Starting phenix.real_space_refine on Fri May 16 07:13:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wo4_37678/05_2025/8wo4_37678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wo4_37678/05_2025/8wo4_37678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wo4_37678/05_2025/8wo4_37678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wo4_37678/05_2025/8wo4_37678.map" model { file = "/net/cci-nas-00/data/ceres_data/8wo4_37678/05_2025/8wo4_37678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wo4_37678/05_2025/8wo4_37678.cif" } resolution = 2.8 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= 0.050 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 74 5.16 5 C 8888 2.51 5 N 2456 2.21 5 O 2770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14188 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1652 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "B" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1689 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 216} Chain: "C" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1652 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Chain: "D" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1689 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 216} Chain: "E" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2817 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "F" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2817 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.18, per 1000 atoms: 0.86 Number of scatterers: 14188 At special positions: 0 Unit cell: (89.08, 150.28, 132.6, 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 74 16.00 O 2770 8.00 N 2456 7.00 C 8888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 215 " - pdb=" SG CYS D 223 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 4 " distance=2.05 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 223 " distance=2.03 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 329 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 312 " distance=2.03 Simple disulfide: pdb=" SG CYS E 313 " - pdb=" SG CYS E 316 " distance=2.04 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 15 " distance=2.04 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 143 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 223 " distance=2.03 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 329 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 312 " distance=2.03 Simple disulfide: pdb=" SG CYS F 313 " - pdb=" SG CYS F 316 " 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 E 401 " - " ASN E 207 " " NAG F 401 " - " ASN F 207 " Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 2.1 seconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 35 sheets defined 12.8% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 4.190A pdb=" N PHE A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.714A pdb=" N SER A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 224 through 228 removed outlier: 3.882A pdb=" N HIS B 227 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.033A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.623A pdb=" N SER C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 190 removed outlier: 3.587A pdb=" N LYS C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.569A pdb=" N ASP D 90 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 224 through 228 removed outlier: 4.029A pdb=" N HIS D 227 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 Processing helix chain 'E' and resid 38 through 53 removed outlier: 3.775A pdb=" N ALA E 44 " --> pdb=" O ARG E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 80 removed outlier: 5.995A pdb=" N GLY E 73 " --> pdb=" O LYS E 69 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 180 through 183 removed outlier: 4.056A pdb=" N VAL E 183 " --> pdb=" O ASP E 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 180 through 183' Processing helix chain 'E' and resid 244 through 248 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'F' and resid 38 through 52 removed outlier: 3.635A pdb=" N GLU F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 82 removed outlier: 3.575A pdb=" N ASN F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY F 73 " --> pdb=" O LYS F 69 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 180 through 183 removed outlier: 3.972A pdb=" N VAL F 183 " --> pdb=" O ASP F 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 180 