 0.6803 (t0) REVERT: B 243 THR cc_start: 0.8019 (p) cc_final: 0.7816 (t) REVERT: C 39 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7907 (mt-10) REVERT: C 63 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7687 (tttm) REVERT: C 64 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8057 (mt-10) REVERT: C 66 SER cc_start: 0.8780 (m) cc_final: 0.8402 (p) REVERT: C 108 SER cc_start: 0.8701 (m) cc_final: 0.8344 (p) REVERT: C 122 SER cc_start: 0.8623 (m) cc_final: 0.8423 (p) REVERT: C 149 TYR cc_start: 0.8553 (m-80) cc_final: 0.8321 (m-80) REVERT: C 213 LYS cc_start: 0.7697 (mtpt) cc_final: 0.7449 (mtmm) REVERT: C 219 ASP cc_start: 0.7979 (m-30) cc_final: 0.7661 (m-30) REVERT: C 234 GLN cc_start: 0.7007 (mt0) cc_final: 0.6766 (mt0) REVERT: C 259 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6574 (ttmm) REVERT: C 263 ASP cc_start: 0.6767 (t0) cc_final: 0.6467 (t0) REVERT: D 106 SER cc_start: 0.7984 (m) cc_final: 0.7578 (p) REVERT: D 115 ASN cc_start: 0.7239 (t0) cc_final: 0.6731 (t0) REVERT: D 183 GLN cc_start: 0.5727 (tm-30) cc_final: 0.5497 (pp30) REVERT: E 99 GLU cc_start: 0.6668 (mp0) cc_final: 0.6210 (mp0) REVERT: E 115 ASN cc_start: 0.7137 (t0) cc_final: 0.6793 (t0) REVERT: E 122 LEU cc_start: 0.8127 (tp) cc_final: 0.7899 (tp) REVERT: F 106 SER cc_start: 0.7999 (m) cc_final: 0.7595 (p) outliers start: 28 outliers final: 15 residues processed: 273 average time/residue: 0.4453 time to fit residues: 133.0118 Evaluate side-chains 222 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 225 ARG Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 225 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 187 ASN C 163 ASN D 35 GLN D 57 ASN D 123 GLN D 131 ASN E 35 GLN E 114 GLN E 123 GLN E 183 GLN F 123 GLN F 131 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.143621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.104052 restraints weight = 14815.286| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.78 r_work: 0.3384 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10590 Z= 0.210 Angle : 0.730 10.150 14418 Z= 0.369 Chirality : 0.053 0.409 1635 Planarity : 0.005 0.051 1908 Dihedral : 8.010 84.674 1832 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.07 % Allowed : 21.11 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.22), residues: 1335 helix: -2.80 (0.44), residues: 93 sheet: -0.16 (0.25), residues: 414 loop : -1.17 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 72 TYR 0.026 0.002 TYR F 176 PHE 0.014 0.002 PHE A 173 TRP 0.017 0.002 TRP E 179 HIS 0.008 0.002 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00477 (10569) covalent geometry : angle 0.68293 (14358) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.10941 ( 6) hydrogen bonds : bond 0.04037 ( 268) hydrogen bonds : angle 6.00075 ( 738) link_NAG-ASN : bond 0.00762 ( 18) link_NAG-ASN : angle 4.25597 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 198 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8057 (t0) cc_final: 0.7633 (t0) REVERT: A 233 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7479 (ptp90) REVERT: A 252 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7690 (t) REVERT: B 57 ASP cc_start: 0.7969 (t0) cc_final: 0.7758 (t70) REVERT: B 209 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8463 (p) REVERT: B 235 LEU cc_start: 0.8844 (tp) cc_final: 0.8628 (tp) REVERT: B 242 ASP cc_start: 0.8325 (t0) cc_final: 0.8105 (t0) REVERT: B 263 ASP cc_start: 0.6710 (t0) cc_final: 0.6491 (t0) REVERT: C 149 TYR cc_start: 0.8917 (m-80) cc_final: 0.8660 (m-80) REVERT: C 263 ASP cc_start: 0.7221 (t0) cc_final: 0.6918 (t0) REVERT: D 87 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7708 (mt0) REVERT: D 115 ASN cc_start: 0.7891 (t0) cc_final: 0.7338 (t0) REVERT: D 183 GLN cc_start: 0.5954 (OUTLIER) cc_final: 0.5656 (pp30) REVERT: D 197 ASN cc_start: 0.6611 (OUTLIER) cc_final: 0.5731 (p0) REVERT: E 65 