Starting phenix.real_space_refine on Sat Oct 11 11:05:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wnp_37670/10_2025/8wnp_37670.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wnp_37670/10_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_37670/10_2025/8wnp_37670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wnp_37670/10_2025/8wnp_37670.map" model { file = "/net/cci-nas-00/data/ceres_data/8wnp_37670/10_2025/8wnp_37670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wnp_37670/10_2025/8wnp_37670.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.53, per 1000 atoms: 0.25 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: 0.94 Conformation dependent library (CDL) restraints added in 628.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.50 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: 2.09 Time building geometry restraints manager: 1.23 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: 0.01 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: 11.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.200 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG D 98 TYR 0.013 0.001 TYR D 95 PHE 0.013 0.001 PHE F 133 TRP 0.027 0.001 TRP H 35 HIS 0.005 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.02368 (14477) covalent geometry : angle 1.03504 (19649) SS BOND : bond 0.00510 ( 24) SS BOND : angle 1.65729 ( 48) hydrogen bonds : bond 0.26699 ( 408) hydrogen bonds : angle 10.06000 ( 1077) link_NAG-ASN : bond 0.00690 ( 1) link_NAG-ASN : angle 7.20062 ( 3) *********************** 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 : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 159 average time/residue: 0.1420 time to fit residues: 31.9352 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 : 0.548 ------------------------------------------------------------------------------- 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 98 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN C 167 GLN C 211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.223660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.182763 restraints weight = 17725.281| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.69 r_work: 0.4077 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14502 Z= 0.124 Angle : 0.622 11.890 19700 Z= 0.323 Chirality : 0.044 0.200 2139 Planarity : 0.005 0.080 2531 Dihedral : 5.794 57.954 2042 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.77 % Favored : 95.18 % Rotamer: Outliers : 1.66 % Allowed : 12.61 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.20), residues: 1804 helix: -0.66 (0.56), residues: 85 sheet: -0.10 (0.21), residues: 628 loop : -0.95 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 212 TYR 0.012 0.001 TYR F 175 PHE 0.012 0.001 PHE E 323 TRP 0.027 0.001 TRP H 35 HIS 0.007 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00273 (14477) covalent geometry : angle 0.61073 (19649) SS BOND : bond 0.00384 ( 24) SS BOND : angle 1.22234 ( 48) hydrogen bonds : bond 0.03923 ( 408) hydrogen bonds : angle 6.63225 ( 1077) link_NAG-ASN : bond 0.01291 ( 1) link_NAG-ASN : angle 8.60809 ( 3) *********************** 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 171 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: D 76 LYS cc_start: 0.5424 (tppt) cc_final: 0.4871 (tttm) REVERT: D 195 GLN cc_start: 0.6587 (mp10) cc_final: 0.6353 (mp10) REVERT: E 34 TYR cc_start: 0.5330 (OUTLIER) cc_final: 0.4986 (m-80) outliers start: 26 outliers final: 16 residues processed: 166 average time/residue: 0.1346 time to fit residues: 31.9954 Evaluate side-chains 145 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain C residue 157 SER 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 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 6 SER 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 175 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 123 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.223787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.182773 restraints weight = 17825.724| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 3.02 r_work: 0.4086 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14502 Z= 0.115 Angle : 0.586 12.182 19700 Z= 0.301 Chirality : 0.043 0.197 2139 Planarity : 0.004 0.065 2531 Dihedral : 5.394 57.716 2037 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.82 % Favored : 95.12 % Rotamer: Outliers : 2.37 % Allowed : 13.06 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.20), residues: 1804 helix: -0.41 (0.56), residues: 87 sheet: 0.04 (0.21), residues: 652 loop : -0.83 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 214 TYR 0.011 0.001 TYR A 50 PHE 0.013 0.001 PHE E 323 TRP 0.029 0.001 TRP H 35 HIS 0.006 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00259 (14477) covalent geometry : angle 0.57402 (19649) SS BOND : bond 0.00405 ( 24) SS BOND : angle 1.23526 ( 48) hydrogen bonds : bond 0.03347 ( 408) hydrogen bonds : angle 6.01320 ( 1077) link_NAG-ASN : bond 0.01284 ( 1) link_NAG-ASN : angle 8.59787 ( 3) *********************** 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 183 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6952 (pt0) REVERT: A 144 GLU cc_start: 0.5135 (OUTLIER) cc_final: 0.4256 (tm-30) REVERT: D 195 GLN cc_start: 0.6489 (mp10) cc_final: 0.6112 (mp10) REVERT: E 34 TYR cc_start: 0.5351 (OUTLIER) cc_final: 0.4982 (m-80) REVERT: E 202 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6701 (mt) REVERT: G 102 PHE cc_start: 0.4188 (m-80) cc_final: 0.3754 (m-80) outliers start: 37 outliers