Starting phenix.real_space_refine on Tue May 13 11:38:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gh5_51347/05_2025/9gh5_51347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gh5_51347/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gh5_51347/05_2025/9gh5_51347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gh5_51347/05_2025/9gh5_51347.map" model { file = "/net/cci-nas-00/data/ceres_data/9gh5_51347/05_2025/9gh5_51347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gh5_51347/05_2025/9gh5_51347.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.41, per 1000 atoms: 0.71 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: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.55 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: 3.39 Time building geometry restraints manager: 2.95 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: 0.02 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: 3.830 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: 0.620 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.630 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (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 TRP 0.014 0.001 TRP D 179 HIS 0.001 0.000 HIS D 139 PHE 0.009 0.001 PHE B 173 TYR 0.017 0.001 TYR F 176 ARG 0.013 0.001 ARG B 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00903 ( 18) link_NAG-ASN : angle 5.31966 ( 54) hydrogen bonds : bond 0.22840 ( 268) hydrogen bonds : angle 8.88851 ( 738) SS BOND : bond 0.00440 ( 3) SS BOND : angle 1.24172 ( 6) covalent geometry : bond 0.00956 (10569) covalent geometry : angle 0.82913 (14358) *********************** 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 : 1.006 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: 0.9668 time to fit residues: 288.6863 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 : 1.080 ------------------------------------------------------------------------------- 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 111 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.142734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103279 restraints weight = 14750.923| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.77 r_work: 0.3370 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10590 Z= 0.282 Angle : 0.760 10.190 14418 Z= 0.387 Chirality : 0.056 0.401 1635 Planarity : 0.005 0.048 1908 Dihedral : 8.183 88.931 1832 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.98 % Allowed : 20.92 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.22), residues: 1335 helix: -2.92 (0.43), residues: 93 sheet: -0.33 (0.23), residues: 465 loop : -1.24 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 269 HIS 0.011 0.003 HIS C 180 PHE 0.017 0.002 PHE A 173 TYR 0.027 0.002 TYR F 176 ARG 0.005 0.001 ARG F 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 18) link_NAG-ASN : angle 4.03925 ( 54) hydrogen bonds : bond 0.04476 ( 268) hydrogen bonds : angle 5.97033 ( 738) SS BOND : bond 0.00371 ( 3) SS BOND : angle 1.09582 ( 6) covalent geometry : bond 0.00649 (10569) covalent geometry : angle 0.72027 (14358) *********************** 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 273 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 207 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8047 (t0) cc_final: 0.7609 (t0) REVERT: A 233 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7459 (ptp90) REVERT: B 57 ASP cc_start: 0.7974 (t0) cc_final: 0.7746 (t70) REVERT: B 209 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8461 (p) REVERT: B 227 SER cc_start: 0.8502 (p) cc_final: 0.8285 (m) REVERT: B 235 LEU cc_start: 0.8877 (tp) cc_final: 0.8650 (tp) REVERT: B 242 ASP cc_start: 0.8290 (t0) cc_final: 0.8021 (t0) REVERT: B 263 ASP cc_start: 0.6724 (t0) cc_final: 0.6415 (t0) REVERT: C 187 ASN cc_start: 0.8486 (m-40) cc_final: 0.8262 (m-40) REVERT: C 252 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7790 (t) REVERT: C 263 ASP cc_start: 0.7112 (t0) cc_final: 0.6774 (t0) REVERT: D 87 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: D 115 ASN cc_start: 0.7908 (t0) cc_final: 0.7329 (t0) REVERT: D 197 ASN cc_start: 0.6600 (OUTLIER) cc_final: 0.5721 (p0) REVERT: E 51 VAL cc_start: 0.8653 (p) cc_final: 0.8438 (t) REVERT: E 65 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: E 87 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7743 (mt0) REVERT: E 99 GLU cc_start: 0.7241 (mp0) cc_final: 0.6995 (mp0) REVERT: E 115 ASN cc_start: 0.7957 (t0) cc_final: 0.7537 (t0) REVERT: F 44 ASN cc_start: 0.8376 (m-40) cc_final: 0.8091 (m-40) outliers start: 66 outliers final: 32 residues processed: 250 average time/residue: 0.8439 time to fit residues: 232.8239 Evaluate side-chains 225 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 61 ILE Chi-restraints excluded: chain A residue 66 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 243 THR 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 256 ASN 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 