through 183' Processing helix chain 'F' and resid 237 through 241 removed outlier: 3.517A pdb=" N LEU F 241 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 248 removed outlier: 3.504A pdb=" N ALA F 248 " --> pdb=" O LYS F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 341 through 345 removed outlier: 3.549A pdb=" N ASN F 344 " --> pdb=" O PRO F 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.575A pdb=" N ARG G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.694A pdb=" N VAL A 20 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP A 71 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 68 " --> pdb=" O ASP A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.181A pdb=" N LEU A 12 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 34 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 119 removed outlier: 5.715A pdb=" N TYR A 174 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.572A pdb=" N GLN B 4 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 26 " --> pdb=" O GLN B 4 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.522A pdb=" N ALA B 92 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET B 35 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 51 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP B 37 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.522A pdb=" N ALA B 92 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE B 109 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.312A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 138 through 139 removed outlier: 6.312A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.265A pdb=" N TYR B 201 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.545A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 115 through 119 removed outlier: 5.935A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB6, first strand: chain 'D' and resid 5 through 8 Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.222A pdb=" N GLY D 11 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER D 36 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET D 35 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL D 51 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.222A pdb=" N GLY D 11 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 127 through 131 removed outlier: 6.232A pdb=" N TYR D 183 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.232A pdb=" N TYR D 183 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.531A pdb=" N TYR D 201 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.973A pdb=" N VAL F 2 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG F 14 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 87 through 90 removed outlier: 6.467A pdb=" N THR E 87 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL E 135 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL E 89 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLY E 56 " --> pdb=" O ALA E 149 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 153 through 157 removed outlier: 6.982A pdb=" N TRP E 168 " --> pdb=" O GLU E 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 329 through 331 removed outlier: 6.559A pdb=" N GLU E 203 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA E 215 " --> pdb=" O TRP E 201 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP E 201 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU F 192 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLU F 205 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU F 212 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N LYS F 213 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE F 277 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 284 through 285 removed outlier: 6.275A pdb=" N LYS E 284 " --> pdb=" O TRP E 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.176A pdb=" N GLY F 56 " --> pdb=" O ALA F 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 87 through 91 removed outlier: 6.500A pdb=" N THR F 87 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL F 135 " --> pdb=" O THR F 87 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL F 89 " --> pdb=" O VAL F 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 284 through 287 Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.522A pdb=" N CYS G 22 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 78 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU G 18 " --> pdb=" O MET G 82 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.522A