Starting phenix.real_space_refine on Fri May 16 06:23:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wnp_37670/05_2025/8wnp_37670.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wnp_37670/05_2025/8wnp_37670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wnp_37670/05_2025/8wnp_37670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wnp_37670/05_2025/8wnp_37670.map" model { file = "/net/cci-nas-00/data/ceres_data/8wnp_37670/05_2025/8wnp_37670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wnp_37670/05_2025/8wnp_37670.cif" } resolution = 3.1 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= -0.000 sd= 0.010 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 8848 2.51 5 N 2444 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14142 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1673 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 212} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Chain: "D" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1673 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2818 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2818 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 923 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 923 Classifications: {'peptide': 120} Modifications used: {'COO': 1} 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: 10.62, per 1000 atoms: 0.75 Number of scatterers: 14142 At special positions: 0 Unit cell: (86.36, 155.72, 138.04, 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 2776 8.00 N 2444 7.00 C 8848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, 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 219 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 143 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 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 219 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 143 " - pdb=" SG CYS D 199 " 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 313 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 15 " distance=2.05 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 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 95 " distance=2.04 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 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.7 seconds 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3344 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 37 sheets defined 10.0% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 122 through 128 Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.525A pdb=" N GLU A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 188' Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 204 through 207 Processing helix chain 'C' and resid 122 through 128 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'D' and resid 29 through 33 removed outlier: 3.565A pdb=" N ASN D 33 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 130 through 134 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 190 through 194 removed outlier: 3.806A pdb=" N GLY D 193 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 207 Processing helix chain 'E' and resid 38 through 51 removed outlier: 3.726A pdb=" N GLU E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 82 removed outlier: 3.639A pdb=" N SER E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 72 " --> pdb=" O TRP E 68 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLY E 73 " --> pdb=" O LYS E 69 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) 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 237 through 241 removed outlier: 3.564A pdb=" N LEU E 241 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 248 removed outlier: 3.563A pdb=" N ALA E 248 " --> pdb=" O LYS E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 52 removed outlier: 3.668A pdb=" N GLU F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 71 through 80 removed outlier: 3.777A pdb=" N LEU F 79 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 148 Processing helix chain 'F' and resid 226 through 230 removed outlier: 3.623A pdb=" N HIS F 229 " --> pdb=" O PRO F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 241 removed outlier: 3.677A pdb=" N LEU F 241 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 248 Processing helix chain 'G' and resid 27 through 31 removed outlier: 3.979A pdb=" N ARG G 30 " --> pdb=" O THR G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'H' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 4.304A pdb=" N VAL A 20 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 76 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 24 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE A 72 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A 71 