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 197 ASN Chi-restraints excluded: chain D residue 205 VAL 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 112 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 65 TYR 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 96 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 28 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN B 148 GLN D 35 GLN D 57 ASN D 78 GLN D 114 GLN D 183 GLN E 35 GLN E 78 GLN ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.143121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.103591 restraints weight = 14813.476| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.78 r_work: 0.3383 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10590 Z= 0.173 Angle : 0.669 11.123 14418 Z= 0.340 Chirality : 0.052 0.374 1635 Planarity : 0.004 0.051 1908 Dihedral : 7.438 75.708 1815 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.53 % Allowed : 22.28 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.22), residues: 1335 helix: -2.83 (0.43), residues: 93 sheet: -0.37 (0.24), residues: 444 loop : -1.19 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 269 HIS 0.006 0.001 HIS C 180 PHE 0.013 0.001 PHE A 173 TYR 0.016 0.001 TYR F 176 ARG 0.004 0.000 ARG F 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 18) link_NAG-ASN : angle 3.44464 ( 54) hydrogen bonds : bond 0.03467 ( 268) hydrogen bonds : angle 5.42939 ( 738) SS BOND : bond 0.00374 ( 3) SS BOND : angle 1.16789 ( 6) covalent geometry : bond 0.00394 (10569) covalent geometry : angle 0.63527 (14358) *********************** 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 239 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8017 (t0) cc_final: 0.7645 (t0) REVERT: A 233 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7446 (ptp90) REVERT: A 243 THR cc_start: 0.8711 (t) cc_final: 0.8443 (m) REVERT: B 235 LEU cc_start: 0.8829 (tp) cc_final: 0.8610 (tp) REVERT: B 263 ASP cc_start: 0.6788 (t0) cc_final: 0.6337 (t0) REVERT: C 29 ILE cc_start: 0.8109 (tp) cc_final: 0.7906 (tp) REVERT: C 263 ASP cc_start: 0.7124 (t0) cc_final: 0.6756 (t0) REVERT: C 273 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7502 (mp) REVERT: D 41 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7642 (mmm) REVERT: D 55 VAL cc_start: 0.8601 (t) cc_final: 0.8401 (t) REVERT: D 87 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: D 115 ASN cc_start: 0.7862 (t0) cc_final: 0.7377 (t0) REVERT: D 217 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7041 (pp) REVERT: E 55 VAL cc_start: 0.8544 (t) cc_final: 0.8311 (t) REVERT: E 65 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: E 87 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: E 99 GLU cc_start: 0.7215 (mp0) cc_final: 0.7010 (mp0) REVERT: F 87 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: F 197 ASN cc_start: 0.6978 (OUTLIER) cc_final: 0.5449 (m-40) outliers start: 61 outliers final: 36 residues processed: 221 average time/residue: 0.8283 time to fit residues: 202.2737 Evaluate side-chains 218 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 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 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 128 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 230 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 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 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 112 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 197 ASN 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 110 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 39 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 44 ASN C 47 ASN C 148 GLN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.141388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102094 restraints weight = 14593.857| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.76 r_work: 0.3364 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10590 Z= 0.264 Angle : 0.695 11.017 14418 Z= 0.354 Chirality : 0.053 0.352 1635 Planarity : 0.004 0.052 1908 Dihedral : 7.115 54.325 1815 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 7.07 % Allowed : 20.65 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.22), residues: 1335 helix: -3.04 (0.39), residues: 102 sheet: -0.52 (0.24), residues: 444 loop : -1.27 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 269 HIS 0.008 0.002 HIS C 180 PHE 0.015 0.002 PHE A 173 TYR 0.014 0.002 TYR F 176 ARG 0.003 0.000 ARG F 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 18) link_NAG-ASN : angle 3.39361 ( 54) hydrogen bonds : bond 0.03712 ( 268) hydrogen bonds : angle 5.29117 ( 738) SS BOND : bond 0.00327 ( 3) SS BOND : angle 1.14278 ( 6) covalent geometry : bond 0.00616 (10569) covalent geometry : angle 0.66378 (14358) *********************** 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 261 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 183 time to