pdb=" N CYS G 22 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 78 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.547A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA G 33 " --> pdb=" O ASP G 95 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP G 101 " --> pdb=" O ILE G 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.547A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA G 33 " --> pdb=" O ASP G 95 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.669A pdb=" N GLN H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.534A pdb=" N PHE H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR H 102 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.534A pdb=" N PHE H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 14430 1.57 - 1.93: 100 1.93 - 2.28: 0 2.28 - 2.63: 0 2.63 - 2.98: 1 Bond restraints: 14531 Sorted by residual: bond pdb=" C ARG A 109 " pdb=" N THR A 110 " ideal model delta sigma weight residual 1.329 2.983 -1.655 1.44e-02 4.82e+03 1.32e+04 bond pdb=" N THR A 110 " pdb=" CA THR A 110 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.17e+00 bond pdb=" N THR C 110 " pdb=" CA THR C 110 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 bond pdb=" N SER B 1 " pdb=" CA SER B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 ... (remaining 14526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.40: 19708 6.40 - 12.81: 3 12.81 - 19.21: 0 19.21 - 25.62: 1 25.62 - 32.02: 1 Bond angle restraints: 19713 Sorted by residual: angle pdb=" O ARG A 109 " pdb=" C ARG A 109 " pdb=" N THR A 110 " ideal model delta sigma weight residual 123.33 101.03 22.30 1.13e+00 7.83e-01 3.89e+02 angle pdb=" C ARG A 109 " pdb=" N THR A 110 " pdb=" CA THR A 110 " ideal model delta sigma weight residual 122.03 90.01 32.02 2.01e+00 2.48e-01 2.54e+02 angle pdb=" C ASP F 136 " pdb=" CA ASP F 136 " pdb=" CB ASP F 136 " ideal model delta sigma weight residual 117.23 111.52 5.71 1.36e+00 5.41e-01 1.76e+01 angle pdb=" C1 NAG F 401 " pdb=" O5 NAG F 401 " pdb=" C5 NAG F 401 " ideal model delta sigma weight residual 113.21 124.37 -11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA CYS E 4 " pdb=" CB CYS E 4 " pdb=" SG CYS E 4 " ideal model delta sigma weight residual 114.40 120.84 -6.44 2.30e+00 1.89e-01 7.84e+00 ... (remaining 19708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 8073 17.81 - 35.62: 465 35.62 - 53.44: 120 53.44 - 71.25: 35 71.25 - 89.06: 8 Dihedral angle restraints: 8701 sinusoidal: 3454 harmonic: 5247 Sorted by residual: dihedral pdb=" CB CYS E 4 " pdb=" SG CYS E 4 " pdb=" SG CYS F 4 " pdb=" CB CYS F 4 " ideal model delta sinusoidal sigma weight residual -86.00 -15.55 -70.45 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CA LYS E 33 " pdb=" C LYS E 33 " pdb=" N TYR E 34 " pdb=" CA TYR E 34 " ideal model delta harmonic sigma weight residual -180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA TRP E 28 " pdb=" C TRP E 28 " pdb=" N ARG E 29 " pdb=" CA ARG E 29 " ideal model delta harmonic sigma weight residual -180.00 -154.52 -25.48 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 8698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1596 0.040 - 0.080: 356 0.080 - 0.121: 160 0.121 - 0.161: 23 0.161 - 0.201: 1 Chirality restraints: 2136 Sorted by residual: chirality pdb=" C1 NAG F 401 " pdb=" ND2 ASN F 207 " pdb=" C2 NAG F 401 " pdb=" O5 NAG F 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL H 2 " pdb=" N VAL H 2 " pdb=" C VAL H 2 " pdb=" CB VAL H 2 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE C 22 " pdb=" N ILE C 22 " pdb=" C ILE C 22 " pdb=" CB ILE C 22 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2133 not shown) Planarity restraints: 2537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 109 " -0.133 2.00e-02 2.50e+03 1.99e-01 3.95e+02 pdb=" C ARG A 109 " 0.337 2.00e-02 2.50e+03 pdb=" O ARG A 109 " -0.157 2.00e-02 2.50e+03 pdb=" N THR A 110 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 155 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO D 156 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 155 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO B 156 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " 0.023 5.00e-02 4.00e+02 ... (remaining 2534 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 96 2.54 - 3.13: 10829 3.13 - 3.72: 20068 3.72 - 4.31: 28770 4.31 - 4.90: 49852 Nonbonded interactions: 109615 Sorted by model distance: nonbonded pdb=" O GLY F 159 " pdb=" OG SER F 166 " model vdw 1.955 3.040 nonbonded pdb=" OD1 ASP E 234 " pdb=" OG1 THR F 233 " model vdw 1.974 3.040 nonbonded pdb=" NE2 GLN A 101 " pdb=" O GLY A 102 " model vdw 2.003 3.120 nonbonded pdb=" OD1 ASP B 224 " pdb=" OG1 THR B 226 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASP C 18 " pdb=" N ARG C 19 " model vdw 2.228 3.120 ... (remaining 109610 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 13.