Starting phenix.real_space_refine on Thu Jun 12 17:27:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wo4_37678/06_2025/8wo4_37678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wo4_37678/06_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_37678/06_2025/8wo4_37678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wo4_37678/06_2025/8wo4_37678.map" model { file = "/net/cci-nas-00/data/ceres_data/8wo4_37678/06_2025/8wo4_37678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wo4_37678/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.58, per 1000 atoms: 0.82 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: 3.46 Conformation dependent library (CDL) restraints added in 2.0 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: 2.25 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: 5.00 Time building geometry restraints manager: 4.14 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: 30.520 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: 0.030 Extract box with map and model: 0.830 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 38.910 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.090 ------------------------------------------------------------------------------- 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 : 1.911 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: 1.2997 time to fit residues: 204.5071 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 : 1.823 ------------------------------------------------------------------------------- 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 = 17310.581| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.40 r_work: 0.3956 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- 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 : 1.537 Fit side-chains REVERT: A 111 VAL cc_start: 0.5137 (m) cc_final: 0.4785 (t) REVERT: A 127 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5793 (tttm) REVERT: C 76 ILE cc_start: 0.6134 (OUTLIER) cc_final: 0.5367 (tp) REVERT: C 78 SER cc_start: 0.6855 (p) cc_final: 0.6508 (t) REVERT: C 79 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7213 (tm) REVERT: E 85 GLN cc_start: 0.8120 (mt0) cc_final: 0.7688 (mt0) REVERT: F 133 PHE cc_start: 0.7613 (t80) cc_final: 0.7369 (t80) REVERT: F 138 ASP cc_start: 0.7558 (t0) cc_final: 0.7011 (t0) REVERT: H 34 MET cc_start: 0.1462 (tmm) cc_final: 0.1213 (tmm) outliers start: 48 outliers final: 21 residues processed: 164 average time/residue: 1.2313 time to fit residues: 222.5227 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 : 1.654 ------------------------------------------------------------------------------- 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: 0.6980 chunk 178 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 127 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 = 0.4719 r_free = 0.4719 target = 0.236453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.191426 restraints weight = 17338.577| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 3.25 r_work: 0.3952 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14555 Z= 0.151 Angle : 0.634 10.104 19763 Z= 0.330 Chirality : 0.043 0.160 2136 Planarity : 0.005 0.053 2535 Dihedral : 5.408 58.040 2032 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.88 % Allowed : 12.68 % Favored : 84.44 % 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: -0.31 (0.20), residues: 1812 helix: -0.27 (0.49), residues: 114 sheet: 0.48 (0.21), residues: 630 loop : -0.61 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 99 HIS 0.007 0.001 HIS E 195 PHE 0.033 0.002 PHE D 68 TYR 0.019 0.002 TYR F 32 ARG 0.005 0.000 ARG E 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 2) link_NAG-ASN : angle 4.82675 ( 6) hydrogen bonds : bond 0.04397 ( 469) hydrogen bonds : angle 6.12410 ( 1323) SS BOND : bond 0.00842 ( 22) SS BOND : angle 1.79234 ( 44) covalent geometry : bond 0.00343 (14531) covalent geometry : angle 0.62343 (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 167 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 1.479 Fit side-chains REVERT: A 111 VAL cc_start: 0.5346 (m) cc_final: 0.4966 (t) REVERT: C 76 ILE cc_start: 0.6253 (OUTLIER) cc_final: 0.5487 (tp) REVERT: C 78 SER cc_start: 0.6752 (p) cc_final: 0.6394 (t) REVERT: C 79 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7224 (tm) REVERT: C 101 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7395 (mt0) REVERT: D 65 LYS cc_start: 0.7076 (ttpt) cc_final: 0.6480 (tptt) REVERT: D 83 MET cc_start: 0.7374 (mtm) cc_final: 0.7107 (mtm) REVERT: E 11 LYS cc_start: 0.6260 (tppt) cc_final: 0.5069 (mppt) REVERT: F 133 PHE cc_start: 0.7484 (t80) cc_final: 0.7233 (t80) outliers start: 45 outliers final: 20 residues processed: 154 average time/residue: 1.2370 time to fit residues: 209.9266 Evaluate side-chains 128 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 47 GLU 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 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 138 ASP 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: 1.9990 chunk 173 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 94 optimal weight: 0.1980 chunk 16 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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 