evaluate : 0.981 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: 0.8388 (OUTLIER) cc_final: 0.7439 (ptp90) REVERT: A 243 THR cc_start: 0.8721 (t) cc_final: 0.8460 (m) REVERT: B 235 LEU cc_start: 0.8848 (tp) cc_final: 0.8590 (tp) REVERT: B 242 ASP cc_start: 0.8207 (t0) cc_final: 0.7890 (t0) REVERT: B 263 ASP cc_start: 0.6846 (t0) cc_final: 0.6411 (t0) REVERT: C 233 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7486 (ptp90) REVERT: C 263 ASP cc_start: 0.7192 (t0) cc_final: 0.6772 (t0) REVERT: D 41 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7647 (mmm) REVERT: D 87 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7714 (mt0) REVERT: D 99 GLU cc_start: 0.7014 (mp0) cc_final: 0.6677 (mp0) REVERT: D 115 ASN cc_start: 0.7904 (t0) cc_final: 0.7330 (t0) REVERT: D 133 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7449 (mt-10) REVERT: D 217 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7153 (pp) REVERT: E 55 VAL cc_start: 0.8602 (t) cc_final: 0.8381 (t) REVERT: E 65 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: E 87 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: F 44 ASN cc_start: 0.8507 (m-40) cc_final: 0.8209 (m-40) REVERT: F 87 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: F 131 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7978 (m-40) REVERT: F 221 VAL cc_start: 0.8192 (p) cc_final: 0.7982 (t) outliers start: 78 outliers final: 50 residues processed: 237 average time/residue: 0.8764 time to fit residues: 228.7228 Evaluate side-chains 248 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 39 GLU 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 B residue 268 LYS 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 230 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 255 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 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 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 41 MET Chi-restraints excluded: chain F residue 65 TYR Chi-restraints excluded: chain F residue 87 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 219 ASN 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 112 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 186 ASN D 35 GLN E 35 GLN F 35 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.142839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.103395 restraints weight = 14560.213| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.76 r_work: 0.3383 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10590 Z= 0.177 Angle : 0.647 9.570 14418 Z= 0.330 Chirality : 0.051 0.344 1635 Planarity : 0.004 0.052 1908 Dihedral : 6.807 53.600 1815 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 6.79 % Allowed : 21.38 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1335 helix: -2.80 (0.40), residues: 102 sheet: -0.47 (0.23), residues: 444 loop : -1.26 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 269 HIS 0.005 0.001 HIS C 180 PHE 0.013 0.001 PHE A 173 TYR 0.011 0.001 TYR F 176 ARG 0.002 0.000 ARG F 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 18) link_NAG-ASN : angle 3.36551 ( 54) hydrogen bonds : bond 0.03148 ( 268) hydrogen bonds : angle 5.13541 ( 738) SS BOND : bond 0.00342 ( 3) SS BOND : angle 1.19323 ( 6) covalent geometry : bond 0.00407 (10569) covalent geometry : angle 0.61405 (14358) *********************** 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 260 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 185 time to evaluate : 1.080 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: A 57 ASP cc_start: 0.8022 (t0) cc_final: 0.7673 (t0) REVERT: A 233 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7434 (ptp90) REVERT: A 243 THR cc_start: 0.8700 (t) cc_final: 0.8451 (m) REVERT: B 57 ASP cc_start: 0.7886 (t0) cc_final: 0.7535 (t0) REVERT: B 227 SER cc_start: 0.8467 (p) cc_final: 0.8252 (m) REVERT: B 235 LEU cc_start: 0.8815 (tp) cc_final: 0.8571 (tp) REVERT: B 242 ASP cc_start: 0.8179 (t0) cc_final: 0.7834 (t0) REVERT: B 263 ASP cc_start: 0.6878 (t0) cc_final: 0.6461 (t0) REVERT: C 149 TYR cc_start: 0.8878 (m-80) cc_final: 0.8661 (m-80) REVERT: C 263 ASP cc_start: 0.7179 (t0) cc_final: 0.6792 (t0) REVERT: D 41 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7633 (mmm) REVERT: D 76 ASN cc_start: 0.7966 (m-40) cc_final: 0.7731 (m-40) REVERT: D 87 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: D 115 ASN cc_start: 0.7796 (t0) cc_final: 0.7407 (t0) REVERT: D 133 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7436 (mt-10) REVERT: D 221 VAL cc_start: 0.8142 (t) cc_final: 0.7906 (t) REVERT: E 55 VAL cc_start: 0.8595 (t) cc_final: 0.8389 (t) REVERT: E 60 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7095 (mm-40) REVERT: E 65 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: E 87 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: F 44 ASN cc_start: 0.8533 (m-40) cc_final: 0.8210 (m-40) REVERT: F 129 LEU cc_start: 0.8446 (mp) cc_final: 0.8181 (mp) REVERT: F 198 