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.850 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 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 : 0.014 1.655 14555 Z= 0.961 Angle : 0.604 32.023 19763 Z= 0.342 Chirality : 0.042 0.201 2136 Planarity : 0.005 0.199 2535 Dihedral : 12.778 89.062 5283 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.96 % Allowed : 8.39 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1810 helix: 0.49 (0.51), residues: 105 sheet: 0.58 (0.22), residues: 589 loop : -0.32 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 99 HIS 0.003 0.001 HIS E 195 PHE 0.009 0.001 PHE G 99 TYR 0.022 0.001 TYR H 91 ARG 0.004 0.000 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 2) link_NAG-ASN : angle 3.55065 ( 6) hydrogen bonds : bond 0.24879 ( 469) hydrogen bonds : angle 9.62659 ( 1323) SS BOND : bond 0.00623 ( 22) SS BOND : angle 1.47973 ( 44) covalent geometry : bond 0.01397 (14531) covalent geometry : angle 0.59732 (19713) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.663 Fit side-chains REVERT: D 65 LYS cc_start: 0.6649 (ttpt) cc_final: 0.6342 (tptt) REVERT: F 138 ASP cc_start: 0.7366 (t0) cc_final: 0.6812 (t0) outliers start: 15 outliers final: 2 residues processed: 143 average time/residue: 1.3370 time to fit residues: 210.1439 Evaluate side-chains 103 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain F residue 4 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 56 GLN A 159 ASN C 91 GLN C 211 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.235376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.190565 restraints weight = 17310.582| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.40 r_work: 0.3957 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 14555 Z= 0.217 Angle : 0.759 11.138 19763 Z= 0.395 Chirality : 0.047 0.192 2136 Planarity : 0.006 0.053 2535 Dihedral : 5.718 58.445 2033 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.07 % Allowed : 9.22 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1812 helix: -0.58 (0.47), residues: 114 sheet: 0.47 (0.21), residues: 629 loop : -0.60 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP D 99 HIS 0.008 0.002 HIS E 195 PHE 0.031 0.002 PHE D 68 TYR 0.020 0.002 TYR F 32 ARG 0.005 0.001 ARG A 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 2) link_NAG-ASN : angle 5.27207 ( 6) hydrogen bonds : bond 0.05420 ( 469) hydrogen bonds : angle 6.75680 ( 1323) SS BOND : bond 0.01137 ( 22) SS BOND : angle 2.35448 ( 44) covalent geometry : bond 0.00498 (14531) covalent geometry : angle 0.74577 (19713) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 1.690 Fit side-chains REVERT: A 111 VAL cc_start: 0.5140 (m) cc_final: 0.4787 (t) REVERT: A 127 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5798 (tttm) REVERT: C 76 ILE cc_start: 0.6137 (OUTLIER) cc_final: 0.5370 (tp) REVERT: C 78 SER cc_start: 0.6856 (p) cc_final: 0.6508 (t) REVERT: C 79 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7211 (tm) REVERT: E 85 GLN cc_start: 0.8121 (mt0) cc_final: 0.7690 (mt0) REVERT: F 133 PHE cc_start: 0.7613 (t80) cc_final: 0.7369 (t80) REVERT: F 138 ASP cc_start: 0.7556 (t0) cc_final: 0.7008 (t0) REVERT: H 34 MET cc_start: 0.1466 (tmm) cc_final: 0.1215 (tmm) outliers start: 48 outliers final: 21 residues processed: 164 average time/residue: 1.2965 time to fit residues: 234.0342 Evaluate side-chains 131 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 349 MET Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 138 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 173 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 150 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.238121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.193235 restraints weight = 17353.964| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 3.33 r_work: 0.3993 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14555 Z= 0.125 Angle : 0.593 9.568 19763 Z= 0.308 Chirality : 0.042 0.155 2136 Planarity : 0.004 0.049 2535 Dihedral : 5.219 57.914 2032 