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: E 87 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: E 99 GLU cc_start: 0.7252 (mp0) cc_final: 0.6990 (mp0) REVERT: E 115 ASN cc_start: 0.7814 (t0) cc_final: 0.7380 (t0) outliers start: 67 outliers final: 33 residues processed: 244 average time/residue: 0.4428 time to fit residues: 118.7022 Evaluate side-chains 225 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 ARG Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 65 TYR Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 225 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 0.0870 chunk 127 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 148 GLN B 148 GLN B 234 GLN C 47 ASN D 35 GLN D 57 ASN D 78 GLN E 78 GLN E 183 GLN F 35 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.141469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.102158 restraints weight = 14729.649| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.76 r_work: 0.3365 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10590 Z= 0.255 Angle : 0.700 11.077 14418 Z= 0.357 Chirality : 0.053 0.365 1635 Planarity : 0.005 0.052 1908 Dihedral : 7.452 73.003 1818 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.25 % Allowed : 20.92 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.22), residues: 1335 helix: -3.06 (0.40), residues: 99 sheet: -0.37 (0.24), residues: 444 loop : -1.21 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 72 TYR 0.017 0.002 TYR F 176 PHE 0.015 0.002 PHE A 173 TRP 0.019 0.002 TRP B 269 HIS 0.009 0.002 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00592 (10569) covalent geometry : angle 0.67043 (14358) SS BOND : bond 0.00362 ( 3) SS BOND : angle 1.11362 ( 6) hydrogen bonds : bond 0.04051 ( 268) hydrogen bonds : angle 5.48985 ( 738) link_NAG-ASN : bond 0.00490 ( 18) link_NAG-ASN : angle 3.36103 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 188 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8058 (t0) cc_final: 0.7660 (t0) REVERT: A 233 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7427 (ptp90) REVERT: A 243 THR cc_start: 0.8659 (t) cc_final: 0.8442 (m) REVERT: B 235 LEU cc_start: 0.8868 (tp) cc_final: 0.8633 (tp) REVERT: B 242 ASP cc_start: 0.8254 (t0) cc_final: 0.8045 (t0) REVERT: B 263 ASP cc_start: 0.6760 (t0) cc_final: 0.6346 (t0) REVERT: C 29 ILE cc_start: 0.8148 (tp) cc_final: 0.7941 (tp) REVERT: C 187 ASN cc_start: 0.8482 (m-40) cc_final: 0.8240 (m-40) REVERT: C 263 ASP cc_start: 0.7101 (t0) cc_final: 0.6725 (t0) REVERT: C 273 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7569 (mp) REVERT: D 41 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7662 (mmm) REVERT: D 87 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: D 115 ASN cc_start: 0.7883 (t0) cc_final: 0.7290 (t0) REVERT: D 217 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7044 (pp) REVERT: E 55 VAL cc_start: 0.8561 (t) cc_final: 0.8329 (t) REVERT: E 65 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: E 87 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: E 99 GLU cc_start: 0.7222 (mp0) cc_final: 0.6988 (mp0) REVERT: E 135 THR cc_start: 0.8248 (t) cc_final: 0.7978 (m) REVERT: E 198 ARG cc_start: 0.6176 (OUTLIER) cc_final: 0.5828 (ttm170) REVERT: F 44 ASN cc_start: 0.8421 (m-40) cc_final: 0.8110 (m-40) REVERT: F 87 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: F 221 VAL cc_start: 0.8328 (p) cc_final: 0.8076 (t) outliers start: 69 outliers final: 41 residues processed: 236 average time/residue: 0.3957 time to fit residues: 103.5287 Evaluate side-chains 222 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 65 TYR Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 225 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 2.9990 chunk 57 optimal weight: 0.0270 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 148 GLN C 44 ASN C 148 GLN C 234 GLN D 35 GLN D 57 ASN D 183 