ARG cc_start: 0.5423 (OUTLIER) cc_final: 0.4962 (ptp-110) REVERT: F 225 ARG cc_start: 0.6010 (OUTLIER) cc_final: 0.5510 (tpp-160) outliers start: 75 outliers final: 55 residues processed: 232 average time/residue: 0.8792 time to fit residues: 225.0891 Evaluate side-chains 247 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 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 39 GLU Chi-restraints excluded: chain B residue 103 ASP 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 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 D residue 225 ARG Chi-restraints excluded: chain E residue 35 GLN 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 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 65 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 125 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 D 35 GLN E 35 GLN F 155 ASN F 232 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.141368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.101705 restraints weight = 14599.536| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.82 r_work: 0.3377 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2773 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= 0.210 Angle : 0.649 8.043 14418 Z= 0.335 Chirality : 0.052 0.330 1635 Planarity : 0.004 0.054 1908 Dihedral : 6.723 55.142 1815 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.34 % Allowed : 22.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1335 helix: -2.70 (0.40), residues: 102 sheet: -0.47 (0.23), residues: 444 loop : -1.28 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 269 HIS 0.006 0.002 HIS C 180 PHE 0.013 0.002 PHE A 173 TYR 0.011 0.001 TYR F 176 ARG 0.003 0.000 ARG D 225 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 18) link_NAG-ASN : angle 3.17181 ( 54) hydrogen bonds : bond 0.03244 ( 268) hydrogen bonds : angle 5.08129 ( 738) SS BOND : bond 0.00320 ( 3) SS BOND : angle 1.11210 ( 6) covalent geometry : bond 0.00491 (10569) covalent geometry : angle 0.62008 (14358) *********************** 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 252 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 182 time to evaluate : 1.138 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: A 233 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7466 (ptp90) REVERT: A 243 THR cc_start: 0.8702 (t) cc_final: 0.8458 (m) REVERT: A 263 ASP cc_start: 0.7129 (t0) cc_final: 0.6626 (t0) REVERT: B 57 ASP cc_start: 0.7871 (t0) cc_final: 0.7509 (t0) REVERT: B 227 SER cc_start: 0.8473 (p) cc_final: 0.8266 (m) REVERT: B 235 LEU cc_start: 0.8821 (tp) cc_final: 0.8580 (tp) REVERT: B 263 ASP cc_start: 0.6868 (t0) cc_final: 0.6404 (t0) REVERT: C 263 ASP cc_start: 0.7157 (t0) cc_final: 0.6776 (t0) REVERT: D 41 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7630 (mmm) REVERT: D 76 ASN cc_start: 0.7966 (m-40) cc_final: 0.7745 (m-40) REVERT: D 87 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7709 (mt0) REVERT: D 115 ASN cc_start: 0.7767 (t0) cc_final: 0.7367 (t0) REVERT: D 133 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7415 (mt-10) REVERT: D 221 VAL cc_start: 0.8100 (t) cc_final: 0.7861 (t) REVERT: E 55 VAL cc_start: 0.8604 (t) cc_final: 0.8397 (t) REVERT: E 60 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7059 (mm-40) REVERT: E 65 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: E 87 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7796 (mt0) REVERT: F 44 ASN cc_start: 0.8533 (m-40) cc_final: 0.8220 (m-40) REVERT: F 87 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7733 (mt0) REVERT: F 198 ARG cc_start: 0.5506 (OUTLIER) cc_final: 0.5045 (ptp-110) REVERT: F 225 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.5537 (tpp-160) outliers start: 70 outliers final: 53 residues processed: 225 average time/residue: 0.8779 time to fit residues: 217.7072 Evaluate side-chains 244 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 39 GLU 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 B residue 268 LYS 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 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 35 GLN 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 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 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 41 optimal weight: 0.0770 chunk 124 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 57 ASN F 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.141371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.101786 restraints weight = 14669.310| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.82 r_work: 0.3370 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10590 Z= 0.204 Angle : 0.643 7.860 14418 Z= 0.332 Chirality : 0.051 0.317 1635 Planarity : 0.004 0.054 1908 Dihedral : 6.681 56.416 1815 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.88 % Allowed : 22.92 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.22), residues: 1335 helix: -2.58 (0.41), residues: 99 