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.713A pdb=" N LEU A 12 " --> pdb=" O GLU A 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.932A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 86 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.594A pdb=" N ASN A 139 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR A 174 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.608A pdb=" N LYS A 146 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.156A pdb=" N GLY B 11 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 92 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP B 99 " --> pdb=" O TYR B 34 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR B 34 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP B 37 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 50 " --> pdb=" O TRP B 37 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG B 39 " --> pdb=" O TRP B 48 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TRP B 48 " --> pdb=" O ARG B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 127 removed outlier: 3.664A pdb=" N VAL B 145 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 184 " --> pdb=" O HIS B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.664A pdb=" N VAL B 145 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 157 removed outlier: 4.702A pdb=" N TYR B 197 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 7 through 8 removed outlier: 3.526A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS C 24 " --> pdb=" O PHE C 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.545A pdb=" N LEU C 12 " --> pdb=" O GLU C 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.639A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 119 removed outlier: 3.594A pdb=" N LEU C 136 " --> pdb=" O PHE C 117 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 134 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.526A pdb=" N VAL C 206 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 8 removed outlier: 4.000A pdb=" N GLN D 4 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER D 26 " --> pdb=" O GLN D 4 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.703A pdb=" N ALA D 92 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR D 34 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET D 35 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 51 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.703A pdb=" N ALA D 92 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR D 105 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 127 removed outlier: 3.738A pdb=" N GLY D 142 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 145 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR D 179 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 123 through 127 removed outlier: 3.738A pdb=" N GLY D 142 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 145 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR D 179 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 154 through 157 Processing sheet with id=AC4, first strand: chain 'E' and resid 18 through 20 Processing sheet with id=AC5, first strand: chain 'E' and resid 32 through 34 removed outlier: 7.890A pdb=" N LYS E 33 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N LEU E 169 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TRP E 168 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU E 156 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 56 through 57 removed outlier: 7.336A pdb=" N GLY E 56 " --> pdb=" O ALA E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 87 through 90 removed outlier: 6.760A pdb=" N THR E 87 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL E 135 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL E 89 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 329 through 331 removed outlier: 3.597A pdb=" N SER E 322 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU E 203 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA E 215 " --> pdb=" O TRP E 201 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP E 201 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 192 " --> pdb=" O LYS E 189 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP F 201 " --> pdb=" O HIS F 216 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU F 205 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU F 212 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N LYS F 213 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE F 277 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 311 through 312 Processing sheet with id=AD1, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.725A pdb=" N GLY F 3 " --> pdb=" O GLY F 16 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG F 14 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 