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.50 % Allowed : 12.68 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1812 helix: -0.00 (0.50), residues: 114 sheet: 0.54 (0.21), residues: 630 loop : -0.50 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 99 HIS 0.006 0.001 HIS E 195 PHE 0.030 0.002 PHE D 68 TYR 0.019 0.001 TYR H 91 ARG 0.004 0.000 ARG E 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 2) link_NAG-ASN : angle 4.58845 ( 6) hydrogen bonds : bond 0.03996 ( 469) hydrogen bonds : angle 6.00326 ( 1323) SS BOND : bond 0.00677 ( 22) SS BOND : angle 1.57028 ( 44) covalent geometry : bond 0.00276 (14531) covalent geometry : angle 0.58370 (19713) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 1.540 Fit side-chains REVERT: A 111 VAL cc_start: 0.5143 (m) cc_final: 0.4789 (t) REVERT: C 76 ILE cc_start: 0.6217 (OUTLIER) cc_final: 0.5388 (tp) REVERT: C 78 SER cc_start: 0.6675 (p) cc_final: 0.6311 (t) REVERT: C 79 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7189 (tm) REVERT: C 101 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: D 58 THR cc_start: 0.7959 (p) cc_final: 0.7672 (p) REVERT: D 65 LYS cc_start: 0.6921 (ttpt) cc_final: 0.6337 (tptt) REVERT: E 11 LYS cc_start: 0.6171 (tppt) cc_final: 0.4970 (mppt) REVERT: E 85 GLN cc_start: 0.8065 (mt0) cc_final: 0.7354 (mm110) REVERT: F 133 PHE cc_start: 0.7481 (t80) cc_final: 0.7274 (t80) outliers start: 39 outliers final: 16 residues processed: 151 average time/residue: 1.2265 time to fit residues: 204.0809 Evaluate side-chains 129 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 141 LYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 142 optimal weight: 3.9990 chunk 177 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 131 optimal weight: 0.3980 chunk 64 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 16 optimal weight: 0.0040 chunk 73 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.239354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.186238 restraints weight = 17407.163| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.44 r_work: 0.4048 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14555 Z= 0.110 Angle : 0.556 7.628 19763 Z= 0.287 Chirality : 0.042 0.161 2136 Planarity : 0.004 0.050 2535 Dihedral : 4.865 57.118 2031 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.14 % Allowed : 12.93 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1812 helix: 0.46 (0.52), residues: 110 sheet: 0.64 (0.21), residues: 632 loop : -0.44 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 99 HIS 0.006 0.001 HIS E 195 PHE 0.023 0.001 PHE D 68 TYR 0.018 0.001 TYR H 91 ARG 0.005 0.000 ARG E 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 2) link_NAG-ASN : angle 3.73607 ( 6) hydrogen bonds : bond 0.03367 ( 469) hydrogen bonds : angle 5.53656 ( 1323) SS BOND : bond 0.00609 ( 22) SS BOND : angle 1.40924 ( 44) covalent geometry : bond 0.00244 (14531) covalent geometry : angle 0.54838 (19713) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 1.505 Fit side-chains REVERT: A 111 VAL cc_start: 0.5288 (m) cc_final: 0.4911 (t) REVERT: C 76 ILE cc_start: 0.6278 (OUTLIER) cc_final: 0.5396 (tp) REVERT: C 79 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7175 (tm) REVERT: C 101 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: D 65 LYS cc_start: 0.6824 (ttpt) cc_final: 0.6265 (tptt) REVERT: E 11 LYS cc_start: 0.6010 (tppt) cc_final: 0.4789 (mppt) outliers start: 49 outliers final: 25 residues processed: 163 average time/residue: 1.1356 time to fit residues: 204.8207 Evaluate side-chains 138 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 172 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN C 167 GLN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.233963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.189338 restraints weight = 17513.579| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 3.56 r_work: 0.3920 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 14555 Z= 0.198 Angle : 0.704 10.219 19763 Z= 0.365 Chirality : 0.045 0.177 2136 Planarity : 0.005 0.053 2535 Dihedral : 5.424 58.767 2031 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.65 % Allowed : 14.21 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1812 helix: -0.08 (0.50), residues: 103 sheet: 0.41 (0.21), residues: 637 loop : -0.66 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 99 HIS 0.008 0.001 HIS E 195 PHE 0.044 0.002 PHE D 68 TYR 0.025 0.002 TYR F 32 ARG 0.005 0.001 ARG C 