sheet: -0.46 (0.23), residues: 444 loop : -1.29 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 269 HIS 0.006 0.002 HIS C 180 PHE 0.013 0.002 PHE A 173 TYR 0.011 0.001 TYR F 176 ARG 0.002 0.000 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 18) link_NAG-ASN : angle 3.03322 ( 54) hydrogen bonds : bond 0.03205 ( 268) hydrogen bonds : angle 5.06752 ( 738) SS BOND : bond 0.00342 ( 3) SS BOND : angle 1.11213 ( 6) covalent geometry : bond 0.00476 (10569) covalent geometry : angle 0.61621 (14358) *********************** 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 259 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 183 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7465 (ptp90) REVERT: A 243 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8448 (m) REVERT: A 263 ASP cc_start: 0.7182 (t0) cc_final: 0.6679 (t0) REVERT: B 57 ASP cc_start: 0.7872 (t0) cc_final: 0.7506 (t0) REVERT: B 235 LEU cc_start: 0.8810 (tp) cc_final: 0.8585 (tp) REVERT: B 242 ASP cc_start: 0.8192 (t0) cc_final: 0.7895 (t0) REVERT: B 263 ASP cc_start: 0.6874 (t0) cc_final: 0.6402 (t0) REVERT: C 263 ASP cc_start: 0.7208 (t0) cc_final: 0.6807 (t0) REVERT: D 41 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7616 (mmm) REVERT: D 87 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: D 133 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7409 (mt-10) REVERT: D 221 VAL cc_start: 0.8089 (t) cc_final: 0.7858 (t) REVERT: E 60 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7069 (mm-40) REVERT: E 65 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: E 87 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: F 44 ASN cc_start: 0.8536 (m-40) cc_final: 0.8209 (m-40) REVERT: F 87 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: F 131 ASN cc_start: 0.8181 (m-40) cc_final: 0.7945 (m-40) REVERT: F 198 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.5123 (ptp-110) REVERT: F 225 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5570 (tpp-160) outliers start: 76 outliers final: 56 residues processed: 229 average time/residue: 0.8529 time to fit residues: 215.4432 Evaluate side-chains 248 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 183 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE 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 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 243 THR 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 39 GLU Chi-restraints excluded: chain B residue 103 ASP 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 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 35 GLN 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 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 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 218 GLN 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 78 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.141056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.101819 restraints weight = 14691.949| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.79 r_work: 0.3374 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2980 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= 0.229 Angle : 0.649 7.762 14418 Z= 0.337 Chirality : 0.052 0.301 1635 Planarity : 0.004 0.054 1908 Dihedral : 6.701 57.109 1815 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 6.52 % Allowed : 23.10 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.21), residues: 1335 helix: -2.56 (0.40), residues: 99 sheet: -0.46 (0.23), residues: 444 loop : -1.32 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 269 HIS 0.006 0.002 HIS C 180 PHE 0.014 0.002 PHE A 173 TYR 0.012 0.001 TYR F 176 ARG 0.003 0.000 ARG D 225 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 18) link_NAG-ASN : angle 2.98121 ( 54) hydrogen bonds : bond 0.03338 ( 268) hydrogen bonds : angle 5.08057 ( 738) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.97454 ( 6) covalent geometry : bond 0.00536 (10569) covalent geometry : angle 0.62393 (14358) *********************** 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 251 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 179 time to evaluate : 0.986 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: 0.8390 (OUTLIER) cc_final: 0.7455 (ptp90) REVERT: A 243 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8454 (m) REVERT: A 263 ASP cc_start: 0.7214 (t0) cc_final: 0.6719 (t0) REVERT: B 57 ASP cc_start: 0.7874 (t0) cc_final: 0.7495 (t0) REVERT: B 235 LEU cc_start: 0.8824 (tp) cc_final: 0.8606 (tp) REVERT: B 242 ASP cc_start: 0.8199 (t0) cc_final: 0.7918 (t0) REVERT: B 263 ASP cc_start: 0.6882 (t0) cc_final: 0.6403 (t0) REVERT: C 263 ASP cc_start: 0.7206 (t0) cc_final: 0.6801 (t0) REVERT: D 41 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7625 (mmm) REVERT: D 87 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: D 133 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7403 (mt-10) REVERT: D 221 VAL cc_start: 0.8073 (t) cc_final: 0.7838 (t) REVERT: E 