Starting phenix.real_space_refine on Fri Feb 6 19:55:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jqq_22441/02_2026/7jqq_22441.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jqq_22441/02_2026/7jqq_22441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jqq_22441/02_2026/7jqq_22441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jqq_22441/02_2026/7jqq_22441.map" model { file = "/net/cci-nas-00/data/ceres_data/7jqq_22441/02_2026/7jqq_22441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jqq_22441/02_2026/7jqq_22441.cif" } resolution = 4.1 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= 0.005 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: 6 Type Number sf(0) Gaussians P 709 5.49 5 Mg 3 5.21 5 S 58 5.16 5 C 15415 2.51 5 N 4880 2.21 5 O 7351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28416 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 43, 'rna3p_pyr': 55} Link IDs: {'rna2p': 17, 'rna3p': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 47, 'rna3p_pyr': 56} Link IDs: {'rna2p': 13, 'rna3p': 103} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 47, 'rna3p_pyr': 57} Link IDs: {'rna2p': 12, 'rna3p': 104} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 48, 'rna3p_pyr': 57} Link IDs: {'rna2p': 11, 'rna3p': 105} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "O" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 47, 'rna3p_pyr': 53} Link IDs: {'rna2p': 15, 'rna3p': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "G" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.14, per 1000 atoms: 0.22 Number of scatterers: 28416 At special positions: 0 Unit cell: (146.59, 150.87, 218.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 709 15.00 Mg 3 11.99 O 7351 8.00 N 4880 7.00 C 15415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 678.4 milliseconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 18 sheets defined 40.4% alpha, 13.0% beta 251 base pairs and 313 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.673A pdb=" N ASP A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 44 Proline residue: A 38 - end of helix Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.620A pdb=" N ALA A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.508A pdb=" N GLU A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.851A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.892A pdb=" N TYR A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 4.056A pdb=" N GLN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.634A pdb=" N TYR A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'B' and resid 9 through 14 Processing helix chain 'B' and resid 29 through 45 Proline residue: B 38 - end of helix Processing helix chain 'B' and resid 60 through 65 removed outlier: 3.718A pdb=" N ASN B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 60 through 65' Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 193 through 207 Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.122A pdb=" N GLY B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.540A pdb=" N ASP B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 removed outlier: 4.077A pdb=" N PHE B 230 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 231 " --> pdb=" O GLN B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 231' Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.774A pdb=" N ASN B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'B' and resid 315 through 330 Processing helix chain 'C' and resid 9 through 16 removed outlier: 4.191A pdb=" N TYR C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP C 16 " --> pdb=" O MET C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 46 removed outlier: 3.706A pdb=" N TYR C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Proline residue: C 38 - end of helix removed outlier: 3.939A pdb=" N LYS C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.616A pdb=" N TYR C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 164 through 171 Processing helix chain 'C' and resid 193 through 207 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 216 through 222 removed outlier: 3.627A pdb=" N ASP C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'C' and resid 315 through 330 removed outlier: 3.755A pdb=" N ARG C 330 " --> pdb=" O PHE C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 removed outlier: 4.002A pdb=" N MET D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 45 Proline residue: D 38 - end of helix Processing helix chain 'D' and resid 56 through 61 removed outlier: 4.001A pdb=" N ALA D 60 " --> pdb=" O PRO D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 104 removed outlier: 4.268A pdb=" N SER D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 145 Processing helix chain 'D' and resid 164 through 170 removed outlier: 3.618A pdb=" N LEU D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 207 removed outlier: 4.622A pdb=" N LYS D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.778A pdb=" N GLY D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.951A pdb=" N GLN D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D 224 " --> pdb=" O ASP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.920A pdb=" N ASN D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'D' and resid 317 through 330 removed outlier: 3.826A pdb=" N ILE D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 15 Processing helix chain 'E' and resid 29 through 46 removed outlier: 3.966A pdb=" N TYR E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Proline residue: E 38 - end of helix Processing helix chain 'E' and resid 55 through 62 removed outlier: 3.564A pdb=" N ALA E 60 " --> pdb=" O PRO E 57 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 62 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 69 removed outlier: 3.719A pdb=" N ASP E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 101 through 106 removed outlier: 4.303A pdb=" N SER E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 145 removed outlier: 4.355A pdb=" N ASN E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 192 through 207 removed outlier: 4.163A pdb=" N THR E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG E 204 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 216 through 222 removed outlier: 3.687A pdb=" N ASP E 220 " --> pdb=" O GLU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 279 through 283 Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'E' and resid 316 through 330 removed outlier: 3.574A pdb=" N ARG E 330 " --> pdb=" O PHE E 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 7.616A pdb=" N VAL A 22 " --> pdb=" O SER A 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 80 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.813A pdb=" N MET A 288 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N TYR A 276 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER A 243 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 240 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 255 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 242 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N MET A 262 " --> pdb=" O ARG A 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 117 removed outlier: 6.352A pdb=" N ILE B 115 