Starting phenix.real_space_refine on Mon Jun 9 09:39:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gh5_51347/06_2025/9gh5_51347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gh5_51347/06_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_51347/06_2025/9gh5_51347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gh5_51347/06_2025/9gh5_51347.map" model { file = "/net/cci-nas-00/data/ceres_data/9gh5_51347/06_2025/9gh5_51347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gh5_51347/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.66, per 1000 atoms: 0.74 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: 2.77 Conformation dependent library (CDL) restraints added in 1.4 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: 1.88 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: 3.24 Time building geometry restraints manager: 3.24 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: 3.710 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.480 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.650 ------------------------------------------------------------------------------- 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 : 1.152 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: 1.0809 time to fit residues: 323.9136 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 : 2.041 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103278 restraints weight = 14750.929| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.77 r_work: 0.3370 rms_B_bonded: 1.93 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: 0.8012 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 10.191 14418 Z= 0.387 Chirality : 0.056 0.401 1635 Planarity : 0.005 0.048 1908 Dihedral : 8.183 88.932 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 4.03915 ( 54) hydrogen bonds : bond 0.04476 ( 268) hydrogen bonds : angle 5.97032 ( 738) SS BOND : bond 0.00371 ( 3) SS BOND : angle 1.09578 ( 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 : 1.141 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: 0.7610 (t0) REVERT: A 233 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7461 (ptp90) REVERT: B 57 ASP cc_start: 0.7974 (t0) cc_final: 0.7745 (t70) REVERT: B 209 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8461 (p) REVERT: B 227 SER cc_start: 0.8501 (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: 0.8020 (t0) REVERT: B 263 ASP cc_start: 0.6728 (t0) cc_final: 0.6420 (t0) REVERT: C 187 ASN cc_start: 0.8484 (m-40) cc_final: 0.8260 (m-40) REVERT: C 252 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7792 (t) REVERT: C 263 ASP cc_start: 0.7115 (t0) cc_final: 0.6778 (t0) REVERT: D 87 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: D 115 ASN cc_start: 0.7910 (t0) cc_final: 0.7332 (t0) REVERT: D 197 ASN cc_start: 0.6600 (OUTLIER) cc_final: 0.5720 (p0) REVERT: E 51 VAL cc_start: 0.8653 (p) cc_final: 0.8438 (t) REVERT: E 65 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: E 87 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7742 (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: 0.7538 (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: 1.0452 time to fit residues: 287.9328 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 : 2.168 ------------------------------------------------------------------------------- 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: 0.5980 chunk 28 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 47 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 50 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN D 35 GLN D 57 ASN D 78 GLN D 114 GLN D 183 GLN E 35 GLN ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.143193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.103703 restraints weight = 14893.474| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.79 r_work: 0.3386 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10590 Z= 0.161 Angle : 0.666 11.159 14418 Z= 0.338 Chirality : 0.052 0.378 1635 Planarity : 0.004 0.050 1908 Dihedral : 7.444 76.415 1815 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.43 % Allowed : 22.37 % 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: -1.54 (0.22), residues: 1335 helix: -2.82 (0.43), residues: 93 sheet: -0.35 (0.24), residues: 444 loop : -1.18 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 269 HIS 0.005 0.001 HIS C 180 PHE 0.012 0.001 PHE A 173 TYR 0.015 0.001 TYR F 176 ARG 0.003 0.000 ARG F 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 18) link_NAG-ASN : angle 3.45094 ( 54) hydrogen bonds : bond 0.03398 ( 268) hydrogen