GLN E 183 GLN F 35 GLN F 78 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.142275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.102938 restraints weight = 14748.866| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.76 r_work: 0.3373 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10590 Z= 0.204 Angle : 0.663 10.471 14418 Z= 0.337 Chirality : 0.052 0.358 1635 Planarity : 0.004 0.052 1908 Dihedral : 6.949 53.924 1813 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.70 % Allowed : 20.74 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.22), residues: 1335 helix: -2.97 (0.39), residues: 99 sheet: -0.53 (0.23), residues: 474 loop : -1.15 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.013 0.001 TYR F 176 PHE 0.013 0.002 PHE A 173 TRP 0.009 0.001 TRP B 269 HIS 0.006 0.002 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00472 (10569) covalent geometry : angle 0.63100 (14358) SS BOND : bond 0.00344 ( 3) SS BOND : angle 1.16657 ( 6) hydrogen bonds : bond 0.03439 ( 268) hydrogen bonds : angle 5.24736 ( 738) link_NAG-ASN : bond 0.00458 ( 18) link_NAG-ASN : angle 3.36689 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 177 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8059 (t0) cc_final: 0.7655 (t0) REVERT: A 233 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7442 (ptp90) REVERT: B 235 LEU cc_start: 0.8855 (tp) cc_final: 0.8591 (tp) REVERT: B 263 ASP cc_start: 0.6794 (t0) cc_final: 0.6339 (t0) REVERT: C 263 ASP cc_start: 0.7195 (t0) cc_final: 0.6780 (t0) REVERT: D 41 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7626 (mmm) REVERT: D 87 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: D 115 ASN cc_start: 0.7884 (t0) cc_final: 0.7307 (t0) REVERT: D 217 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7077 (pp) REVERT: E 55 VAL cc_start: 0.8587 (t) cc_final: 0.8360 (t) REVERT: E 65 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: E 87 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7769 (mt0) REVERT: E 198 ARG cc_start: 0.6182 (OUTLIER) cc_final: 0.5834 (ttm170) REVERT: F 87 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: F 197 ASN cc_start: 0.7241 (OUTLIER) cc_final: 0.5467 (m-40) REVERT: F 221 VAL cc_start: 0.8352 (p) cc_final: 0.7918 (t) outliers start: 74 outliers final: 46 residues processed: 227 average time/residue: 0.3893 time to fit residues: 97.6737 Evaluate side-chains 230 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 65 TYR Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 225 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 148 GLN B 187 ASN C 186 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN D 57 ASN D 183 GLN E 57 ASN E 183 GLN F 35 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.141604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.102168 restraints weight = 14698.786| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.77 r_work: 0.3367 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10590 Z= 0.251 Angle : 0.669 8.951 14418 Z= 0.344 Chirality : 0.053 0.343 1635 Planarity : 0.004 0.053 1908 Dihedral : 6.791 53.974 1813 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 7.34 % Allowed : 21.11 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.22), residues: 1335 helix: -2.83 (0.40), residues: 99 sheet: -0.47 (0.23), residues: 444 loop : -1.27 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 225 TYR 0.013 0.001 TYR F 176 PHE 0.015 0.002 PHE A 173 TRP 0.014 0.002 TRP B 269 HIS 0.008 0.002 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00587 (10569) covalent geometry : angle 0.63876 (14358) SS BOND : bond 0.00317 ( 3) SS BOND : angle 1.14910 ( 6) hydrogen bonds : bond 0.03577 ( 268) hydrogen bonds : angle 5.19437 ( 738) link_NAG-ASN : bond 0.00431 ( 18) link_NAG-ASN : angle 3.30236 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 180 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8065 (t0) cc_final: 0.7683 (t0) REVERT: A 233 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7443 (ptp90) REVERT: B 235 LEU cc_start: 0.8864 (tp) cc_final: 0.8612 (tp) REVERT: B 263 ASP cc_start: 0.6831 (t0) cc_final: 0.6415 (t0) REVERT: B 272 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8282 (ttpp) REVERT: C 263 ASP cc_start: 0.7213 (t0) cc_final: 0.6806 (t0) REVERT: D 41 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7632 (mmm) REVERT: D 76 ASN cc_start: 0.7980 (m-40) cc_final: 0.7739 (m-40) REVERT: D 87 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: D 99 GLU cc_start: 0.6995 (mp0) cc_final: 0.6661 (mp0) REVERT: D 115 ASN cc_start: 0.7833 (t0) cc_final: 0.7446 (t0) REVERT: D 133 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7457 (mt-10) REVERT: D 217 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7181 (pp) REVERT: D 221 VAL cc_start: 0.8183 (t) cc_final: 0.7944 (t) REVERT: E 55 VAL cc_start: 0.8608 (t) cc_final: 0.8398 (t) REVERT: E 60 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7156 (mm-40) REVERT: E 65 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: E 87 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7783 (mt0) REVERT: E 198 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5902 (ttm170) REVERT: F 44 ASN cc_start: 0.8499 (m-40) cc_final: 0.8176 (m-40) REVERT: F 87 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7681 (mt0) REVERT: F 131 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.8009 (m-40) REVERT: F 198 ARG cc_start: 0.5523 (OUTLIER) cc_final: 0.5020 (ptp-110) REVERT: F 221 VAL cc_start: 0.8210 (p) cc_final: 0.8004 (t) REVERT: F 225 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5594 (tpp-160) outliers start: 81 outliers final: 52 residues processed: 233 average time/residue: 0.4243 time to fit residues: 108.6974 Evaluate side-chains 259 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 196 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 65 TYR Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 225 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 97 optimal weight: 0.0270 chunk 123 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN D 35 GLN D 57 ASN D 183 GLN E 57 ASN E 183 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.142653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.103298 restraints weight = 14737.282| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.77 r_work: 0.3383 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10590 Z= 0.168 Angle : 0.629 7.269 14418 Z= 0.324 Chirality : 0.051 0.333 1635 Planarity : 0.004 0.054 1908 Dihedral : 6.649 54.926 1813 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.88 % Allowed : 22.10 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.22), residues: 1335 helix: -2.59 (0.41), residues: 99 sheet: -0.47 (0.23), residues: 444 loop : -1.24 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 225 TYR 0.011 0.001 TYR F 176 PHE 0.012 0.001 PHE A 173 TRP 0.008 0.001 TRP B 269 HIS 0.004 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00389 (10569) covalent geometry : angle 0.59991 (14358) SS BOND : bond 0.00323 ( 3) SS BOND : angle 1.16329 ( 6) hydrogen bonds : bond 0.03060 ( 268) hydrogen bonds : angle 5.08086 ( 738) link_NAG-ASN : bond 0.00488 ( 18) link_NAG-ASN : angle 3.13326 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 198 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8045 (t0) cc_final: 0.7669 (t0) REVERT: A 233 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7449 (ptp90) REVERT: A 263 ASP cc_start: 0.7123 (t0) cc_final: 0.6660 (t0) REVERT: B 57 ASP cc_start: 0.7855 (t0) cc_final: 0.7489 (t0) REVERT: B 235 LEU cc_start: 0.8823 (tp) cc_final: 0.8586 (tp) REVERT: B 242 ASP cc_start: 0.8194 (t0) cc_final: 0.7902 (t0) REVERT: B 263 ASP cc_start: 0.6834 (t0) cc_final: 0.6388 (t0) REVERT: B 272 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8291 (ttpp) REVERT: C 263 ASP cc_start: 0.7221 (t0) cc_final: 0.6832 (t0) REVERT: D 41 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7592 (mmm) REVERT: D 76 ASN cc_start: 0.7962 (m-40) cc_final: 0.7746 (m-40) REVERT: D 87 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: D 99 GLU cc_start: 0.7013 (mp0) cc_final: 0.6677 (mp0) REVERT: D 115 ASN cc_start: 0.7771 (t0) cc_final: 0.7366 (t0) REVERT: D 133 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7428 (mt-10) REVERT: D 221 VAL cc_start: 0.8139 (t) cc_final: 0.7903 (t) REVERT: E 55 VAL cc_start: 0.8605 (t) cc_final: 0.8393 (t) REVERT: E 60 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7090 (mm-40) REVERT: E 65 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.6966 (m-80) REVERT: E 87 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: E 100 THR cc_start: 0.8393 (p) cc_final: 0.8139 (t) REVERT: E 135 THR cc_start: 0.8249 (t) cc_final: 0.7943 (m) REVERT: E 198 ARG cc_start: 0.6257 (OUTLIER) cc_final: 0.5834 (ttm170) REVERT: F 44 ASN cc_start: 0.8530 (m-40) cc_final: 0.8185 (m-40) REVERT: F 129 LEU cc_start: 0.8426 (mp) cc_final: 0.8193 (mp) REVERT: F 131 ASN cc_start: 0.8173 (m-40) cc_final: 0.7944 (m-40) REVERT: F 135 THR cc_start: 0.8351 (t) cc_final: 0.8010 (p) REVERT: F 198 ARG cc_start: 0.5489 (OUTLIER) cc_final: 0.5019 (ptp-110) REVERT: F 225 ARG cc_start: 0.6059 (OUTLIER) cc_final: 0.5537 (tpp-160) outliers start: 76 outliers final: 56 residues processed: 241 average time/residue: 0.3907 time to fit residues: 104.1993 Evaluate side-chains 259 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 65 TYR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 225 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 148 GLN D 35 GLN D 57 ASN D 183 GLN E 57 ASN E 183 GLN F 155 ASN F 232 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.142121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.102799 restraints weight = 14564.525| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.76 r_work: 0.3377 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10590 Z= 0.205 Angle : 0.640 7.166 14418 Z= 0.331 Chirality : 0.051 0.316 1635 Planarity : 0.004 0.054 1908 Dihedral : 6.550 56.467 1813 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 7.16 % Allowed : 22.74 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.22), residues: 1335 helix: -2.60 (0.41), residues: 99 sheet: -0.46 (0.23), residues: 444 loop : -1.26 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 225 TYR 0.011 0.001 TYR F 176 PHE 0.013 0.002 PHE A 173 TRP 0.011 0.001 TRP B 269 HIS 0.006 0.002 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00480 (10569) covalent geometry : angle 0.61373 (14358) SS BOND : bond 0.00330 ( 3) SS BOND : angle 1.08270 ( 6) hydrogen bonds : bond 0.03198 ( 268) hydrogen bonds : angle 5.06850 ( 738) link_NAG-ASN : bond 0.00451 ( 18) link_NAG-ASN : angle 3.03689 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 190 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8054 (t0) cc_final: 0.7665 (t0) REVERT: A 233 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7451 (ptp90) REVERT: A 263 ASP cc_start: 0.7136 (t0) cc_final: 0.6550 (t0) REVERT: B 235 LEU cc_start: 0.8841 (tp) cc_final: 0.8590 (tp) REVERT: B 242 ASP cc_start: 0.8206 (t0) cc_final: 0.7901 (t0) REVERT: B 263 ASP cc_start: 0.6839 (t0) cc_final: 0.6369 (t0) REVERT: C 263 ASP cc_start: 0.7216 (t0) cc_final: 0.6825 (t0) REVERT: D 41 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7611 (mmm) REVERT: D 87 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: D 99 GLU cc_start: 0.7017 (mp0) cc_final: 0.6685 (mp0) REVERT: D 115 ASN cc_start: 0.7769 (t0) cc_final: 0.7367 (t0) REVERT: D 133 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7394 (mm-30) REVERT: D 221 VAL cc_start: 0.8104 (t) cc_final: 0.7866 (t) REVERT: E 55 VAL cc_start: 0.8608 (t) cc_final: 0.8397 (t) REVERT: E 60 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7104 (mm-40) REVERT: E 65 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: E 87 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: E 100 THR cc_start: 0.8397 (p) cc_final: 0.8146 (t) REVERT: E 135 THR cc_start: 0.8255 (t) cc_final: 0.7948 (m) REVERT: E 198 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5894 (ttm170) REVERT: F 44 ASN cc_start: 0.8536 (m-40) cc_final: 0.8183 (m-40) REVERT: F 87 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7737 (mt0) REVERT: F 131 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7976 (m-40) REVERT: F 135 THR cc_start: 0.8338 (t) cc_final: 0.7994 (p) REVERT: F 198 ARG cc_start: 0.5563 (OUTLIER) cc_final: 0.5110 (ptp-110) outliers start: 79 outliers final: 56 residues processed: 237 average time/residue: 0.3936 time to fit residues: 102.8982 Evaluate side-chains 256 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 191 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 65 TYR Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 225 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 127 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 124 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN D 35 GLN D 183 GLN E 57 ASN E 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.141392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.101913 restraints weight = 14542.358| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.80 r_work: 0.3379 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10590 Z= 0.199 Angle : 0.628 7.406 14418 Z= 0.326 Chirality : 0.051 0.307 1635 Planarity : 0.004 0.054 1908 Dihedral : 6.509 57.223 1813 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.79 % Allowed : 23.28 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.22), residues: 1335 helix: -2.56 (0.40), residues: 99 sheet: -0.44 (0.23), residues: 453 loop : -1.21 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 225 TYR 0.011 0.001 TYR F 176 PHE 0.013 0.002 PHE A 173 TRP 0.010 0.001 TRP B 269 HIS 0.005 0.002 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00462 (10569) covalent geometry : angle 0.60130 (14358) SS BOND : bond 0.00298 ( 3) SS BOND : angle 1.13731 ( 6) hydrogen bonds : bond 0.03154 ( 268) hydrogen bonds : angle 5.03271 ( 738) link_NAG-ASN : bond 0.00452 ( 18) link_NAG-ASN : angle 2.98867 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 191 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8060 (t0) cc_final: 0.7681 (t0) REVERT: A 233 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7445 (ptp90) REVERT: A 263 ASP cc_start: 0.7208 (t0) cc_final: 0.6712 (t0) REVERT: B 235 LEU cc_start: 0.8830 (tp) cc_final: 0.8579 (tp) REVERT: B 242 ASP cc_start: 0.8208 (t0) cc_final: 0.7891 (t0) REVERT: B 263 ASP cc_start: 0.6856 (t0) cc_final: 0.6389 (t0) REVERT: C 263 ASP cc_start: 0.7228 (t0) cc_final: 0.6825 (t0) REVERT: D 41 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7593 (mmm) REVERT: D 87 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: D 99 GLU cc_start: 0.6993 (mp0) cc_final: 0.6650 (mp0) REVERT: D 115 ASN cc_start: 0.7732 (t0) cc_final: 0.7330 (t0) REVERT: D 133 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7388 (mm-30) REVERT: D 221 VAL cc_start: 0.8075 (t) cc_final: 0.7839 (t) REVERT: E 55 VAL cc_start: 0.8613 (t) cc_final: 0.8408 (t) REVERT: E 60 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7087 (mm-40) REVERT: E 65 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: E 87 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: E 100 THR cc_start: 0.8395 (p) cc_final: 0.8168 (t) REVERT: E 135 THR cc_start: 0.8252 (t) cc_final: 0.7958 (m) REVERT: E 198 ARG cc_start: 0.6262 (OUTLIER) cc_final: 0.5887 (ttm170) REVERT: F 44 ASN cc_start: 0.8534 (m-40) cc_final: 0.8175 (m-40) REVERT: F 87 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: F 131 ASN