33 through 36 removed outlier: 3.557A pdb=" N LEU F 169 " --> pdb=" O HIS F 35 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP F 157 " --> pdb=" O TRP F 168 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS F 170 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL F 155 " --> pdb=" O LYS F 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 88 through 90 removed outlier: 6.391A pdb=" N VAL F 89 " --> pdb=" O VAL F 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 284 through 285 removed outlier: 5.940A pdb=" N LYS F 284 " --> pdb=" O TRP F 311 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.608A pdb=" N SER G 6 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.739A pdb=" N VAL G 11 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ARG G 37 " --> pdb=" O PHE G 46 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE G 46 " --> pdb=" O ARG G 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.739A pdb=" N VAL G 11 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N CYS G 95 " --> pdb=" O TRP G 110 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP G 110 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE G 97 " --> pdb=" O ASP G 108 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD9, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.517A pdb=" N GLY H 9 " --> pdb=" O THR H 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.448A pdb=" N PHE H 46 " --> pdb=" O ARG H 37 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG H 37 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR H 109 " --> pdb=" O ILE H 97 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 3.54 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: 14374 1.57 - 1.93: 100 1.93 - 2.28: 0 2.28 - 2.63: 0 2.63 - 2.99: 3 Bond restraints: 14477 Sorted by residual: bond pdb=" C THR B 119 " pdb=" N LYS B 120 " ideal model delta sigma weight residual 1.332 2.916 -1.584 1.31e-02 5.83e+03 1.46e+04 bond pdb=" C THR D 119 " pdb=" N LYS D 120 " ideal model delta sigma weight residual 1.332 2.976 -1.644 1.40e-02 5.10e+03 1.38e+04 bond pdb=" C ARG A 109 " pdb=" N THR A 110 " ideal model delta sigma weight residual 1.327 2.987 -1.660 1.47e-02 4.63e+03 1.27e+04 bond pdb=" CA LEU B 127 " pdb=" CB LEU B 127 " ideal model delta sigma weight residual 1.525 1.552 -0.027 1.47e-02 4.63e+03 3.48e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 ... (remaining 14472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.10: 19644 16.10 - 32.20: 3 32.20 - 48.30: 0 48.30 - 64.40: 0 64.40 - 80.50: 2 Bond angle restraints: 19649 Sorted by residual: angle pdb=" O THR D 119 " pdb=" C THR D 119 " pdb=" N LYS D 120 " ideal model delta sigma weight residual 122.59 42.09 80.50 1.33e+00 5.65e-01 3.66e+03 angle pdb=" O ARG A 109 " pdb=" C ARG A 109 " pdb=" N THR A 110 " ideal model delta sigma weight residual 122.59 57.99 64.60 1.33e+00 5.65e-01 2.36e+03 angle pdb=" CA THR B 119 " pdb=" C THR B 119 " pdb=" N LYS B 120 " ideal model delta sigma weight residual 116.39 86.00 30.39 1.26e+00 6.30e-01 5.82e+02 angle pdb=" C THR B 119 " pdb=" N LYS B 120 " pdb=" CA LYS B 120 " ideal model delta sigma weight residual 122.95 150.92 -27.97 1.44e+00 4.82e-01 3.77e+02 angle pdb=" C THR D 119 " pdb=" N LYS D 120 " pdb=" CA LYS D 120 " ideal model delta sigma weight residual 121.54 102.63 18.91 1.91e+00 2.74e-01 9.81e+01 ... (remaining 19644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7800 17.91 - 35.81: 699 35.81 - 53.71: 154 53.71 - 71.62: 29 71.62 - 89.52: 17 Dihedral angle restraints: 8699 sinusoidal: 3466 harmonic: 5233 Sorted by residual: dihedral pdb=" CB CYS E 313 " pdb=" SG CYS E 313 " pdb=" SG CYS E 316 " pdb=" CB CYS E 316 " ideal model delta sinusoidal sigma weight residual -86.00 -170.54 84.54 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS F 313 " pdb=" SG CYS F 313 " pdb=" SG CYS F 316 " pdb=" CB CYS F 316 " ideal model delta sinusoidal sigma weight residual -86.00 -152.81 66.81 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CA ARG A 109 " pdb=" C ARG A 109 " pdb=" N THR A 110 " pdb=" CA THR A 110 " ideal model delta harmonic sigma weight residual 180.00 145.63 34.37 0 5.00e+00 4.00e-02 4.73e+01 ... (remaining 8696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1559 0.039 - 0.078: 383 0.078 - 0.117: 148 0.117 - 0.156: 47 0.156 - 0.194: 2 Chirality restraints: 2139 Sorted by residual: chirality pdb=" CA PRO E 320 " pdb=" N PRO E 320 " pdb=" C PRO E 320 " pdb=" CB PRO E 320 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CA ILE E 21 " pdb=" N ILE E 21 " pdb=" C ILE E 21 " pdb=" CB ILE E 21 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE A 49 " pdb=" N ILE A 49 " pdb=" C ILE A 49 " pdb=" CB ILE A 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.71e-01 ... (remaining 2136 not shown) Planarity restraints: 2532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 109 " -0.182 2.00e-02 2.50e+03 2.73e-01 7.44e+02 pdb=" C ARG A 109 " 0.438 2.00e-02 2.50e+03 pdb=" O ARG A 109 " -0.269 2.00e-02 2.50e+03 pdb=" N THR A 110 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 119 " 0.145 2.00e-02 2.50e+03 2.59e-01 6.69e+02 pdb=" C THR D 119 " -0.396 2.00e-02 2.50e+03 pdb=" O THR D 119 " 0.296 2.00e-02 2.50e+03 pdb=" N LYS D 120 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 119 " -0.082 2.00e-02 2.50e+03 1.76e-01 3.10e+02 pdb=" C THR B 119 " 0.296 2.00e-02 2.50e+03 pdb=" O THR B 119 " -0.165 2.00e-02 2.50e+03 pdb=" N LYS B 120 " -0.048 2.00e-02 2.50e+03 ... (remaining 2529 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 112 2.54 - 3.13: 10724 3.13 - 3.72: 19550 3.72 - 4.31: 27431 4.31 - 4.90: 48659 Nonbonded interactions: 106476 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" OE1 GLN C 90 " model vdw 1.951 3.040 nonbonded pdb=" O GLU F 258 " pdb=" OG1 THR F 317 " model vdw 2.026 3.040 nonbonded pdb=" OG SER G 99 " pdb=" OG SER G 104 " model vdw 2.084 3.040 nonbonded pdb=" O LEU E 212 " pdb=" NH1 ARG E 257 " model vdw 2.104 3.120 nonbonded pdb=" OE1 GLN G 38 " pdb=" OH TYR G 94 " model vdw 2.109 3.040 ... (remaining 106471 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: 0.03 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: 19.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.750 Find NCS groups from input model: 0.410 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 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 : 0.024 1.660 14502 Z= 1.692 Angle : 1.041 80.499 19700 Z= 0.709 Chirality : 0.043 0.194 2139 Planarity : 0.009 0.273 2531 Dihedral : 14.690 89.525 5283 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.12 % Favored : 92.77 % Rotamer: Outliers : 0.38 % Allowed : 11.91 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.20), residues: 1798 helix: -1.44 (0.53), residues: 86 sheet: -0.54 (0.21), residues: 595 loop : -1.11 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 35 HIS 0.005 0.001 HIS F 113 PHE 0.013 0.001 PHE F 133 TYR 0.013 0.001 TYR D 95 ARG 0.004 0.000 ARG D 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 1) link_NAG-ASN : angle 7.20062 ( 3) hydrogen bonds : bond 0.26699 ( 408) hydrogen bonds : angle 10.06000 ( 1077) SS BOND : bond 0.00510 ( 24) SS BOND : angle 1.65729 ( 48) covalent geometry : bond 0.02368 (14477) covalent geometry : angle 1.03504 (19649) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 159 average time/residue: 0.2965 time to fit residues: 66.5779 Evaluate side-chains 142 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain F residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 203 HIS C 167 GLN C 199 HIS C 211 ASN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 HIS F 254 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.218570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.177850 restraints weight = 17779.055| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.61 r_work: 0.4002 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14502 Z= 0.210 Angle : 0.752 12.115 19700 Z= 0.389 Chirality : 0.048 0.210 2139 Planarity : 0.006 0.087 2531 Dihedral : 6.354 59.195 2042 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.60 % Favored : 93.29 % Rotamer: Outliers : 2.82 % Allowed : 13.44 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.19), residues: 1804 helix: -1.39 (0.52), residues: 85 sheet: -0.33 (0.21), residues: 621 loop : -1.27 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 35 HIS 0.009 0.001 HIS F 113 PHE 0.018 0.002 PHE E 323 TYR 0.018 0.002 TYR A 50 ARG 0.008 0.001 ARG F 276 Details of bonding type rmsd link_NAG-ASN : bond 0.00891 ( 1) link_NAG-ASN : angle 9.06025 ( 3) hydrogen bonds : bond 0.04788 ( 408) hydrogen bonds : angle 7.14084 ( 1077) SS BOND : bond 0.00692 ( 24) SS BOND : angle 1.82641 ( 48) covalent geometry : bond 0.00492 (14477) covalent geometry : angle 0.73895 (19649) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 1.583 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6383 (tp) REVERT: A 167 GLN cc_start: 0.5732 (pm20) cc_final: 0.5481 (tt0) REVERT: A 168 ASP cc_start: 0.6963 (t0) cc_final: 0.6719 (t0) REVERT: D 195 GLN cc_start: 0.6582 (mp10) cc_final: 0.6352 (mp10) REVERT: E 34 TYR cc_start: 0.5767 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: F 233 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7292 (p) REVERT: F 323 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.5311 (m-80) REVERT: H 51 ARG cc_start: 0.6355 (mtt180) cc_final: 0.6108 (mtt180) outliers start: 44 outliers final: 27 residues processed: 181 average time/residue: 0.2721 time to fit residues: 71.8804 Evaluate side-chains 167 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 172 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 1 optimal weight: 8.