bonds : angle 5.44908 ( 738) SS BOND : bond 0.00367 ( 3) SS BOND : angle 1.17603 ( 6) covalent geometry : bond 0.00362 (10569) covalent geometry : angle 0.63238 (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 238 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8016 (t0) cc_final: 0.7618 (t0) REVERT: A 233 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7438 (ptp90) REVERT: A 243 THR cc_start: 0.8712 (t) cc_final: 0.8438 (m) REVERT: B 57 ASP cc_start: 0.7903 (t0) cc_final: 0.7688 (t70) REVERT: B 235 LEU cc_start: 0.8824 (tp) cc_final: 0.8603 (tp) REVERT: B 242 ASP cc_start: 0.8207 (t0) cc_final: 0.8002 (t0) REVERT: B 263 ASP cc_start: 0.6772 (t0) cc_final: 0.6327 (t0) REVERT: C 263 ASP cc_start: 0.7124 (t0) cc_final: 0.6765 (t0) REVERT: C 273 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7446 (mp) REVERT: D 41 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7657 (mmm) REVERT: D 87 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: D 115 ASN cc_start: 0.7865 (t0) cc_final: 0.7277 (t0) REVERT: D 217 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7050 (pp) REVERT: E 55 VAL cc_start: 0.8541 (t) cc_final: 0.8307 (t) REVERT: E 65 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: E 87 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: E 99 GLU cc_start: 0.7221 (mp0) cc_final: 0.7012 (mp0) REVERT: F 197 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.5461 (m-40) outliers start: 60 outliers final: 36 residues processed: 221 average time/residue: 0.8748 time to fit residues: 214.4159 Evaluate side-chains 217 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 148 GLN B 148 GLN B 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 E 78 GLN ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.140856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.101388 restraints weight = 14579.165| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.76 r_work: 0.3356 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 10590 Z= 0.299 Angle : 0.714 11.092 14418 Z= 0.364 Chirality : 0.054 0.353 1635 Planarity : 0.004 0.053 1908 Dihedral : 7.169 56.042 1815 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.61 % Allowed : 21.01 % Favored : 72.37 % 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: -1.78 (0.22), residues: 1335 helix: -3.11 (0.38), residues: 102 sheet: -0.54 (0.24), residues: 444 loop : -1.28 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 269 HIS 0.010 0.003 HIS C 180 PHE 0.016 0.002 PHE A 173 TYR 0.015 0.002 TYR F 176 ARG 0.003 0.000 ARG F 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 18) link_NAG-ASN : angle 3.40683 ( 54) hydrogen bonds : bond 0.03912 ( 268) hydrogen bonds : angle 5.32960 ( 738) SS BOND : bond 0.00310 ( 3) SS BOND : angle 1.16129 ( 6) covalent geometry : bond 0.00700 (10569) covalent geometry : angle 0.68388 (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 259 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 186 time to evaluate : 1.201 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: 0.8394 (OUTLIER) cc_final: 0.7448 (ptp90) REVERT: A 243 THR cc_start: 0.8723 (t) cc_final: 0.8462 (m) REVERT: B 57 ASP cc_start: 0.7965 (t0) cc_final: 0.7606 (t0) REVERT: B 235 LEU cc_start: 0.8858 (tp) cc_final: 0.8596 (tp) REVERT: B 263 ASP cc_start: 0.6860 (t0) cc_final: 0.6463 (t0) REVERT: C 233 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7488 (ptp90) REVERT: C 263 ASP cc_start: 0.7200 (t0) cc_final: 0.6775 (t0) REVERT: D 41 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7637 (mmm) REVERT: D 87 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: D 99 GLU cc_start: 0.7002 (mp0) cc_final: 0.6673 (mp0) REVERT: D 115 ASN cc_start: 0.7892 (t0) cc_final: 0.7300 (t0) REVERT: D 133 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7450 (mt-10) REVERT: D 197 ASN cc_start: 0.6349 (OUTLIER) cc_final: 0.5797 (p0) REVERT: D 217 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7170 (pp) REVERT: E 55 VAL cc_start: 0.8603 (t) cc_final: 0.8395 (t) REVERT: E 60 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7154 (mm-40) REVERT: E 65 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: E 87 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: F 44 ASN cc_start: 0.8512 (m-40) cc_final: 0.8222 (m-40) REVERT: F 87 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: F 107 LEU cc_start: 0.8332 (tp) cc_final: 0.8106 (tp) REVERT: F 131 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.8001 (m-40) REVERT: F 221 VAL cc_start: 0.8213 (p) cc_final: 0.7997 (t) outliers start: 73 outliers final: 46 