final: 22 residues processed: 178 average time/residue: 0.1281 time to fit residues: 33.2885 Evaluate side-chains 161 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 144 GLU 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 124 VAL 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 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 186 THR Chi-restraints excluded: chain E residue 202 ILE 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 71 VAL 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 H residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 101 optimal weight: 4.9990 chunk 143 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 53 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS C 199 HIS F 207 ASN F 254 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.216182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.175698 restraints weight = 17827.840| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.68 r_work: 0.4012 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14502 Z= 0.216 Angle : 0.742 12.307 19700 Z= 0.381 Chirality : 0.047 0.175 2139 Planarity : 0.006 0.086 2531 Dihedral : 6.033 58.905 2037 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.76 % Favored : 93.13 % Rotamer: Outliers : 3.84 % Allowed : 14.40 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.20), residues: 1804 helix: -1.18 (0.49), residues: 91 sheet: -0.07 (0.21), residues: 627 loop : -1.19 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 98 TYR 0.021 0.002 TYR A 50 PHE 0.022 0.002 PHE E 323 TRP 0.032 0.002 TRP H 35 HIS 0.009 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00516 (14477) covalent geometry : angle 0.72806 (19649) SS BOND : bond 0.00720 ( 24) SS BOND : angle 1.99416 ( 48) hydrogen bonds : bond 0.04291 ( 408) hydrogen bonds : angle 6.49655 ( 1077) link_NAG-ASN : bond 0.00920 ( 1) link_NAG-ASN : angle 9.00440 ( 3) *********************** 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 198 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 138 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.6748 (m-80) cc_final: 0.6461 (m-80) REVERT: A 144 GLU cc_start: 0.5194 (OUTLIER) cc_final: 0.4316 (tm-30) REVERT: B 195 GLN cc_start: 0.3844 (OUTLIER) cc_final: 0.3570 (mp10) REVERT: D 76 LYS cc_start: 0.5782 (tppt) cc_final: 0.5177 (mmtp) REVERT: D 195 GLN cc_start: 0.6514 (mp10) cc_final: 0.6233 (mp10) REVERT: E 34 TYR cc_start: 0.5740 (OUTLIER) cc_final: 0.5344 (m-80) REVERT: E 202 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6819 (mt) REVERT: F 131 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6967 (p0) REVERT: F 233 THR cc_start: 0.7594 (OUTLIER) cc_final: 0.7347 (p) REVERT: G 102 PHE cc_start: 0.4422 (m-80) cc_final: 0.3902 (m-80) outliers start: 60 outliers final: 38 residues processed: 188 average time/residue: 0.1245 time to fit residues: 34.1800 Evaluate side-chains 174 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 144 GLU 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 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 C residue 23 THR Chi-restraints excluded: chain C residue 53 SER 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 203 SER Chi-restraints excluded: chain D residue 69 THR 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 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 57 ILE Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 104 LEU 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 233 THR Chi-restraints excluded: chain G residue 11 VAL 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 175 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 GLN F 216 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.217612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.177354 restraints weight = 17892.646| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.99 r_work: 0.4013 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14502 Z= 0.180 Angle : 0.687 12.407 19700 Z= 0.352 Chirality : 0.045 0.183 2139 Planarity : 0.005 0.085 2531 Dihedral : 5.924 59.375 2037 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.26 % Favored : 93.63 % Rotamer: Outliers : 3.71 % Allowed : 16.07 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.20), residues: 1804 helix: -1.04 (0.50), residues: 91 sheet: -0.03 (0.21), residues: 639 loop : -1.28 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 98 TYR 0.018 0.002 TYR A 50 PHE 0.017 0.002 PHE A 63 TRP 0.023 0.002 TRP H 35 HIS 0.007 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00424 (14477) covalent geometry : angle 0.67332 (19649) SS BOND : bond 0.00592 ( 24) SS BOND : angle 1.72854 ( 48) hydrogen bonds : bond 0.03810 ( 408) hydrogen bonds : angle 6.27220 ( 1077) link_NAG-ASN : bond 0.01017 ( 1) link_NAG-ASN : angle 9.07077 ( 3) *********************** 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 194 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 136 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 141 TYR cc_start: 0.5423 (t80) cc_final: 0.5212 (t80) REVERT: A 144 GLU cc_start: 0.5223 (OUTLIER) cc_final: 0.4315 (tm-30) REVERT: B 195 GLN cc_start: 0.3710 (OUTLIER) cc_final: 0.3465 (mp10) REVERT: D 76 LYS cc_start: 0.5725 (tppt) cc_final: 0.5129 (mmtp) REVERT: D 195 GLN cc_start: 0.6510 (mp10) cc_final: 0.6207 (mp10) REVERT: E 34 TYR cc_start: 0.5709 (OUTLIER) cc_final: 0.5324 (m-80) REVERT: E 202 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6820 (mt) REVERT: F 131 ASN cc_start: 0.7221 (OUTLIER) cc_final: 0.7006 (p0) REVERT: F 233 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7304 (p) REVERT: G 102 PHE cc_start: 0.4511 (m-80) cc_final: 0.4054 (m-80) outliers start: 58 outliers final: 40 residues processed: 185 average time/residue: 0.1208 time to fit residues: 33.2057 Evaluate side-chains 174 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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 B residue 195 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 53 SER 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 D residue 69 THR 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 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 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 104 LEU 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 233 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 19 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4596 r_free = 0.4596 target = 0.215944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.175823 restraints weight = 17957.039| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.63 r_work: 0.3986 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.2422 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= 0.224 Angle : 0.763 12.395 19700 Z= 0.390 Chirality : 0.047 0.182 2139 Planarity : 0.006 0.107 2531 Dihedral : 6.287 59.603 2037 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.98 % Favored : 91.96 % Rotamer: Outliers : 4.23 % Allowed : 17.22 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.19), residues: 1804 helix: -1.22 (0.52), residues: 79 sheet: -0.28 (0.21), residues: 658 loop : -1.38 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 98 TYR 0.020 0.002 TYR A 50 PHE 0.020 0.002 PHE A 63 TRP 0.028 0.002 TRP E 115 HIS 0.010 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00532 (14477) covalent geometry : angle 0.74922 (19649) SS BOND : bond 0.00786 ( 24) SS BOND : angle 1.97143 ( 48) hydrogen bonds : bond 0.04291 ( 408) hydrogen bonds : angle 6.52628 ( 1077) link_NAG-ASN : bond 0.00895 ( 1) link_NAG-ASN : angle 9.26002 ( 3) *********************** 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 197 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 131 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7060 (m-80) cc_final: 0.6373 (m-80) REVERT: A 144 GLU cc_start: 0.5481 (OUTLIER) cc_final: 0.4506 (tm-30) REVERT: B 195 GLN cc_start: 0.3810 (OUTLIER) cc_final: 0.3571 (mp10) REVERT: D 76 LYS cc_start: 0.5628 (tppt) cc_final: 0.5043 (mmtp) REVERT: D 195 GLN cc_start: 0.6525 (mp10) cc_final: 0.6192 (mp10) REVERT: E 34 TYR cc_start: 0.6015 (OUTLIER) cc_final: 0.5638 (m-80) REVERT: E 202 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6903 (mt) REVERT: E 331 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.7187 (m-10) REVERT: F 131 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6893 (p0) REVERT: F 233 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7345 (p) REVERT: G 102 PHE cc_start: 0.4632 (m-80) cc_final: 0.4156 (m-80) outliers start: 66 outliers final: 47 residues processed: 185 average time/residue: 0.1192 time to fit residues: 32.6852 Evaluate side-chains 176 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 122 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 13 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 53 SER 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 D residue 69 THR 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 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 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 E residue 331 TYR 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 67 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 104 LEU 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 233 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 28 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4659 r_free = 0.4659 target = 0.218046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.178945 restraints weight = 17758.366| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 2.53 r_work: 0.4073 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3950 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14502 Z= 0.201 Angle : 0.726 12.465 19700 Z= 0.371 Chirality : 0.046 0.165 2139 Planarity : 0.006 0.082 2531 Dihedral : 6.199 59.174 2037 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.98 % Favored : 92.90 % Rotamer: Outliers : 4.10 % Allowed : 17.54 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.20), residues: 1804 helix: -1.09 (0.54), residues: 79 sheet: -0.30 (0.21), residues: 664 loop : -1.40 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 98 TYR 0.017 0.002 TYR A 50 PHE 0.017 0.002 PHE E 323 TRP 0.024 0.002 TRP E 115 HIS 0.008 0.002 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00477 (14477) covalent geometry : angle 0.71215 (19649) SS BOND : bond 0.00707 ( 24) SS BOND : angle 1.86064 ( 48) hydrogen bonds : bond 0.03993 ( 408) hydrogen bonds : angle 6.39607 ( 1077) link_NAG-ASN : bond 0.00922 ( 1) link_NAG-ASN : angle 9.31776 ( 3) *********************** 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 194 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 130 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.6991 (m-80) cc_final: 0.6330 (m-80) REVERT: A 144 GLU cc_start: 0.5616 (OUTLIER) cc_final: 0.4731 (tm-30) REVERT: D 67 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6920 (mtm110) REVERT: D 76 LYS cc_start: 0.5783 (tppt) cc_final: 0.5212 (mmtp) REVERT: D 195 GLN cc_start: 0.6523 (mp10) cc_final: 0.6215 (mp10) REVERT: E 34 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5712 (m-80) REVERT: E 202 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6953 (mt) REVERT: F 131 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6997 (p0) REVERT: F 233 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7381 (p) REVERT: G 102 PHE cc_start: 0.4793 (m-80) cc_final: 0.4291 (m-80) outliers start: 64 outliers final: 48 residues processed: 184 average time/residue: 0.1227 time to fit residues: 33.6170 Evaluate side-chains 179 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 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 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 53 SER 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 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 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 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 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 85 GLN Chi-restraints excluded: chain F residue 104 LEU 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 202 ILE Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 165 optimal weight: 9.9990 chunk 131 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** C 139 ASN D 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.219419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.180397 restraints weight = 17642.389| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.56 r_work: 0.4090 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14502 Z= 0.166 Angle : 0.679 12.411 19700 Z= 0.347 Chirality : 0.045 0.170 2139 Planarity : 0.005 0.073 2531 Dihedral : 5.984 58.499 2037 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.71 % Favored : 93.24 % Rotamer: Outliers : 4.29 % Allowed : 17.73 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.20), residues: 1804 helix: -0.63 (0.59), residues: 73 sheet: -0.26 (0.21), residues: 665 loop : -1.31 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 98 TYR 0.016 0.002 TYR D 95 PHE 0.016 0.002 PHE A 140 TRP 0.020 0.002 TRP E 115 HIS 0.007 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00390 (14477) covalent geometry : angle 0.66581 (19649) SS BOND : bond 0.00623 ( 24) SS BOND : angle 1.62582 ( 48) hydrogen bonds : bond 0.03637 ( 408) hydrogen bonds : angle 6.17656 ( 1077) link_NAG-ASN : bond 0.01035 ( 1) link_NAG-ASN : angle 9.16603 ( 3) *********************** 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 192 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 125 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7006 (m-80) cc_final: 0.6288 (m-80) REVERT: A 144 GLU cc_start: 0.5546 (OUTLIER) cc_final: 0.4688 (tm-30) REVERT: D 67 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6939 (mtm110) REVERT: D 195 GLN cc_start: 0.6535 (mp10) cc_final: 0.6243 (mp10) REVERT: E 34 TYR cc_start: 0.5965 (OUTLIER) cc_final: 0.5620 (m-80) REVERT: E 202 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6918 (mt) REVERT: E 331 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.7015 (m-10) REVERT: F 131 ASN cc_start: 0.7309 (OUTLIER) cc_final: 0.7038 (p0) REVERT: F 233 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7297 (p) REVERT: G 102 PHE cc_start: 0.4788 (m-80) cc_final: 0.4307 (m-80) outliers start: 67 outliers final: 51 residues processed: 181 average time/residue: 0.1234 time to fit residues: 33.1434 Evaluate side-chains 180 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 122 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 20 VAL 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 34 TYR 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 79 LEU 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 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 53 SER 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 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 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 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 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 85 GLN Chi-restraints excluded: chain F residue 104 LEU 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 202 ILE Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 97 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4653 r_free = 0.4653 target = 0.217601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.178709 restraints weight = 17815.043| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.54 r_work: 0.4068 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14502 Z= 0.203 Angle : 0.735 12.494 19700 Z= 0.375 Chirality : 0.047 0.180 2139 Planarity : 0.006 0.072 2531 Dihedral : 6.232 59.339 2037 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.15 % Favored : 91.74 % Rotamer: Outliers : 4.29 % Allowed : 17.99 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.19), residues: 1804 helix: -0.83 (0.57), residues: 73 sheet: -0.31 (0.21), residues: 653 loop : -1.41 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 101 TYR 0.017 0.002 TYR A 50 PHE 0.019 0.002 PHE E 323 TRP 0.019 0.002 TRP E 115 HIS 0.008 0.002 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00484 (14477) covalent geometry : angle 0.72132 (19649) SS BOND : bond 0.00740 ( 24) SS BOND : angle 1.82275 ( 48) hydrogen bonds : bond 0.04042 ( 408) hydrogen bonds : angle 6.38919 ( 1077) link_NAG-ASN : bond 0.01011 ( 1) link_NAG-ASN : angle 9.23873 ( 3) *********************** 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 189 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 122 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 TYR cc_start: 0.7015 (m-80) cc_final: 0.6301 (m-80) REVERT: A 144 