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN F 216 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.216191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.176030 restraints weight = 17743.789| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.59 r_work: 0.4014 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14502 Z= 0.204 Angle : 0.735 12.322 19700 Z= 0.379 Chirality : 0.047 0.241 2139 Planarity : 0.006 0.079 2531 Dihedral : 6.447 59.967 2040 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.98 % Favored : 92.90 % Rotamer: Outliers : 4.16 % Allowed : 14.79 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 1804 helix: -1.32 (0.52), residues: 85 sheet: -0.23 (0.21), residues: 613 loop : -1.40 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 35 HIS 0.008 0.002 HIS F 113 PHE 0.020 0.002 PHE E 323 TYR 0.018 0.002 TYR A 50 ARG 0.007 0.001 ARG D 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 1) link_NAG-ASN : angle 9.26606 ( 3) hydrogen bonds : bond 0.04391 ( 408) hydrogen bonds : angle 6.71483 ( 1077) SS BOND : bond 0.00792 ( 24) SS BOND : angle 1.92234 ( 48) covalent geometry : bond 0.00481 (14477) covalent geometry : angle 0.72092 (19649) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 138 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6353 (tp) REVERT: A 144 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4423 (tm-30) REVERT: A 167 GLN cc_start: 0.5825 (pm20) cc_final: 0.5585 (tt0) REVERT: D 76 LYS cc_start: 0.5552 (tppt) cc_final: 0.5088 (mmtp) REVERT: D 195 GLN cc_start: 0.6536 (mp10) cc_final: 0.6180 (mp10) REVERT: E 34 TYR cc_start: 0.5890 (OUTLIER) cc_final: 0.5532 (m-80) REVERT: E 150 TRP cc_start: 0.6618 (t60) cc_final: 0.6354 (t-100) REVERT: F 131 ASN cc_start: 0.7138 (OUTLIER) cc_final: 0.6895 (p0) outliers start: 65 outliers final: 40 residues processed: 198 average time/residue: 0.2591 time to fit residues: 75.3457 Evaluate side-chains 169 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.221974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.182338 restraints weight = 17754.647| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.56 r_work: 0.4073 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14502 Z= 0.111 Angle : 0.591 12.334 19700 Z= 0.304 Chirality : 0.043 0.195 2139 Planarity : 0.005 0.070 2531 Dihedral : 5.674 57.607 2038 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.71 % Favored : 95.18 % Rotamer: Outliers : 2.50 % Allowed : 16.90 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 1804 helix: -0.67 (0.53), residues: 87 sheet: 0.02 (0.22), residues: 613 loop : -1.17 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 330 HIS 0.006 0.001 HIS F 113 PHE 0.012 0.001 PHE A 140 TYR 0.011 0.001 TYR D 95 ARG 0.012 0.000 ARG F 62 Details of bonding type rmsd link_NAG-ASN : bond 0.01275 ( 1) link_NAG-ASN : angle 8.88420 ( 3) hydrogen bonds : bond 0.03079 ( 408) hydrogen bonds : angle 5.97326 ( 1077) SS BOND : bond 0.00384 ( 24) SS BOND : angle 1.21927 ( 48) covalent geometry : bond 0.00251 (14477) covalent geometry : angle 0.57880 (19649) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.5268 (OUTLIER) cc_final: 0.4430 (tm-30) REVERT: B 195 GLN cc_start: 0.3632 (OUTLIER) cc_final: 0.3399 (mp10) REVERT: D 76 LYS cc_start: 0.5546 (tppt) cc_final: 0.5144 (mmtp) REVERT: D 195 GLN cc_start: 0.6458 (mp10) cc_final: 0.6192 (mp10) REVERT: E 34 TYR cc_start: 0.5441 (OUTLIER) cc_final: 0.5075 (m-80) REVERT: E 202 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6632 (mt) REVERT: F 233 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7141 (p) outliers start: 39 outliers final: 23 residues processed: 171 average time/residue: 0.2671 time to fit residues: 65.8777 Evaluate side-chains 155 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain H residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 159 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.215938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.175987 restraints weight = 17968.223| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.63 r_work: 0.3983 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 14502 Z= 0.240 Angle : 0.768 12.247 19700 Z= 0.395 Chirality : 0.048 0.202 2139 Planarity : 0.006 0.103 2531 Dihedral : 6.406 59.418 2038 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.82 % Favored : 92.07 % Rotamer: Outliers : 4.42 % Allowed : 16.45 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1804 helix: -1.28 (0.52), residues: 79 sheet: -0.19 (0.22), residues: 622 loop : -1.42 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 210 HIS 0.009 