residues processed: 235 average time/residue: 0.8987 time to fit residues: 232.7356 Evaluate side-chains 236 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 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 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 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 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 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: 0.7980 chunk 103 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 67 optimal weight: 0.2980 chunk 123 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 99 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.143451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.104030 restraints weight = 14539.926| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.77 r_work: 0.3394 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10590 Z= 0.145 Angle : 0.635 10.045 14418 Z= 0.323 Chirality : 0.051 0.393 1635 Planarity : 0.004 0.052 1908 Dihedral : 6.767 53.519 1815 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.98 % Allowed : 22.10 % Favored : 71.92 % 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: -1.61 (0.22), residues: 1335 helix: -2.68 (0.42), residues: 99 sheet: -0.53 (0.23), residues: 474 loop : -1.17 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 269 HIS 0.003 0.001 HIS C 180 PHE 0.011 0.001 PHE A 173 TYR 0.011 0.001 TYR F 176 ARG 0.002 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 18) link_NAG-ASN : angle 3.41241 ( 54) hydrogen bonds : bond 0.02938 ( 268) hydrogen bonds : angle 5.10616 ( 738) SS BOND : bond 0.00357 ( 3) SS BOND : angle 1.20837 ( 6) covalent geometry : bond 0.00329 (10569) covalent geometry : angle 0.60046 (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 253 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 187 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7986 (t0) cc_final: 0.7626 (t0) REVERT: A 233 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7439 (ptp90) REVERT: A 243 THR cc_start: 0.8668 (t) cc_final: 0.8427 (m) REVERT: B 57 ASP cc_start: 0.7875 (t0) cc_final: 0.7523 (t0) REVERT: B 227 SER cc_start: 0.8446 (p) cc_final: 0.8241 (m) REVERT: B 235 LEU cc_start: 0.8803 (tp) cc_final: 0.8560 (tp) REVERT: B 242 ASP cc_start: 0.8172 (t0) cc_final: 0.7876 (t0) REVERT: B 263 ASP cc_start: 0.6823 (t0) cc_final: 0.6360 (t0) REVERT: B 272 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8284 (ttpp) REVERT: C 263 ASP cc_start: 0.7186 (t0) cc_final: 0.6791 (t0) REVERT: D 41 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7601 (mmm) REVERT: D 76 ASN cc_start: 0.7954 (m-40) cc_final: 0.7715 (m-40) REVERT: D 87 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: D 115 ASN cc_start: 0.7810 (t0) cc_final: 0.7422 (t0) REVERT: D 133 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7403 (mt-10) REVERT: D 217 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7127 (pp) REVERT: D 221 VAL cc_start: 0.8123 (t) cc_final: 0.7884 (t) REVERT: E 55 VAL cc_start: 0.8586 (t) cc_final: 0.8382 (t) REVERT: E 60 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7040 (mm-40) REVERT: E 65 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: E 87 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7778 (mt0) REVERT: E 99 GLU cc_start: 0.7085 (mp0) cc_final: 0.6885 (mp0) REVERT: F 44 ASN cc_start: 0.8527 (m-40) cc_final: 0.8139 (m-40) REVERT: F 129 LEU cc_start: 0.8432 (mp) cc_final: 0.8170 (mp) REVERT: F 198 ARG cc_start: 0.5401 (OUTLIER) cc_final: 0.4949 (ptp-110) REVERT: F 221 VAL cc_start: 0.8185 (p) cc_final: 0.7947 (t) REVERT: F 225 ARG cc_start: 0.5990 (OUTLIER) cc_final: 0.5483 (tpp-160) outliers start: 66 outliers final: 43 residues processed: 232 average time/residue: 1.1122 time to fit residues: 284.6846 Evaluate side-chains 231 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 197 VAL 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 226 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain 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 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: 6.9990 chunk 45 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 D 35 GLN E 35 GLN F 155 ASN F 232 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.140791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101355 restraints weight = 14613.532| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.81 r_work: 0.3367 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10590 Z= 0.254 Angle : 0.666 8.404 14418 Z= 0.343 Chirality : 0.052 0.321 1635 Planarity : 0.004 0.055 1908 Dihedral : 6.747 55.407 1815 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.16 % Allowed : 22.74 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.68 (0.39), residues: 99 sheet: -0.48 (0.23), residues: 444 loop : -1.30 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 269 HIS 0.007 0.002 HIS C 180 PHE 0.015 0.002 PHE A 173 TYR 0.012 0.001 TYR F 176 ARG 0.003 0.000 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 18) link_NAG-ASN : angle 3.12560 ( 54) hydrogen bonds : bond 0.03516 ( 268) hydrogen bonds : angle 5.13411 ( 738) SS BOND : bond 0.00316 ( 3) SS BOND : angle 1.14756 ( 6) covalent geometry : bond 0.00591 (10569) covalent geometry : angle 0.63855 (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 241 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 173 time to evaluate : 1.481 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: 0.8388 (OUTLIER) cc_final: 0.7447 (ptp90) REVERT: A 243 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8477 (m) REVERT: A 263 ASP cc_start: 0.7150 (t0) cc_final: 0.6651 (t0) REVERT: B 57 ASP cc_start: 0.7875 (t0) cc_final: 0.7499 (t0) REVERT: B 227 SER cc_start: 0.8473 (p) cc_final: 0.8265 (m) REVERT: B 235 LEU cc_start: 0.8853 (tp) cc_final: 0.8605 (tp) REVERT: B 242 ASP cc_start: 0.8192 (t0) cc_final: 0.7853 (t0) REVERT: B 263 ASP cc_start: 0.6859 (t0) cc_final: 0.6418 (t0) REVERT: B 272 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8324 (ttpp) REVERT: C 263 ASP cc_start: 0.7149 (t0) cc_final: 0.6766 (t0) REVERT: D 41 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7632 (mmm) REVERT: D 76 ASN cc_start: 0.7968 (m-40) cc_final: 0.7755 (m-40) REVERT: D 87 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: D 115 ASN cc_start: 0.7789 (t0) cc_final: 0.7365 (t0) REVERT: D 133 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7432 (mt-10) REVERT: D 221 VAL cc_start: 0.8132 (t) cc_final: 0.7898 (t) REVERT: E 60 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7067 (mm-40) REVERT: E 65 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: E 87 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7789 (mt0) REVERT: F 44 ASN cc_start: 0.8541 (m-40) cc_final: 0.8227 (m-40) REVERT: F 87 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: F 131 ASN cc_start: 0.8225 (m-40) cc_final: 0.7981 (m-40) REVERT: F 198 ARG cc_start: 0.5563 (OUTLIER) cc_final: 0.5075 (ptp-110) REVERT: F 225 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5567 (tpp-160) outliers start: 68 outliers final: 51 residues processed: 217 average time/residue: 1.1435 time to fit residues: 275.3428 Evaluate side-chains 236 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 176 time to evaluate : 2.090 ------------------------------------------------------------------------------- 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 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 37 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 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 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: 0.0270 chunk 124 optimal weight: 0.0570 chunk 127 optimal weight: 0.0030 chunk 108 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.3166 ------------------------------------------------------------------------------- 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 E 35 GLN E 57 ASN F 35 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.142780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103631 restraints weight = 14831.111| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.80 r_work: 0.3399 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10590 Z= 0.130 Angle : 0.611 7.504 14418 Z= 0.315 Chirality : 0.050 0.314 1635 Planarity : 0.004 0.054 1908 Dihedral : 6.560 56.624 1815 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.89 % Allowed : 23.55 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.48 (0.22), residues: 1335 helix: -2.17 (0.46), residues: 90 sheet: -0.29 (0.23), residues: 444 loop : -1.26 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 178 HIS 0.003 0.001 HIS B 92 PHE 0.011 0.001 PHE A 173 TYR 0.009 0.001 TYR F 176 ARG 0.002 0.000 ARG E 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 18) link_NAG-ASN : angle 3.00055 ( 54) hydrogen bonds : bond 0.02708 ( 268) hydrogen bonds : angle 4.96341 ( 738) SS BOND : bond 0.00356 ( 3) SS BOND : angle 1.24510 ( 6) covalent geometry : bond 0.00297 (10569) covalent geometry : angle 0.58351 (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 245 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 180 