60 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7173 (mm-40) REVERT: E 62 LEU cc_start: 0.8620 (mt) cc_final: 0.8338 (mp) REVERT: E 65 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: E 87 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: E 225 ARG cc_start: 0.5379 (OUTLIER) cc_final: 0.5125 (tpt-90) REVERT: F 44 ASN cc_start: 0.8546 (m-40) cc_final: 0.8226 (m-40) REVERT: F 87 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: F 131 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7973 (m-40) REVERT: F 198 ARG cc_start: 0.5615 (OUTLIER) cc_final: 0.5164 (ptp-110) outliers start: 72 outliers final: 55 residues processed: 222 average time/residue: 0.9250 time to fit residues: 225.7877 Evaluate side-chains 241 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 176 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE 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 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 243 THR 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 39 GLU Chi-restraints excluded: chain B residue 103 ASP 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 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 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 35 GLN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 51 optimal weight: 0.2980 chunk 81 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN C 44 ASN D 35 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.141629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.102563 restraints weight = 14617.460| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.76 r_work: 0.3378 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10590 Z= 0.154 Angle : 0.636 10.605 14418 Z= 0.326 Chirality : 0.050 0.298 1635 Planarity : 0.004 0.060 1908 Dihedral : 6.593 57.138 1815 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.16 % Allowed : 23.37 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.22), residues: 1335 helix: -2.39 (0.42), residues: 99 sheet: -0.47 (0.23), residues: 474 loop : -1.21 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 269 HIS 0.004 0.001 HIS C 180 PHE 0.012 0.001 PHE A 173 TYR 0.010 0.001 TYR F 176 ARG 0.002 0.000 ARG E 225 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 18) link_NAG-ASN : angle 3.47506 ( 54) hydrogen bonds : bond 0.02859 ( 268) hydrogen bonds : angle 4.95017 ( 738) SS BOND : bond 0.00371 ( 3) SS BOND : angle 1.09885 ( 6) covalent geometry : bond 0.00357 (10569) covalent geometry : angle 0.59979 (14358) *********************** 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 243 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 175 time to evaluate : 1.089 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: A 121 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8671 (m) REVERT: A 233 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7457 (ptp90) REVERT: A 243 THR cc_start: 0.8656 (t) cc_final: 0.8440 (m) REVERT: A 263 ASP cc_start: 0.7210 (t0) cc_final: 0.6723 (t0) REVERT: B 57 ASP cc_start: 0.7866 (t0) cc_final: 0.7483 (t0) REVERT: B 235 LEU cc_start: 0.8741 (tp) cc_final: 0.8530 (tp) REVERT: B 242 ASP cc_start: 0.8196 (t0) cc_final: 0.7896 (t0) REVERT: B 263 ASP cc_start: 0.6872 (t0) cc_final: 0.6380 (t0) REVERT: C 263 ASP cc_start: 0.7221 (t0) cc_final: 0.6807 (t0) REVERT: D 87 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: D 221 VAL cc_start: 0.7973 (t) cc_final: 0.7745 (t) REVERT: E 55 VAL cc_start: 0.8582 (t) cc_final: 0.8373 (t) REVERT: E 60 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7091 (mm-40) REVERT: E 62 LEU cc_start: 0.8548 (mt) cc_final: 0.8231 (mp) REVERT: E 65 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: E 87 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: E 100 THR cc_start: 0.8342 (p) cc_final: 0.8124 (t) REVERT: E 225 ARG cc_start: 0.5210 (OUTLIER) cc_final: 0.4938 (tpt-90) REVERT: F 44 ASN cc_start: 0.8503 (m-40) cc_final: 0.8161 (m-40) REVERT: F 87 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: F 129 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8169 (mp) REVERT: F 131 ASN cc_start: 0.8171 (m-40) cc_final: 0.7937 (m-40) REVERT: F 198 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.5139 (ptp-110) outliers start: 68 outliers final: 52 residues processed: 218 average time/residue: 0.8457 time to fit residues: 204.3270 Evaluate side-chains 233 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 172 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE 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 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 39 GLU Chi-restraints excluded: chain B residue 103 ASP 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 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 38 THR 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 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 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 129 LEU 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 