0.002 HIS E 35 PHE 0.022 0.003 PHE E 323 TYR 0.020 0.002 TYR A 50 ARG 0.011 0.001 ARG F 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00878 ( 1) link_NAG-ASN : angle 9.19103 ( 3) hydrogen bonds : bond 0.04398 ( 408) hydrogen bonds : angle 6.58015 ( 1077) SS BOND : bond 0.00779 ( 24) SS BOND : angle 1.95631 ( 48) covalent geometry : bond 0.00567 (14477) covalent geometry : angle 0.75400 (19649) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 137 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.6918 (m-80) cc_final: 0.6641 (m-80) REVERT: A 144 GLU cc_start: 0.5505 (OUTLIER) cc_final: 0.4563 (tm-30) REVERT: B 72 ARG cc_start: 0.6491 (ptt180) cc_final: 0.5988 (ptt180) REVERT: B 195 GLN cc_start: 0.3890 (OUTLIER) cc_final: 0.3651 (mp10) REVERT: D 67 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7309 (mtm110) REVERT: D 76 LYS cc_start: 0.5563 (tppt) cc_final: 0.5174 (mmtp) REVERT: D 195 GLN cc_start: 0.6521 (mp10) cc_final: 0.6197 (mp10) REVERT: E 34 TYR cc_start: 0.5969 (OUTLIER) cc_final: 0.5590 (m-80) REVERT: E 202 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6854 (mt) REVERT: F 233 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7319 (p) outliers start: 69 outliers final: 50 residues processed: 197 average time/residue: 0.2553 time to fit residues: 73.7549 Evaluate side-chains 180 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 124 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.220942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.182155 restraints weight = 17876.937| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 2.52 r_work: 0.4109 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3984 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14502 Z= 0.143 Angle : 0.644 12.342 19700 Z= 0.330 Chirality : 0.044 0.188 2139 Planarity : 0.005 0.067 2531 Dihedral : 5.976 58.475 2038 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.32 % Favored : 94.57 % Rotamer: Outliers : 3.78 % Allowed : 17.35 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.20), residues: 1804 helix: -0.81 (0.54), residues: 85 sheet: -0.10 (0.21), residues: 624 loop : -1.28 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 115 HIS 0.007 0.001 HIS E 113 PHE 0.014 0.002 PHE A 140 TYR 0.013 0.001 TYR D 95 ARG 0.006 0.000 ARG F 62 Details of bonding type rmsd link_NAG-ASN : bond 0.01138 ( 1) link_NAG-ASN : angle 9.04243 ( 3) hydrogen bonds : bond 0.03416 ( 408) hydrogen bonds : angle 6.10455 ( 1077) SS BOND : bond 0.00546 ( 24) SS BOND : angle 1.58537 ( 48) covalent geometry : bond 0.00331 (14477) covalent geometry : angle 0.63041 (19649) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 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: 59 poor density : 129 time to evaluate : 1.448 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.6836 (m-80) cc_final: 0.6408 (m-80) REVERT: A 144 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.4682 (tm-30) REVERT: B 72 ARG cc_start: 0.6094 (ptt180) cc_final: 0.5688 (ptt180) REVERT: D 67 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7159 (mtm110) REVERT: D 76 LYS cc_start: 0.5603 (tppt) cc_final: 0.5210 (mmtp) REVERT: D 195 GLN cc_start: 0.6553 (mp10) cc_final: 0.6256 (mp10) REVERT: E 34 TYR cc_start: 0.5894 (OUTLIER) cc_final: 0.5497 (m-80) REVERT: E 202 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6844 (mt) REVERT: F 118 TRP cc_start: 0.4674 (OUTLIER) cc_final: 0.4310 (m-90) REVERT: F 233 THR cc_start: 0.7595 (OUTLIER) cc_final: 0.7309 (p) outliers start: 59 outliers final: 38 residues processed: 180 average time/residue: 0.3030 time to fit residues: 80.8213 Evaluate side-chains 167 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 3.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 126 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 160 optimal weight: 0.0040 chunk 93 optimal weight: 0.8980 chunk 129 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 HIS 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 = 0.219786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.180714 restraints weight = 17919.296| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.54 r_work: 0.4091 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14502 Z= 0.164 Angle : 0.673 12.246 19700 Z= 0.344 Chirality : 0.045 0.184 2139 Planarity : 0.006 0.104 2531 Dihedral : 6.022 58.995 2038 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.48 % Favored : 92.46 % Rotamer: Outliers : 4.23 % Allowed : 17.29 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.20), residues: 1804 helix: -0.52 (0.59), residues: 73 sheet: -0.13 (0.22), residues: 619 loop : -1.28 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 115 HIS 0.007 0.001 HIS F 113 PHE 0.016 0.002 PHE A 140 TYR 0.015 0.002 TYR A 50 ARG 