C 167 GLN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.234516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.189656 restraints weight = 17445.147| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 3.64 r_work: 0.3935 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14555 Z= 0.182 Angle : 0.682 9.710 19763 Z= 0.355 Chirality : 0.045 0.205 2136 Planarity : 0.005 0.055 2535 Dihedral : 5.536 57.870 2031 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.78 % Allowed : 13.32 % Favored : 82.91 % 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: -0.12 (0.51), residues: 103 sheet: 0.40 (0.21), residues: 628 loop : -0.76 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 99 HIS 0.007 0.002 HIS E 195 PHE 0.037 0.002 PHE D 68 TYR 0.023 0.002 TYR F 32 ARG 0.005 0.001 ARG E 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 2) link_NAG-ASN : angle 4.67003 ( 6) hydrogen bonds : bond 0.04466 ( 469) hydrogen bonds : angle 5.95255 ( 1323) SS BOND : bond 0.01010 ( 22) SS BOND : angle 2.05032 ( 44) covalent geometry : bond 0.00415 (14531) covalent geometry : angle 0.67145 (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 179 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 120 time to evaluate : 1.631 Fit side-chains REVERT: A 19 ARG cc_start: 0.6497 (mmm-85) cc_final: 0.6164 (tpt-90) REVERT: A 111 VAL cc_start: 0.5572 (m) cc_final: 0.5244 (t) REVERT: C 76 ILE cc_start: 0.6334 (OUTLIER) cc_final: 0.5581 (tp) REVERT: C 78 SER cc_start: 0.6758 (p) cc_final: 0.6418 (t) REVERT: C 79 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7205 (tm) REVERT: C 101 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: D 19 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6378 (tt) REVERT: E 11 LYS cc_start: 0.6136 (tppt) cc_final: 0.5168 (mppt) REVERT: F 133 PHE cc_start: 0.7496 (t80) cc_final: 0.7218 (t80) outliers start: 59 outliers final: 30 residues processed: 165 average time/residue: 1.3222 time to fit residues: 240.8801 Evaluate side-chains 148 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 116 VAL 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 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 E residue 6 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 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 140 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 172 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 = 0.4689 r_free = 0.4689 target = 0.232951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.170548 restraints weight = 17515.100| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.20 r_work: 0.3955 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 14555 Z= 0.197 Angle : 0.697 10.150 19763 Z= 0.363 Chirality : 0.045 0.169 2136 Planarity : 0.005 0.060 2535 Dihedral : 5.634 58.050 2031 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.35 % Allowed : 14.02 % Favored : 81.63 % 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: -0.65 (0.20), residues: 1812 helix: -0.28 (0.50), residues: 105 sheet: 0.35 (0.21), residues: 624 loop : -0.93 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 99 HIS 0.008 0.002 HIS E 195 PHE 0.042 0.002 PHE D 68 TYR 0.028 0.002 TYR F 32 ARG 0.006 0.001 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 2) link_NAG-ASN : angle 4.86108 ( 6) hydrogen bonds : bond 0.04553 ( 469) hydrogen bonds : angle 5.95684 ( 1323) SS BOND : bond 0.00960 ( 22) SS BOND : angle 2.05966 ( 44) covalent geometry : bond 0.00456 (14531) covalent geometry : angle 0.68571 (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 188 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 120 time to evaluate : 1.724 Fit side-chains REVERT: A 5 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6416 (mtp) REVERT: A 19 ARG cc_start: 0.6616 (mmm-85) cc_final: 0.6225 (tpt-90) REVERT: A 111 VAL cc_start: 0.5972 (m) cc_final: 0.5680 (t) REVERT: C 76 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.5673 (tp) REVERT: C 78 SER cc_start: 0.6765 (p) cc_final: 0.6418 (t) REVERT: C 79 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7290 (tm) REVERT: C 101 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: D 19 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6308 (tt) REVERT: D 99 TRP cc_start: 0.7183 (t-100) cc_final: 0.6898 (t-100) REVERT: E 11 LYS cc_start: 0.6248 (tppt) cc_final: 0.5323 (mppt) REVERT: E 85 GLN cc_start: 0.8066 (mt0) cc_final: 0.7384 (mm110) REVERT: F 21 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7171 (mp) REVERT: F 133 PHE cc_start: 0.7454 (t80) cc_final: 0.7194 (t80) outliers start: 68 outliers final: 36 residues processed: 173 average time/residue: 1.2036 time to fit residues: 230.4200 Evaluate side-chains 154 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET 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 30 VAL Chi-restraints excluded: chain B residue 47 GLU 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 79 LEU 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 D residue 47 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 162 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 102 optimal weight: 0.0870 chunk 71 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 overall best weight: 2.7364 ------------------------------------------------------------------------------- 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 = 0.4667 r_free = 0.4667 target = 0.230793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.168637 restraints weight = 17610.942| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.18 r_work: 0.3931 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 14555 Z= 0.237 Angle : 0.775 11.332 19763 Z= 0.405 Chirality : 0.047 0.199 2136 Planarity : 0.006 0.065 2535 Dihedral : 5.954 57.738 2031 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.74 % Allowed : 14.40 % Favored : 80.86 % 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: -0.96 (0.20), residues: 1812 helix: -0.57 (0.50), residues: 104 sheet: 0.29 (0.21), residues: 614 loop : -1.23 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP D 99 HIS 0.008 0.002 HIS E 195 PHE 0.051 0.003 PHE D 68 TYR 0.017 0.002 TYR A 87 ARG 0.006 0.001 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00776 ( 2) link_NAG-ASN : angle 5.56627 ( 6) hydrogen bonds : bond 0.05048 ( 469) hydrogen bonds : angle 6.18331 ( 1323) SS BOND : bond 0.01202 ( 22) SS BOND : angle 2.30039 ( 44) covalent geometry : bond 0.00547 (14531) covalent geometry : angle 0.76175 (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 197 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 123 time to evaluate : 1.612 Fit side-chains REVERT: A 5 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6554 (mtp) REVERT: A 111 VAL cc_start: 0.6402 (m) cc_final: 0.6140 (t) REVERT: A 127 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.6011 (tttm) REVERT: B 7 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: C 76 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.5746 (tp) REVERT: C 78 SER cc_start: 0.6854 (p) cc_final: 0.6530 (t) REVERT: C 79 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7246 (tm) REVERT: C 101 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: D 19 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6341 (tt) REVERT: E 11 LYS cc_start: 0.6432 (tppt) cc_final: 0.5665 (mppt) REVERT: E 85 GLN cc_start: 0.8045 (mt0) cc_final: 0.7363 (mm110) REVERT: F 8 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.5859 (m-80) REVERT: F 21 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7244 (mp) outliers start: 74 outliers final: 46 residues processed: 185 average time/residue: 1.4630 time to fit residues: 304.3009 Evaluate side-chains 174 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 119 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET 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 127 LYS 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 47 GLU 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 B residue 117 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 20 VAL 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 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 47 GLU Chi-restraints excluded: chain D residue 114 THR 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 138 ASP Chi-restraints excluded: chain E residue 162 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 8 PHE 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 60 VAL 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 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: 1.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4675 r_free = 0.4675 target = 0.231918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.176120 restraints weight = 17453.091| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.72 r_work: 0.3969 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 14555 Z= 0.186 Angle : 0.686 9.659 19763 Z= 0.359 Chirality : 0.045 0.159 2136 Planarity : 0.005 0.063 2535 Dihedral : 5.604 57.531 2031 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.55 % Allowed : 15.94 % 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: -0.84 (0.20), residues: 1812 helix: -0.15 (0.52), residues: 103 sheet: 0.19 (0.21), residues: 637 loop : -1.08 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 99 HIS 0.007 0.001 HIS E 195 PHE 0.051 0.002 PHE D 68 TYR 0.024 0.002 TYR B 152 ARG 0.004 0.001 ARG E 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 2) link_NAG-ASN : angle 4.82559 ( 6) hydrogen bonds : bond 0.04354 ( 469) hydrogen bonds : angle 5.96440 ( 1323) SS BOND : bond 0.01016 ( 22) SS BOND : angle 1.96485 ( 44) covalent geometry : bond 0.00430 (14531) covalent geometry : angle 0.67582 (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 197 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 126 time to evaluate : 2.965 Fit side-chains REVERT: A 111 VAL cc_start: 0.6418 (m) cc_final: 0.5946 (t) REVERT: A 127 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.5990 (pttm) REVERT: A 200 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6271 (mp-120) REVERT: B 7 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: C 76 ILE cc_start: 0.6458 (OUTLIER) cc_final: 0.5687 (tp) REVERT: C 78 SER cc_start: 0.6781 (p) cc_final: 0.6452 (t) REVERT: C 79 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7235 (tm) REVERT: C 91 GLN cc_start: 0.5194 (mt0) cc_final: 0.4918 (mt0) REVERT: C 101 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: D 99 TRP cc_start: 0.7172 (t-100) cc_final: 0.6933 (t-100) REVERT: E 11 LYS cc_start: 0.6582 (tppt) cc_final: 0.5798 (mppt) REVERT: E 85 GLN cc_start: 0.8008 (mt0) cc_final: 0.7284 (mm110) REVERT: E 338 ARG cc_start: 0.6934 (mtp-110) cc_final: 0.6378 (ptm160) REVERT: F 8 PHE cc_start: 0.6234 (OUTLIER) cc_final: 0.5833 (m-80) REVERT: F 21 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7011 (mp) outliers start: 71 outliers final: 50 residues processed: 185 average time/residue: 1.6332 time to fit residues: 340.1565 Evaluate side-chains 176 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 118 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 127 LYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 GLN 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 47 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 20 VAL 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 79 LEU 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 111 VAL 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 D residue 114 THR 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 88 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 202 ILE 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 8 PHE 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 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: 0.7980 chunk 47 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 178 optimal weight: 0.0370 chunk 123 optimal weight: 0.0040 chunk 111 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 overall best weight: 0.5470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN 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 = 0.4719 r_free = 0.4719 target = 0.236709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.193191 restraints weight = 17361.360| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 3.42 r_work: 0.3984 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3431 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 : 0.563 8.986 19763 Z= 0.294 Chirality : 0.042 0.153 2136 Planarity : 0.005 0.055 2535 Dihedral : 4.925 56.728 2031 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.75 % Allowed : 18.18 % Favored : 79.07 % 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: -0.41 (0.20), residues: 1812 helix: 0.51 (0.52), residues: 106 sheet: 0.47 (0.20), residues: 645 loop : -0.83 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 168 HIS 0.007 0.001 HIS E 195 PHE 0.020 0.001 PHE D 68 TYR 0.019 0.001 TYR B 152 ARG 0.010 0.000 ARG F 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 2) link_NAG-ASN : angle 3.01585 ( 6) hydrogen bonds : bond 0.03143 ( 469) hydrogen bonds : angle 5.43164 ( 1323) SS BOND : bond 0.00546 ( 22) SS BOND : angle 1.30672 ( 44) covalent geometry : bond 0.00248 (14531) covalent geometry : angle 0.55817 (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 173 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 1.600 Fit side-chains REVERT: B 83 MET cc_start: 0.7532 (mtm) cc_final: 0.7278 (mmm) REVERT: C 5 MET cc_start: 0.5072 (mtp) cc_final: 0.4600 (mmm) REVERT: C 76 ILE cc_start: 0.6287 (OUTLIER) cc_final: 0.5633 (tp) REVERT: C 101 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7405 (mt0) REVERT: E 85 GLN cc_start: 0.7956 (mt0) cc_final: 0.7332 (mm110) REVERT: E 168 TRP cc_start: 0.6027 (m100) cc_final: 0.5721 (m100) REVERT: E 338 ARG cc_start: 0.6797 (mtp-110) cc_final: 0.6456 (ptp-170) REVERT: G 44 GLU cc_start: 0.2998 (OUTLIER) cc_final: 0.2696 (mp0) outliers start: 43 outliers final: 24 residues processed: 162 average time/residue: 1.8257 time to fit residues: 327.5805 Evaluate side-chains 144 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 13 ILE 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 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 D residue 47 GLU 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 293 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER 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 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 169 optimal weight: 20.0000 chunk 141 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** 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 = 0.4671 r_free = 0.4671 target = 0.231481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.187010 restraints weight = 17278.175| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 3.52 r_work: 0.3912 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 14555 Z= 0.203 Angle : 0.701 9.428 19763 Z= 0.365 Chirality : 0.045 0.182 2136 Planarity : 0.005 0.059 2535 Dihedral : 5.405 58.219 2031 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.52 % Allowed : 18.37 % Favored : 78.10 % 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: -0.63 (0.20), residues: 1812 helix: 0.05 (0.51), residues: 103 sheet: 0.33 (0.21), residues: 642 loop : -0.95 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 99 HIS 0.007 0.001 HIS E 195 PHE 0.049 0.002 PHE D 68 TYR 0.023 0.002 TYR E 200 ARG 0.012 0.001 ARG F 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 2) link_NAG-ASN : angle 4.03877 ( 6) hydrogen bonds : bond 0.04401 ( 469) hydrogen bonds : angle 5.80976 ( 1323) SS BOND : bond 0.01029 ( 22) SS BOND : angle 1.94600 ( 44) covalent geometry : bond 0.00471 (14531) covalent geometry : angle 0.69193 (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 