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 2) link_NAG-ASN : angle 4.63862 ( 6) hydrogen bonds : bond 0.04644 ( 469) hydrogen bonds : angle 5.90559 ( 1323) SS BOND : bond 0.00894 ( 22) SS BOND : angle 2.04091 ( 44) covalent geometry : bond 0.00455 (14531) covalent geometry : angle 0.69324 (19713) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 119 time to evaluate : 1.491 Fit side-chains REVERT: A 111 VAL cc_start: 0.5636 (m) cc_final: 0.5336 (t) REVERT: C 76 ILE cc_start: 0.6291 (OUTLIER) cc_final: 0.5566 (tp) REVERT: C 78 SER cc_start: 0.6757 (p) cc_final: 0.6378 (t) REVERT: C 79 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7158 (tm) REVERT: C 101 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: D 19 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6383 (tt) REVERT: E 11 LYS cc_start: 0.6238 (tppt) cc_final: 0.5373 (mppt) REVERT: E 338 ARG cc_start: 0.6551 (mtp-110) cc_final: 0.6301 (mtm110) outliers start: 57 outliers final: 27 residues processed: 161 average time/residue: 1.3544 time to fit residues: 242.1807 Evaluate side-chains 142 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 0.0070 chunk 19 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 96 optimal weight: 0.0050 chunk 69 optimal weight: 1.9990 overall best weight: 1.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.234852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.172887 restraints weight = 17564.089| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.19 r_work: 0.3977 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14555 Z= 0.158 Angle : 0.637 8.535 19763 Z= 0.331 Chirality : 0.043 0.157 2136 Planarity : 0.005 0.054 2535 Dihedral : 5.202 58.124 2031 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.46 % Allowed : 15.36 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1812 helix: 0.12 (0.52), residues: 105 sheet: 0.40 (0.21), residues: 640 loop : -0.71 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 99 HIS 0.007 0.001 HIS E 195 PHE 0.044 0.002 PHE D 68 TYR 0.016 0.002 TYR H 91 ARG 0.003 0.000 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 2) link_NAG-ASN : angle 4.18665 ( 6) hydrogen bonds : bond 0.04016 ( 469) hydrogen bonds : angle 5.71860 ( 1323) SS BOND : bond 0.00916 ( 22) SS BOND : angle 1.83988 ( 44) covalent geometry : bond 0.00363 (14531) covalent geometry : angle 0.62737 (19713) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 114 time to evaluate : 1.534 Fit side-chains REVERT: A 19 ARG cc_start: 0.6643 (mmm-85) cc_final: 0.6346 (tpt-90) REVERT: A 111 VAL cc_start: 0.5870 (m) cc_final: 0.5582 (t) REVERT: B 7 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: C 76 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.5665 (tp) REVERT: C 78 SER cc_start: 0.6735 (p) cc_final: 0.6340 (t) REVERT: C 101 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: D 19 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6419 (tt) REVERT: E 11 LYS cc_start: 0.6308 (tppt) cc_final: 0.5547 (mppt) REVERT: E 338 ARG cc_start: 0.6633 (mtp-110) cc_final: 0.6369 (mtm110) REVERT: F 21 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7089 (mp) REVERT: F 156 GLU cc_start: 0.6979 (tt0) cc_final: 0.6771 (tm-30) outliers start: 54 outliers final: 34 residues processed: 155 average time/residue: 1.1722 time to fit residues: 202.4093 Evaluate side-chains 151 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 22 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 135 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.235603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.173351 restraints weight = 17466.159| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.22 r_work: 0.4007 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14555 Z= 0.126 Angle : 0.587 8.537 19763 Z= 0.303 Chirality : 0.042 0.151 2136 Planarity : 0.005 0.050 2535 Dihedral : 4.935 57.549 2031 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.33 % Allowed : 15.94 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1812 helix: 0.43 (0.52), residues: 106 sheet: 0.47 (0.21), residues: 640 loop : -0.64 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 99 HIS 0.006 0.001 HIS E 195 PHE 0.035 0.002 PHE D 68 TYR 0.016 0.001 TYR H 91 ARG 0.005 0.000 ARG E 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 2) link_NAG-ASN : angle 3.48063 ( 6) hydrogen bonds : bond 0.03533 ( 469) hydrogen bonds : angle 5.50078 ( 1323) SS BOND : bond 0.00733 ( 22) SS BOND : angle 1.55985 ( 44) covalent geometry : bond 0.00286 (14531) covalent geometry : angle 0.57949 (19713) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 1.669 Fit side-chains REVERT: A 111 VAL cc_start: 0.5912 (m) cc_final: 0.5653 (t) REVERT: B 7 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: B 83 MET cc_start: 0.7557 (mtm) cc_final: 0.7261 (mmm) REVERT: C 5 MET cc_start: 0.5250 (mtp) cc_final: 0.4743 (mmm) REVERT: C 76 ILE cc_start: 0.6379 (OUTLIER) cc_final: 0.5629 (tp) REVERT: C 101 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7479 (mt0) REVERT: D 65 LYS cc_start: 0.6957 (ttpt) cc_final: 0.6293 (tptt) REVERT: E 11 LYS cc_start: 0.6381 (tppt) cc_final: 0.5623 (mppt) REVERT: E 338 ARG cc_start: 0.6687 (mtp-110) cc_final: 0.6401 (mtm110) REVERT: F 21 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7001 (mp) outliers start: 52 outliers final: 32 residues processed: 157 average time/residue: 1.1958 time to fit residues: 208.1563 Evaluate side-chains 150 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.232922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.170402 restraints weight = 17341.015| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.19 r_work: 0.3973 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 14555 Z= 0.179 Angle : 0.669 9.632 19763 Z= 0.347 Chirality : 0.044 0.171 2136 Planarity : 0.005 0.057 2535 Dihedral : 5.284 58.739 2031 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.46 % Allowed : 16.26 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1812 helix: 0.01 (0.50), residues: 105 sheet: 0.41 (0.21), residues: 632 loop : -0.79 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 99 HIS 0.007 0.001 HIS F 195 PHE 0.048 0.002 PHE D 68 TYR 0.017 0.002 TYR F 32 ARG 0.005 0.001 ARG E 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 2) link_NAG-ASN : angle 3.90730 ( 6) hydrogen bonds : bond 0.04243 ( 469) hydrogen bonds : angle 5.75367 ( 1323) SS BOND : bond 0.00931 ( 22) SS BOND : angle 1.98688 ( 44) covalent geometry : bond 0.00413 (14531) covalent geometry : angle 0.65955 (19713) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 1.680 Fit side-chains REVERT: A 111 VAL cc_start: 0.6061 (m) cc_final: 0.5839 (t) REVERT: B 7 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: C 76 ILE cc_start: 0.6430 (OUTLIER) cc_final: 0.5649 (tp) REVERT: C 78 SER cc_start: 0.6746 (p) cc_final: 0.6387 (t) REVERT: C 101 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: D 19 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6303 (tt) REVERT: D 99 TRP cc_start: 0.7146 (t-100) cc_final: 0.6790 (t-100) REVERT: E 11 LYS cc_start: 0.6321 (tppt) cc_final: 0.5691 (mppt) REVERT: E 168 TRP cc_start: 0.6144 (m100) cc_final: 0.5823 (m100) REVERT: E 338 ARG cc_start: 0.6681 (mtp-110) cc_final: 0.6427 (mtm110) REVERT: F 21 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7031 (mp) outliers start: 54 outliers final: 38 residues processed: 155 average time/residue: 1.1299 time to fit residues: 194.8894 Evaluate side-chains 152 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 174 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.231864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.187880 restraints weight = 17275.495| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.58 r_work: 0.3914 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 14555 Z= 0.201 Angle : 0.709 9.913 19763 Z= 0.369 Chirality : 0.046 0.172 2136 Planarity : 0.005 0.059 2535 Dihedral : 5.510 58.628 2031 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.84 % Allowed : 16.33 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1812 helix: -0.22 (0.50), residues: 105 sheet: 0.29 (0.21), residues: 640 loop : -0.93 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP D 99 HIS 0.007 0.002 HIS E 195 PHE 0.054 0.002 PHE D 68 TYR 0.023 0.002 TYR F 200 ARG 0.005 0.001 ARG D 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 2) link_NAG-ASN : angle 4.17255 ( 6) hydrogen bonds : bond 0.04521 ( 469) hydrogen bonds : angle 5.89196 ( 1323) SS BOND : bond 0.01087 ( 22) SS BOND : angle 2.03370 ( 44) covalent geometry : bond 0.00467 (14531) covalent geometry : angle 0.69988 (19713) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 116 time to evaluate : 1.525 Fit side-chains REVERT: A 111 VAL cc_start: 0.6295 (m) cc_final: 0.6057 (t) REVERT: B 7 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: B 34 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7166 (m-10) REVERT: B 83 MET cc_start: 0.7614 (mtm) cc_final: 