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8637 (m) REVERT: A 233 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7434 (ptp90) REVERT: A 243 THR cc_start: 0.8667 (t) cc_final: 0.8455 (m) REVERT: A 263 ASP cc_start: 0.7182 (t0) cc_final: 0.6675 (t0) REVERT: B 235 LEU cc_start: 0.8749 (tp) cc_final: 0.8534 (tp) REVERT: B 242 ASP cc_start: 0.8180 (t0) cc_final: 0.7817 (t0) REVERT: B 263 ASP cc_start: 0.6856 (t0) cc_final: 0.6382 (t0) REVERT: B 265 ASP cc_start: 0.7641 (p0) cc_final: 0.7411 (p0) REVERT: C 263 ASP cc_start: 0.7173 (t0) cc_final: 0.6788 (t0) REVERT: D 41 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7560 (mmm) REVERT: D 76 ASN cc_start: 0.7947 (m-40) cc_final: 0.7732 (m-40) REVERT: D 87 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7640 (mt0) REVERT: D 115 ASN cc_start: 0.7708 (t0) cc_final: 0.7313 (t0) REVERT: D 221 VAL cc_start: 0.7987 (t) cc_final: 0.7754 (t) REVERT: E 60 GLN cc_start: 0.7420 (mm-40) cc_final: 0.7038 (mm-40) REVERT: E 65 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: E 87 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: E 225 ARG cc_start: 0.5165 (OUTLIER) cc_final: 0.4901 (tpt-90) REVERT: F 44 ASN cc_start: 0.8512 (m-40) cc_final: 0.8163 (m-40) REVERT: F 87 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: F 131 ASN cc_start: 0.8123 (m-40) cc_final: 0.7918 (m-40) REVERT: F 198 ARG cc_start: 0.5483 (OUTLIER) cc_final: 0.5054 (ptp-110) outliers start: 65 outliers final: 50 residues processed: 221 average time/residue: 1.0189 time to fit residues: 250.7886 Evaluate side-chains 237 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 226 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 235 LEU 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 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 226 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 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 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 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 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 88 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: 1.9990 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 A 177 ASN B 187 ASN C 44 ASN D 35 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 218 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.139265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100143 restraints weight = 14531.565| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.76 r_work: 0.3342 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 10590 Z= 0.326 Angle : 0.704 8.719 14418 Z= 0.365 Chirality : 0.055 0.302 1635 Planarity : 0.004 0.059 1908 Dihedral : 6.760 57.518 1815 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 6.70 % Allowed : 22.46 % Favored : 70.83 % 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: -1.76 (0.21), residues: 1335 helix: -2.67 (0.39), residues: 99 sheet: -0.36 (0.23), residues: 423 loop : -1.44 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 269 HIS 0.009 0.003 HIS C 180 PHE 0.016 0.002 PHE A 173 TYR 0.014 0.002 TYR F 176 ARG 0.003 0.000 ARG A 73 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 18) link_NAG-ASN : angle 2.98645 ( 54) hydrogen bonds : bond 0.03873 ( 268) hydrogen bonds : angle 5.23188 ( 738) SS BOND : bond 0.00264 ( 3) SS BOND : angle 0.87059 ( 6) covalent geometry : bond 0.00763 (10569) covalent geometry : angle 0.68115 (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 260 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 186 time to evaluate : 1.177 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: 0.8429 (OUTLIER) cc_final: 0.7477 (ptp90) REVERT: A 243 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8459 (m) REVERT: A 263 ASP cc_start: 0.7176 (t0) cc_final: 0.6700 (t0) REVERT: B 57 ASP cc_start: 0.7944 (t0) cc_final: 0.7585 (t0) REVERT: B 235 LEU cc_start: 0.8841 (tp) cc_final: 0.8604 (tp) REVERT: B 263 ASP cc_start: 0.6864 (t0) cc_final: 0.6369 (t0) REVERT: C 263 ASP cc_start: 0.7139 (t0) cc_final: 0.6756 (t0) REVERT: D 41 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7667 (mmm) REVERT: D 87 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: D 115 ASN cc_start: 0.7754 (t0) cc_final: 0.7338 (t0) REVERT: D 133 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7401 (mt-10) REVERT: D 221 VAL cc_start: 0.8133 (t) cc_final: 0.7896 (t) REVERT: E 60 GLN cc_start: 0.7434 (mm-40) cc_final: 0.7121 (mm-40) REVERT: E 65 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: E 87 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: F 44 ASN