0.007 0.000 ARG F 62 Details of bonding type rmsd link_NAG-ASN : bond 0.01109 ( 1) link_NAG-ASN : angle 8.96735 ( 3) hydrogen bonds : bond 0.03632 ( 408) hydrogen bonds : angle 6.14309 ( 1077) SS BOND : bond 0.00618 ( 24) SS BOND : angle 1.64789 ( 48) covalent geometry : bond 0.00385 (14477) covalent geometry : angle 0.65937 (19649) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 123 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.5633 (OUTLIER) cc_final: 0.4722 (tm-30) REVERT: D 67 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7189 (mtm110) REVERT: D 76 LYS cc_start: 0.5678 (tppt) cc_final: 0.5315 (mmtp) REVERT: D 195 GLN cc_start: 0.6516 (mp10) cc_final: 0.6203 (mp10) REVERT: E 34 TYR cc_start: 0.5911 (OUTLIER) cc_final: 0.5631 (m-80) REVERT: E 202 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6900 (mt) REVERT: E 331 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6981 (m-10) REVERT: F 118 TRP cc_start: 0.4663 (OUTLIER) cc_final: 0.4234 (m-90) REVERT: F 233 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7329 (p) REVERT: F 324 ARG cc_start: 0.5494 (OUTLIER) cc_final: 0.3427 (mmm160) outliers start: 66 outliers final: 46 residues processed: 176 average time/residue: 0.2544 time to fit residues: 65.4892 Evaluate side-chains 175 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 121 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 13 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 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 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 = 0.4685 r_free = 0.4685 target = 0.220943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.180831 restraints weight = 17654.913| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 2.70 r_work: 0.4081 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14502 Z= 0.145 Angle : 0.643 12.190 19700 Z= 0.327 Chirality : 0.044 0.173 2139 Planarity : 0.005 0.106 2531 Dihedral : 5.744 58.510 2037 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 4.10 % Allowed : 17.80 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.20), residues: 1804 helix: -0.32 (0.60), residues: 73 sheet: -0.07 (0.21), residues: 626 loop : -1.22 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 115 HIS 0.007 0.001 HIS F 113 PHE 0.014 0.002 PHE E 323 TYR 0.015 0.001 TYR D 95 ARG 0.006 0.000 ARG B 101 Details of bonding type rmsd link_NAG-ASN : bond 0.01172 ( 1) link_NAG-ASN : angle 8.84699 ( 3) hydrogen bonds : bond 0.03371 ( 408) hydrogen bonds : angle 5.96764 ( 1077) SS BOND : bond 0.00536 ( 24) SS BOND : angle 1.42317 ( 48) covalent geometry : bond 0.00339 (14477) covalent geometry : angle 0.63053 (19649) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 121 time to evaluate : 1.479 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.6647 (m-80) cc_final: 0.6017 (m-80) REVERT: A 144 GLU cc_start: 0.5474 (OUTLIER) cc_final: 0.4599 (tm-30) REVERT: D 67 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7084 (mtm110) REVERT: D 195 GLN cc_start: 0.6557 (mp10) cc_final: 0.6266 (mp10) REVERT: D 211 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6239 (m-30) REVERT: E 34 TYR cc_start: 0.5706 (OUTLIER) cc_final: 0.5424 (m-80) REVERT: E 202 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6806 (mt) REVERT: E 331 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6856 (m-10) REVERT: F 118 TRP cc_start: 0.4537 (OUTLIER) cc_final: 0.4015 (m-90) REVERT: F 233 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7316 (p) REVERT: F 324 ARG cc_start: 0.5517 (OUTLIER) cc_final: 0.3399 (mmm160) outliers start: 64 outliers final: 46 residues processed: 174 average time/residue: 0.2523 time to fit residues: 64.5967 Evaluate side-chains 172 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 117 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 124 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 174 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.217600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.177355 restraints weight = 17696.259| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.44 r_work: 0.4072 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14502 Z= 0.211 Angle : 0.741 12.304 19700 Z= 0.379 Chirality : 0.047 0.183 2139 Planarity : 0.006 0.120 2531 Dihedral : 6.234 59.734 2037 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.15 % Favored : 91.80 % Rotamer: Outliers : 4.67 % Allowed : 17.41 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 1804 helix: -0.74 (0.58), residues: 73 sheet: -0.20 (0.21), residues: 615 loop : -1.40 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 115 HIS 0.008 0.002 HIS F 113 PHE 0.021 0.002 PHE E 323 TYR 0.018 0.002 TYR A 50 ARG 0.008 0.001 ARG B 101 Details of bonding type rmsd link_NAG-ASN : bond 0.01010 ( 1) link_NAG-ASN : angle 9.12079 ( 3) hydrogen bonds : bond 0.04118 ( 408) hydrogen bonds : angle 6.40168 ( 1077) SS BOND : bond 0.00747 ( 24) SS BOND : angle 1.84294 ( 48) covalent geometry : bond 0.00502 (14477) covalent geometry : angle 0.72730 (19649) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.6898 (m-80) cc_final: 0.6228 (m-80) REVERT: A 144 GLU cc_start: 0.5640 (OUTLIER) cc_final: 0.4742 (tm-30) REVERT: D 67 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7311 (mtm110) REVERT: D 76 LYS cc_start: 0.5630 (tppt) cc_final: 0.5294 (mmtp) REVERT: D 89 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: E 202 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6916 (mt) REVERT: E 331 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6912 (m-10) REVERT: F 118 TRP cc_start: 0.4848 (OUTLIER) cc_final: 0.4437 (m-90) REVERT: F 233 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7368 (p) REVERT: F 324 ARG cc_start: 0.5485 (OUTLIER) cc_final: 0.3388 (mmm160) outliers start: 73 outliers final: 54 residues processed: 186 average time/residue: 0.2794 time to fit residues: 76.0456 Evaluate side-chains 182 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 120 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 324 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 139 optimal weight: 0.0270 chunk 147 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.222460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.182706 restraints weight = 17708.276| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 2.61 r_work: 0.4136 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14502 Z= 0.122 Angle : 0.619 12.154 19700 Z= 0.316 Chirality : 0.043 0.191 2139 Planarity : 0.005 0.101 2531 Dihedral : 5.641 57.811 2037 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.43 % Favored : 94.51 % Rotamer: Outliers : 3.14 % Allowed : 19.08 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1804 helix: -0.23 (0.58), residues: 79 sheet: -0.07 (0.22), residues: 616 loop : -1.20 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 330 HIS 0.006 0.001 HIS F 113 PHE 0.014 0.001 PHE A 140 TYR 0.016 0.001 TYR D 95 ARG 0.005 0.000 ARG B 101 Details of bonding type rmsd link_NAG-ASN : bond 0.01264 ( 1) link_NAG-ASN : angle 8.79050 ( 3) hydrogen bonds : bond 0.03159 ( 408) hydrogen bonds : angle 5.82854 ( 1077) SS BOND : bond 0.00447 ( 24) SS BOND : angle 1.24916 ( 48) covalent geometry : bond 0.00278 (14477) covalent geometry : angle 0.60714 (19649) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 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: 49 poor density : 118 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.6860 (m-80) cc_final: 0.6161 (m-80) REVERT: A 144 GLU cc_start: 0.5539 (OUTLIER) cc_final: 0.4652 (tm-30) REVERT: D 76 LYS cc_start: 0.5635 (tppt) cc_final: 0.5273 (mmtp) REVERT: E 34 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.5591 (m-80) REVERT: E 202 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6809 (mt) REVERT: E 318 MET cc_start: 0.5668 (tpp) cc_final: 0.4745 (tmm) REVERT: E 331 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: F 118 TRP cc_start: 0.4406 (OUTLIER) cc_final: 0.3841 (m-90) REVERT: F 233 THR cc_start: 0.7486 (OUTLIER) cc_final: 0.7212 (p) REVERT: F 324 ARG cc_start: 0.5562 (OUTLIER) cc_final: 0.3448 (mmm160) outliers start: 49 outliers final: 40 residues processed: 159 average time/residue: 0.2747 time to fit residues: 63.7913 Evaluate side-chains 162 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.216821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.175800 restraints weight = 17942.241| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.79 r_work: 0.4039 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 14502 Z= 0.238 Angle : 0.768 12.255 19700 Z= 0.392 Chirality : 0.048 0.171 2139 Planarity : 0.006 0.117 2531 Dihedral : 6.279 59.787 2037 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.48 % Favored : 91.41 % Rotamer: Outliers : 4.23 % Allowed : 18.25 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.19), residues: 1804 helix: -1.12 (0.53), residues: 79 sheet: -0.20 (0.21), residues: 622 loop : -1.51 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 210 HIS 0.008 0.002 HIS F 113 PHE 0.024 0.003 PHE E 323 TYR 0.020 0.002 TYR A 50 ARG 0.012 0.001 ARG B 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00952 ( 1) link_NAG-ASN : angle 9.16783 ( 3) hydrogen bonds : bond 0.04290 ( 408) hydrogen bonds : angle 6.43382 ( 1077) SS BOND : bond 0.00770 ( 24) SS BOND : angle 1.91831 ( 48) covalent geometry : bond 0.00568 (14477) covalent geometry : angle 0.75438 (19649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8668.85 seconds wall clock time: 151 minutes 11.34 seconds (9071.34 seconds total)