65 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 97 optimal weight: 0.0170 chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 128 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN C 44 ASN D 35 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN E 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.141303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.102113 restraints weight = 14537.163| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.80 r_work: 0.3375 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10590 Z= 0.177 Angle : 0.643 12.040 14418 Z= 0.330 Chirality : 0.051 0.290 1635 Planarity : 0.004 0.057 1908 Dihedral : 6.481 57.714 1815 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.71 % Allowed : 24.09 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1335 helix: -2.18 (0.44), residues: 93 sheet: -0.44 (0.22), residues: 483 loop : -1.20 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 269 HIS 0.005 0.001 HIS B 92 PHE 0.013 0.001 PHE A 173 TYR 0.008 0.001 TYR D 65 ARG 0.004 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 18) link_NAG-ASN : angle 3.47300 ( 54) hydrogen bonds : bond 0.02996 ( 268) hydrogen bonds : angle 4.96233 ( 738) SS BOND : bond 0.00341 ( 3) SS BOND : angle 1.14200 ( 6) covalent geometry : bond 0.00414 (10569) covalent geometry : angle 0.60768 (14358) ********************** 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 251 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7499 (ptp90) REVERT: A 243 THR cc_start: 0.8637 (t) cc_final: 0.8417 (m) REVERT: A 263 ASP cc_start: 0.7239 (t0) cc_final: 0.6763 (t0) REVERT: B 57 ASP cc_start: 0.7835 (t0) cc_final: 0.7475 (t0) REVERT: B 235 LEU cc_start: 0.8766 (tp) cc_final: 0.8537 (tp) REVERT: B 242 ASP cc_start: 0.8187 (t0) cc_final: 0.7912 (t0) REVERT: B 263 ASP cc_start: 0.6893 (t0) cc_final: 0.6407 (t0) REVERT: C 263 ASP cc_start: 0.7239 (t0) cc_final: 0.6838 (t0) REVERT: D 87 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: D 221 VAL cc_start: 0.8025 (t) cc_final: 0.7789 (t) REVERT: E 55 VAL cc_start: 0.8581 (t) cc_final: 0.8364 (t) REVERT: E 60 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7072 (mm-40) REVERT: E 62 LEU cc_start: 0.8570 (mt) cc_final: 0.8265 (mp) REVERT: E 65 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: E 87 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: E 225 ARG cc_start: 0.5211 (OUTLIER) cc_final: 0.4947 (tpt-90) REVERT: F 44 ASN cc_start: 0.8530 (m-40) cc_final: 0.8210 (m-40) REVERT: F 87 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7733 (mt0) REVERT: F 129 LEU cc_start: 0.8478 (mp) cc_final: 0.8232 (mp) REVERT: F 131 ASN cc_start: 0.8184 (m-40) cc_final: 0.7955 (m-40) REVERT: F 135 THR cc_start: 0.8339 (t) cc_final: 0.8008 (m) REVERT: F 198 ARG cc_start: 0.5558 (OUTLIER) cc_final: 0.5176 (ptp-110) REVERT: F 225 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.5859 (ttp-170) outliers start: 63 outliers final: 51 residues processed: 227 average time/residue: 0.8303 time to fit residues: 208.8634 Evaluate side-chains 232 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 173 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 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 39 GLU Chi-restraints excluded: chain B residue 103 ASP 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 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 38 THR 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 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 149 ILE Chi-restraints excluded: chain E residue 183 GLN 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 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 84 optimal weight: 3.9990 chunk 97 optimal weight: 0.0370 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.140605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.101295 restraints weight = 14440.998| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.78 r_work: 0.3367 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10590 Z= 0.215 Angle : 0.662 11.632 14418 Z= 0.340 Chirality : 0.051 0.286 1635 Planarity : 0.004 0.058 1908 Dihedral : 6.535 57.455 1815 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 5.34 % Allowed : 25.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.21), residues: 1335 helix: -2.34 (0.41), residues: 99 sheet: -0.35 (0.22), residues: 453 loop : -1.36 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 269 HIS 0.006 0.002 HIS C 180 PHE 0.014 0.002 PHE A 173 TYR 0.010 0.001 TYR F 176 ARG 0.003 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 18) link_NAG-ASN : angle 3.41577 ( 54) hydrogen bonds : bond 0.03203 ( 268) hydrogen bonds : angle 5.01394 ( 738) SS BOND : bond 0.00333 ( 3) SS BOND : angle 1.08978 ( 6) covalent geometry : bond 0.00504 (10569) covalent geometry : angle 0.62899 (14358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13531.47 seconds wall clock time: 236 minutes 6.64 seconds (14166.64 seconds total)