cc_start: 0.8560 (m-40) cc_final: 0.8270 (m110) REVERT: F 87 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: F 131 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.8012 (m-40) REVERT: F 198 ARG cc_start: 0.5674 (OUTLIER) cc_final: 0.5181 (ptp-110) outliers start: 74 outliers final: 53 residues processed: 229 average time/residue: 0.9125 time to fit residues: 230.3998 Evaluate side-chains 253 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 191 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 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 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 226 SER Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 122 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 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 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 127 SER Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 225 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.0770 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.141430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.102463 restraints weight = 14631.335| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.77 r_work: 0.3376 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10590 Z= 0.162 Angle : 0.644 11.759 14418 Z= 0.329 Chirality : 0.051 0.301 1635 Planarity : 0.004 0.057 1908 Dihedral : 6.682 57.103 1815 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.98 % Allowed : 23.55 % 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: -1.61 (0.22), residues: 1335 helix: -2.34 (0.43), residues: 99 sheet: -0.45 (0.23), residues: 453 loop : -1.26 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 269 HIS 0.004 0.001 HIS C 180 PHE 0.013 0.001 PHE A 173 TYR 0.009 0.001 TYR F 176 ARG 0.002 0.000 ARG F 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00716 ( 18) link_NAG-ASN : angle 3.49502 ( 54) hydrogen bonds : bond 0.02927 ( 268) hydrogen bonds : angle 5.04648 ( 738) SS BOND : bond 0.00315 ( 3) SS BOND : angle 1.12000 ( 6) covalent geometry : bond 0.00374 (10569) covalent geometry : angle 0.60798 (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 256 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 190 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7454 (ptp90) REVERT: A 263 ASP cc_start: 0.7196 (t0) cc_final: 0.6717 (t0) REVERT: B 57 ASP cc_start: 0.7871 (t0) cc_final: 0.7492 (t0) REVERT: B 235 LEU cc_start: 0.8752 (tp) cc_final: 0.8524 (tp) REVERT: B 242 ASP cc_start: 0.8186 (t0) cc_final: 0.7918 (t0) REVERT: B 263 ASP cc_start: 0.6880 (t0) cc_final: 0.6378 (t0) REVERT: C 149 TYR cc_start: 0.8823 (m-80) cc_final: 0.8582 (m-80) REVERT: C 263 ASP cc_start: 0.7216 (t0) cc_final: 0.6811 (t0) REVERT: D 41 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7568 (mmm) REVERT: D 87 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: D 221 VAL cc_start: 0.7980 (t) cc_final: 0.7737 (t) REVERT: E 60 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7110 (mm-40) REVERT: E 65 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7016 (m-80) REVERT: E 87 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: E 100 THR cc_start: 0.8337 (p) cc_final: 0.8118 (t) REVERT: E 225 ARG cc_start: 0.5206 (OUTLIER) cc_final: 0.4933 (tpt-90) REVERT: F 44 ASN cc_start: 0.8525 (m-40) cc_final: 0.8183 (m-40) REVERT: F 87 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: F 129 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8126 (mp) REVERT: F 131 ASN cc_start: 0.8199 (m-40) cc_final: 0.7961 (m-40) REVERT: F 135 THR cc_start: 0.8353 (t) cc_final: 0.8005 (m) REVERT: F 198 ARG cc_start: 0.5593 (OUTLIER) cc_final: 0.5210 (ptp-110) REVERT: F 225 ARG cc_start: 0.6257 (OUTLIER) cc_final: 0.5848 (ttp-170) outliers start: 66 outliers final: 46 residues processed: 230 average time/residue: 0.8576 time to fit residues: 218.6922 Evaluate side-chains 231 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 175 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 233 ARG Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 ASN 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 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 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 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 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 88 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 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: 0.7980 chunk 46 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN B 187 ASN C 44 