169 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: C 76 ILE cc_start: 0.6347 (OUTLIER) cc_final: 0.5638 (tp) REVERT: C 101 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: D 19 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6236 (tt) REVERT: D 99 TRP cc_start: 0.7188 (t-100) cc_final: 0.6967 (t-100) REVERT: E 11 LYS cc_start: 0.6741 (tppt) cc_final: 0.5961 (mppt) REVERT: E 85 GLN cc_start: 0.8012 (mt0) cc_final: 0.7327 (mm110) REVERT: E 338 ARG cc_start: 0.6837 (mtp-110) cc_final: 0.6477 (ptp-170) REVERT: F 21 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7050 (mp) REVERT: G 44 GLU cc_start: 0.2997 (OUTLIER) cc_final: 0.2671 (mp0) outliers start: 55 outliers final: 34 residues processed: 156 average time/residue: 1.1335 time to fit residues: 196.9606 Evaluate side-chains 154 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 A residue 192 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 20 VAL 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 105 VAL 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 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 293 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 ASP 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 108 VAL Chi-restraints excluded: chain F residue 140 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** 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 = 0.4689 r_free = 0.4689 target = 0.233520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.189967 restraints weight = 17367.141| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 3.45 r_work: 0.3942 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14555 Z= 0.140 Angle : 0.621 8.331 19763 Z= 0.323 Chirality : 0.043 0.151 2136 Planarity : 0.005 0.056 2535 Dihedral : 5.158 57.539 2031 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.43 % Allowed : 19.27 % Favored : 78.30 % 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: -0.49 (0.20), residues: 1812 helix: 0.44 (0.52), residues: 103 sheet: 0.39 (0.21), residues: 647 loop : -0.87 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 99 HIS 0.007 0.001 HIS E 195 PHE 0.031 0.002 PHE D 68 TYR 0.022 0.002 TYR B 152 ARG 0.011 0.000 ARG F 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 2) link_NAG-ASN : angle 3.30511 ( 6) hydrogen bonds : bond 0.03715 ( 469) hydrogen bonds : angle 5.60091 ( 1323) SS BOND : bond 0.00764 ( 22) SS BOND : angle 1.69460 ( 44) covalent geometry : bond 0.00321 (14531) covalent geometry : angle 0.61357 (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 153 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.677 Fit side-chains revert: symmetry clash REVERT: B 83 MET cc_start: 0.7606 (mtm) cc_final: 0.7295 (mmm) REVERT: C 76 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5622 (tp) REVERT: C 101 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7484 (mt0) REVERT: E 11 LYS cc_start: 0.6738 (tppt) cc_final: 0.5980 (mppt) REVERT: E 85 GLN cc_start: 0.7931 (mt0) cc_final: 0.7291 (mm110) REVERT: E 168 TRP cc_start: 0.6090 (m100) cc_final: 0.5779 (m100) REVERT: E 338 ARG cc_start: 0.6813 (mtp-110) cc_final: 0.6476 (ptp-170) REVERT: G 44 GLU cc_start: 0.3024 (OUTLIER) cc_final: 0.2673 (mt-10) outliers start: 38 outliers final: 26 residues processed: 144 average time/residue: 1.2154 time to fit residues: 194.3784 Evaluate side-chains 142 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 A residue 173 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 214 GLU 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 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 108 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 30 ASP 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 108 VAL Chi-restraints excluded: chain F residue 140 LEU 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 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 29 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** 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 = 0.4669 r_free = 0.4669 target = 0.231270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.187404 restraints weight = 17475.121| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 3.53 r_work: 0.3888 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 14555 Z= 0.198 Angle : 0.703 9.141 19763 Z= 0.366 Chirality : 0.045 0.215 2136 Planarity : 0.006 0.077 2535 Dihedral : 5.479 58.339 2031 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.14 % Allowed : 18.89 % Favored : 77.98 % 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: -0.70 (0.20), residues: 1812 helix: 0.01 (0.51), residues: 103 sheet: 0.26 (0.21), residues: 647 loop : -0.99 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 99 HIS 0.007 0.001 HIS E 195 PHE 0.043 0.002 PHE D 68 TYR 0.022 0.002 TYR E 200 ARG 0.012 0.001 ARG F 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 2) link_NAG-ASN : angle 3.93550 ( 6) hydrogen bonds : bond 0.04447 ( 469) hydrogen bonds : angle 5.84516 ( 1323) SS BOND : bond 0.01036 ( 22) SS BOND : angle 2.03460 ( 44) covalent geometry : bond 0.00461 (14531) covalent geometry : angle 0.69415 (19713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11339.89 seconds wall clock time: 198 minutes 34.14 seconds (11914.14 seconds total)