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.4761 (tm-30) REVERT: D 67 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7303 (mtm110) REVERT: D 76 LYS cc_start: 0.5897 (tppt) cc_final: 0.5320 (mmtp) REVERT: E 34 TYR cc_start: 0.6023 (OUTLIER) cc_final: 0.5772 (m-80) REVERT: E 202 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6982 (mt) REVERT: E 331 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.7037 (m-10) REVERT: F 131 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.6982 (p0) REVERT: F 233 THR cc_start: 0.7672 (OUTLIER) cc_final: 0.7400 (p) REVERT: G 102 PHE cc_start: 0.4834 (m-80) cc_final: 0.4327 (m-80) outliers start: 67 outliers final: 54 residues processed: 177 average time/residue: 0.1261 time to fit residues: 32.7281 Evaluate side-chains 180 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 119 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 20 VAL 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 57 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 LEU 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 5 MET Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR 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 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 40 ARG 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 E residue 331 TYR 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 85 GLN Chi-restraints excluded: chain F residue 104 LEU 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 202 ILE Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 96 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 76 optimal weight: 0.0980 chunk 91 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.219458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.180411 restraints weight = 17717.328| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.51 r_work: 0.4094 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3972 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14502 Z= 0.159 Angle : 0.671 13.509 19700 Z= 0.342 Chirality : 0.045 0.183 2139 Planarity : 0.005 0.066 2531 Dihedral : 5.930 58.433 2037 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.43 % Favored : 93.46 % Rotamer: Outliers : 3.59 % Allowed : 18.76 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.20), residues: 1804 helix: -0.54 (0.59), residues: 73 sheet: -0.25 (0.21), residues: 665 loop : -1.32 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 214 TYR 0.014 0.001 TYR D 95 PHE 0.015 0.002 PHE E 323 TRP 0.017 0.002 TRP E 115 HIS 0.007 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00375 (14477) covalent geometry : angle 0.65858 (19649) SS BOND : bond 0.00589 ( 24) SS BOND : angle 1.52809 ( 48) hydrogen bonds : bond 0.03552 ( 408) hydrogen bonds : angle 6.10604 ( 1077) link_NAG-ASN : bond 0.01108 ( 1) link_NAG-ASN : angle 9.06740 ( 3) ********************** 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 176 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 33 TYR cc_start: 0.6993 (m-80) cc_final: 0.6275 (m-80) REVERT: A 144 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.4745 (tm-30) REVERT: D 67 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.6936 (mtm110) REVERT: D 76 LYS cc_start: 0.5854 (tppt) cc_final: 0.5275 (mmtp) REVERT: E 34 TYR cc_start: 0.5913 (OUTLIER) cc_final: 0.5617 (m-80) REVERT: E 202 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6915 (mt) REVERT: E 331 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6961 (m-10) REVERT: F 136 ASP cc_start: 0.7550 (t0) cc_final: 0.7341 (t0) REVERT: G 102 PHE cc_start: 0.4851 (m-80) cc_final: 0.4356 (m-80) outliers start: 56 outliers final: 47 residues processed: 167 average time/residue: 0.1219 time to fit residues: 30.1672 Evaluate side-chains 170 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 20 VAL 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 34 TYR 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 79 LEU 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 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR 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 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 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 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 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 109 optimal weight: 0.1980 chunk 139 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.222399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.182593 restraints weight = 17631.429| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 2.69 r_work: 0.4134 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14502 Z= 0.123 Angle : 0.615 12.858 19700 Z= 0.313 Chirality : 0.043 0.179 2139 Planarity : 0.005 0.059 2531 Dihedral : 5.516 57.701 2037 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 3.20 % Allowed : 19.21 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.20), residues: 1804 helix: -0.18 (0.58), residues: 81 sheet: 0.04 (0.21), residues: 632 loop : -1.23 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 214 TYR 0.012 0.001 TYR D 95 PHE 0.013 0.001 PHE A 140 TRP 0.017 0.001 TRP E 115 HIS 0.006 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00284 (14477) covalent geometry : angle 0.60328 (19649) SS BOND : bond 0.00457 ( 24) SS BOND : angle 1.25261 ( 48) hydrogen bonds : bond 0.03090 ( 408) hydrogen bonds : angle 5.72799 ( 1077) link_NAG-ASN : bond 0.01287 ( 1) link_NAG-ASN : angle 8.71766 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4387.87 seconds wall clock time: 75 minutes 45.99 seconds (4545.99 seconds total)