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.140437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.101501 restraints weight = 14658.521| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.76 r_work: 0.3361 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10590 Z= 0.221 Angle : 0.666 11.277 14418 Z= 0.344 Chirality : 0.052 0.291 1635 Planarity : 0.004 0.057 1908 Dihedral : 6.514 57.260 1814 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.34 % Allowed : 24.64 % Favored : 70.02 % 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: -2.34 (0.42), residues: 99 sheet: -0.33 (0.23), residues: 423 loop : -1.43 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 269 HIS 0.006 0.002 HIS C 180 PHE 0.013 0.002 PHE A 173 TYR 0.009 0.001 TYR D 65 ARG 0.003 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 18) link_NAG-ASN : angle 3.35298 ( 54) hydrogen bonds : bond 0.03253 ( 268) hydrogen bonds : angle 5.11817 ( 738) SS BOND : bond 0.00300 ( 3) SS BOND : angle 1.00937 ( 6) covalent geometry : bond 0.00524 (10569) covalent geometry : angle 0.63439 (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 241 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 182 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7465 (ptp90) REVERT: A 263 ASP cc_start: 0.7215 (t0) cc_final: 0.6726 (t0) REVERT: B 57 ASP cc_start: 0.7900 (t0) cc_final: 0.7500 (t0) REVERT: B 235 LEU cc_start: 0.8760 (tp) cc_final: 0.8529 (tp) REVERT: B 242 ASP cc_start: 0.8208 (t0) cc_final: 0.7898 (t0) REVERT: B 263 ASP cc_start: 0.6885 (t0) cc_final: 0.6381 (t0) REVERT: C 263 ASP cc_start: 0.7193 (t0) cc_final: 0.6790 (t0) REVERT: D 41 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7575 (mmm) REVERT: D 87 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: D 133 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7341 (mm-30) REVERT: D 218 GLN cc_start: 0.6304 (tp40) cc_final: 0.6024 (tp40) REVERT: D 221 VAL cc_start: 0.8016 (t) cc_final: 0.7776 (t) REVERT: E 60 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7165 (mm-40) REVERT: E 65 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: E 87 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: E 225 ARG cc_start: 0.5255 (OUTLIER) cc_final: 0.4994 (tpt-90) REVERT: F 44 ASN cc_start: 0.8532 (m-40) cc_final: 0.8185 (m-40) REVERT: F 87 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: F 129 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8205 (mp) REVERT: F 131 ASN cc_start: 0.8244 (m-40) cc_final: 0.7990 (m-40) REVERT: F 198 ARG cc_start: 0.5692 (OUTLIER) cc_final: 0.5288 (ptp-110) REVERT: F 225 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.5973 (ttp-170) outliers start: 59 outliers final: 45 residues processed: 217 average time/residue: 0.9514 time to fit residues: 228.9579 Evaluate side-chains 237 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 182 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 233 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 ASN 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 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 252 VAL Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 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 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 88 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 84 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** D 183 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.139289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100323 restraints weight = 14402.149| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.75 r_work: 0.3348 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 10590 Z= 0.298 Angle : 0.705 11.573 14418 Z= 0.364 Chirality : 0.053 0.283 1635 Planarity : 0.004 0.058 1908 Dihedral : 6.683 58.196 1814 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.89 % Allowed : 24.55 % Favored : 69.57 % 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: -1.82 (0.21), residues: 1335 helix: -2.55 (0.39), residues: 102 sheet: -0.40 (0.23), residues: 423 loop : -1.50 (0.20), residues: 810 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 0.016 0.002 PHE A 173 TYR 0.014 0.002 TYR F 176 ARG 0.002 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 18) link_NAG-ASN : angle 3.45259 ( 54) hydrogen bonds : bond 0.03721 ( 268) hydrogen bonds : angle 5.24249 ( 738) SS BOND : bond 0.00269 ( 3) SS BOND : angle 0.88818 ( 6) covalent geometry : bond 0.00705 (10569) covalent geometry : angle 0.67336 (14358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15256.02 seconds wall clock time: 267 minutes 15.71 seconds (16035.71 seconds total)