cc_start: 0.8231 (m-40) cc_final: 0.7972 (m-40) REVERT: F 135 THR cc_start: 0.8335 (t) cc_final: 0.7995 (p) REVERT: F 198 ARG cc_start: 0.5591 (OUTLIER) cc_final: 0.5162 (ptp-110) outliers start: 75 outliers final: 59 residues processed: 233 average time/residue: 0.3920 time to fit residues: 101.0486 Evaluate side-chains 262 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 195 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 65 TYR Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 225 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 148 GLN D 35 GLN D 183 GLN E 57 ASN E 218 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.140342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.101084 restraints weight = 14627.100| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.76 r_work: 0.3349 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 10590 Z= 0.348 Angle : 0.713 9.290 14418 Z= 0.371 Chirality : 0.055 0.293 1635 Planarity : 0.004 0.057 1908 Dihedral : 6.734 56.947 1813 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 6.79 % Allowed : 23.55 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.21), residues: 1335 helix: -2.72 (0.39), residues: 99 sheet: -0.43 (0.23), residues: 423 loop : -1.45 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 225 TYR 0.015 0.002 TYR F 176 PHE 0.017 0.002 PHE A 173 TRP 0.019 0.002 TRP B 269 HIS 0.010 0.003 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00819 (10569) covalent geometry : angle 0.69062 (14358) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.94176 ( 6) hydrogen bonds : bond 0.03983 ( 268) hydrogen bonds : angle 5.30068 ( 738) link_NAG-ASN : bond 0.00405 ( 18) link_NAG-ASN : angle 2.97683 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7425 (ptp90) REVERT: A 263 ASP cc_start: 0.7219 (t0) cc_final: 0.6737 (t0) REVERT: B 235 LEU cc_start: 0.8890 (tp) cc_final: 0.8639 (tp) REVERT: C 263 ASP cc_start: 0.7205 (t0) cc_final: 0.6790 (t0) REVERT: D 41 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7662 (mmm) REVERT: D 87 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: D 99 GLU cc_start: 0.6947 (mp0) cc_final: 0.6687 (mp0) REVERT: D 133 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7439 (mt-10) REVERT: E 60 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7203 (mm-40) REVERT: E 65 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7141 (m-80) REVERT: E 87 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: E 100 THR cc_start: 0.8436 (p) cc_final: 0.8183 (t) REVERT: E 135 THR cc_start: 0.8292 (t) cc_final: 0.8007 (m) REVERT: F 44 ASN cc_start: 0.8569 (m-40) cc_final: 0.8275 (m-40) REVERT: F 87 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: F 131 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8026 (m-40) REVERT: F 135 THR cc_start: 0.8351 (t) cc_final: 0.8044 (p) REVERT: F 198 ARG cc_start: 0.5745 (OUTLIER) cc_final: 0.5269 (ptp-110) REVERT: F 225 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.6129 (ttp-170) outliers start: 75 outliers final: 57 residues processed: 238 average time/residue: 0.4185 time to fit residues: 109.6466 Evaluate side-chains 257 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 191 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 65 TYR Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 225 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 131 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN D 35 GLN D 137 GLN D 183 GLN E 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.140851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.101534 restraints weight = 14448.628| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.78 r_work: 0.3373 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10590 Z= 0.214 Angle : 0.668 10.894 14418 Z= 0.341 Chirality : 0.052 0.293 1635 Planarity : 0.004 0.058 1908 Dihedral : 6.786 58.454 1813 