0.7231 (mmm) REVERT: C 76 ILE cc_start: 0.6368 (OUTLIER) cc_final: 0.5680 (tp) REVERT: C 78 SER cc_start: 0.6828 (p) cc_final: 0.6491 (t) REVERT: C 101 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7586 (mt0) REVERT: D 19 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6311 (tt) REVERT: E 11 LYS cc_start: 0.6468 (tppt) cc_final: 0.5895 (mppt) REVERT: E 338 ARG cc_start: 0.6661 (mtp-110) cc_final: 0.6405 (mtm110) REVERT: F 21 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7057 (mp) REVERT: F 314 ARG cc_start: 0.6852 (ttm170) cc_final: 0.6651 (mtt-85) outliers start: 60 outliers final: 41 residues processed: 161 average time/residue: 1.0973 time to fit residues: 196.9524 Evaluate side-chains 157 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 110 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 34 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 145 optimal weight: 0.0020 chunk 156 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.233374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.189766 restraints weight = 17345.133| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 3.47 r_work: 0.3933 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14555 Z= 0.160 Angle : 0.644 8.720 19763 Z= 0.336 Chirality : 0.044 0.169 2136 Planarity : 0.005 0.080 2535 Dihedral : 5.298 58.122 2031 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.94 % Allowed : 17.54 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1812 helix: 0.18 (0.51), residues: 105 sheet: 0.35 (0.21), residues: 635 loop : -0.86 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 99 HIS 0.007 0.001 HIS E 195 PHE 0.042 0.002 PHE D 68 TYR 0.017 0.002 TYR F 200 ARG 0.004 0.000 ARG D 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 2) link_NAG-ASN : angle 3.59956 ( 6) hydrogen bonds : bond 0.04010 ( 469) hydrogen bonds : angle 5.72131 ( 1323) SS BOND : bond 0.00897 ( 22) SS BOND : angle 1.78079 ( 44) covalent geometry : bond 0.00371 (14531) covalent geometry : angle 0.63601 (19713) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 1.672 Fit side-chains REVERT: A 111 VAL cc_start: 0.6302 (m) cc_final: 0.6083 (t) REVERT: B 7 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7061 (mt-10) REVERT: B 34 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.6880 (m-10) REVERT: C 5 MET cc_start: 0.5238 (mtt) cc_final: 0.4687 (mmm) REVERT: C 76 ILE cc_start: 0.6353 (OUTLIER) cc_final: 0.5668 (tp) REVERT: C 101 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: D 19 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6241 (tt) REVERT: E 11 LYS cc_start: 0.6548 (tppt) cc_final: 0.6015 (mppt) REVERT: E 338 ARG cc_start: 0.6669 (mtp-110) cc_final: 0.6262 (ptm160) REVERT: F 21 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7011 (mp) outliers start: 46 outliers final: 36 residues processed: 145 average time/residue: 1.1766 time to fit residues: 191.5678 Evaluate side-chains 149 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 34 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 29 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 100 optimal weight: 0.0770 chunk 165 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 4 optimal weight: 0.0170 overall best weight: 0.9778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.235061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.191698 restraints weight = 17575.382| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 3.58 r_work: 0.3951 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14555 Z= 0.126 Angle : 0.599 7.773 19763 Z= 0.311 Chirality : 0.042 0.168 2136 Planarity : 0.005 0.079 2535 Dihedral : 5.034 57.528 2031 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.82 % Allowed : 17.86 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1812 helix: 0.49 (0.52), residues: 106 sheet: 0.48 (0.21), residues: 646 loop : -0.77 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 168 HIS 0.006 0.001 HIS E 195 PHE 0.027 0.002 PHE D 68 TYR 0.016 0.001 TYR F 200 ARG 0.011 0.000 ARG F 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 2) link_NAG-ASN : angle 2.87274 ( 6) hydrogen bonds : bond 0.03520 ( 469) hydrogen bonds : angle 5.52114 ( 1323) SS BOND : bond 0.00722 ( 22) SS BOND : angle 1.51252 ( 44) covalent geometry : bond 0.00291 (14531) covalent geometry : angle 0.59345 (19713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10452.20 seconds wall clock time: 181 minutes 24.80 seconds (10884.80 seconds total)