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.25 % Allowed : 24.09 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.21), residues: 1335 helix: -2.53 (0.41), residues: 99 sheet: -0.42 (0.23), residues: 426 loop : -1.45 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 225 TYR 0.013 0.001 TYR C 149 PHE 0.015 0.002 PHE A 173 TRP 0.010 0.001 TRP B 269 HIS 0.006 0.002 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00501 (10569) covalent geometry : angle 0.63369 (14358) SS BOND : bond 0.00302 ( 3) SS BOND : angle 1.11687 ( 6) hydrogen bonds : bond 0.03298 ( 268) hydrogen bonds : angle 5.16742 ( 738) link_NAG-ASN : bond 0.00658 ( 18) link_NAG-ASN : angle 3.51831 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 191 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7423 (ptp90) REVERT: A 263 ASP cc_start: 0.7237 (t0) cc_final: 0.6758 (t0) REVERT: B 235 LEU cc_start: 0.8837 (tp) cc_final: 0.8579 (tp) REVERT: B 242 ASP cc_start: 0.8194 (t0) cc_final: 0.7945 (t0) REVERT: C 263 ASP cc_start: 0.7218 (t0) cc_final: 0.6807 (t0) REVERT: D 41 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7652 (mmm) REVERT: D 87 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: D 99 GLU cc_start: 0.6975 (mp0) cc_final: 0.6677 (mp0) REVERT: D 133 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7411 (mm-30) REVERT: D 221 VAL cc_start: 0.8073 (t) cc_final: 0.7850 (t) REVERT: E 60 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7201 (mm-40) REVERT: E 65 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7061 (m-80) REVERT: E 87 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: E 100 THR cc_start: 0.8385 (p) cc_final: 0.8167 (t) REVERT: E 135 THR cc_start: 0.8272 (t) cc_final: 0.7983 (m) REVERT: F 44 ASN cc_start: 0.8544 (m-40) cc_final: 0.8236 (m-40) REVERT: F 87 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: F 131 ASN cc_start: 0.8269 (m-40) cc_final: 0.8006 (m-40) REVERT: F 135 THR cc_start: 0.8334 (t) cc_final: 0.8017 (p) REVERT: F 198 ARG cc_start: 0.5673 (OUTLIER) cc_final: 0.5270 (ptp-170) REVERT: F 225 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.6032 (ttp-170) outliers start: 69 outliers final: 57 residues processed: 232 average time/residue: 0.4375 time to fit residues: 111.4581 Evaluate side-chains 256 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 191 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 ARG Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 65 TYR Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 225 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 94 optimal weight: 0.0060 chunk 18 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN D 35 GLN D 137 GLN D 181 ASN E 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.140239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101132 restraints weight = 14507.933| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.79 r_work: 0.3361 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10590 Z= 0.211 Angle : 0.657 11.550 14418 Z= 0.337 Chirality : 0.051 0.286 1635 Planarity : 0.004 0.058 1908 Dihedral : 6.550 58.024 1813 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 6.16 % Allowed : 24.46 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.21), residues: 1335 helix: -2.46 (0.41), residues: 99 sheet: -0.41 (0.23), residues: 426 loop : -1.44 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 225 TYR 0.011 0.001 TYR C 149 PHE 0.015 0.002 PHE A 173 TRP 0.009 0.001 TRP B 269 HIS 0.006 0.002 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00494 (10569) covalent geometry : angle 0.62022 (14358) SS BOND : bond 0.00396 ( 3) SS BOND : angle 1.07954 ( 6) hydrogen bonds : bond 0.03243 ( 268) hydrogen bonds : angle 5.12511 ( 738) link_NAG-ASN : bond 0.00518 ( 18) link_NAG-ASN : angle 3.60569 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6947.29 seconds wall clock time: 118 minutes 34.12 seconds (7114.12 seconds total)