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU B 156 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE B 117 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASN B 20 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU B 19 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU B 189 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE B 21 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.671A pdb=" N TRP B 94 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 85 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 288 through 289 removed outlier: 3.529A pdb=" N VAL B 245 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 253 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 81 removed outlier: 6.955A pdb=" N PHE C 85 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE C 49 " --> pdb=" O TRP C 94 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE C 96 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR C 51 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE C 115 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU C 156 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE C 117 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN C 20 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU C 19 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLU C 189 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE C 21 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 240 through 246 removed outlier: 4.569A pdb=" N PHE C 242 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL C 253 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 276 through 277 removed outlier: 3.558A pdb=" N THR C 277 " --> pdb=" O MET C 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 94 through 97 removed outlier: 3.859A pdb=" N ILE D 50 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP D 118 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE D 115 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU D 156 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE D 117 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU D 19 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N GLU D 189 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE D 21 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 78 through 81 Processing sheet with id=AB5, first strand: chain 'D' and resid 240 through 246 removed outlier: 5.085A pdb=" N PHE D 240 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL D 255 " --> pdb=" O PHE D 240 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 242 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 78 through 81 removed outlier: 6.895A pdb=" N PHE E 85 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLN E 48 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N THR E 114 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE E 50 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL E 116 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER E 113 " --> pdb=" O ARG E 152 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE E 154 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE E 115 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS E 155 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU E 19 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU E 189 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE E 21 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 243 through 246 Processing sheet with id=AB8, first strand: chain 'E' and resid 254 through 255 Processing sheet with id=AB9, first strand: chain 'E' and resid 276 through 277 removed outlier: 4.130A pdb=" N THR E 277 " --> pdb=" O MET E 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 437 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 622 hydrogen bonds 1132 hydrogen bond angles 0 basepair planarities 251 basepair parallelities 313 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7557 1.35 - 1.50: 13166 1.50 - 1.65: 9646 1.65 - 1.80: 66 1.80 - 1.95: 37 Bond restraints: 30472 Sorted by residual: bond pdb=" CA LEU C 299 " pdb=" CB LEU C 299 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.51e-02 4.39e+03 5.88e+00 bond pdb=" CA ASP B 118 " pdb=" CB ASP B 118 " ideal model delta sigma weight residual 1.531 1.561 -0.030 1.48e-02 4.57e+03 4.22e+00 bond pdb=" C2 C N 65 " pdb=" O2 C N 65 " ideal model delta sigma weight residual 1.240 1.204 0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C3' DA G 23 " pdb=" O3' DA G 23 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.06e+00 bond pdb=" O1B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.481 1.516 -0.035 2.00e-02 2.50e+03 3.05e+00 ... (remaining 30467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 42751 1.94 - 3.88: 1487 3.88 - 5.82: 243 5.82 - 7.75: 69 7.75 - 9.69: 18 Bond angle restraints: 44568 Sorted by residual: angle pdb=" O4' A K 99 " pdb=" C1' A K 99 " pdb=" N9 A K 99 " ideal model delta sigma weight residual 108.20 114.58 -6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" C3' G K 11 " pdb=" O3' G K 11 " pdb=" P G K 12 " ideal model delta sigma weight residual 120.20 126.55 -6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" O3' G K 11 " pdb=" C3' G K 11 " pdb=" C2' G K 11 " ideal model delta sigma weight residual 109.50 115.85 -6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" N VAL C 162 " pdb=" CA VAL C 162 " pdb=" C VAL C 162 " ideal model delta sigma weight residual 112.98 107.90 5.08 1.25e+00 6.40e-01 1.65e+01 angle pdb=" C ARG D 200 " pdb=" N ARG D 201 " pdb=" CA ARG D 201 " ideal model delta sigma weight residual 122.06 114.66 7.40 1.86e+00 2.89e-01 1.58e+01 ... (remaining 44563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 15963 35.88 - 71.75: 2432 71.75 - 107.63: 264 107.63 - 143.51: 17 143.51 - 179.38: 13 Dihedral angle restraints: 18689 sinusoidal: 13839 harmonic: 4850 Sorted by residual: dihedral pdb=" O4' U O 69 " pdb=" C1' U O 69 " pdb=" N1 U O 69 " pdb=" C2 U O 69 " ideal model delta sinusoidal sigma weight residual -160.00 -26.11 -133.89 1 1.50e+01 4.44e-03 7.22e+01 dihedral pdb=" O4' U M 76 " pdb=" C1' U M 76 " pdb=" N1 U M 76 " pdb=" C2 U M 76 " ideal model delta sinusoidal sigma weight residual 232.00 88.30 143.70 1 1.70e+01 3.46e-03 6.00e+01 dihedral pdb=" O4' C K 18 " pdb=" C1' C K 18 " pdb=" N1 C K 18 " pdb=" C2 C K 18 " ideal model delta sinusoidal sigma weight residual -160.00 -61.46 -98.54 1 1.50e+01 4.44e-03 4.90e+01 ... (remaining 18686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4317 0.049 - 0.097: 823 0.097 - 0.146: 222 0.146 - 0.194: 35 0.194 - 0.243: 11 Chirality restraints: 5408 Sorted by residual: chirality pdb=" C1' U O 113 " pdb=" O4' U O 113 " pdb=" C2' U O 113 " pdb=" N1 U O 113 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1' A N 46 " pdb=" O4' A N 46 " pdb=" C2' A N 46 " pdb=" N9 A N 46 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE A 190 " pdb=" N ILE A 190 " pdb=" C ILE A 190 " pdb=" CB ILE A 190 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5405 not shown) Planarity restraints: 3128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C N 65 " 0.018 2.00e-02 2.50e+03 3.93e-02 3.47e+01 pdb=" N1 C N 65 " -0.015 2.00e-02 2.50e+03 pdb=" C2 C N 65 " -0.095 2.00e-02 2.50e+03 pdb=" O2 C N 65 " 0.060 2.00e-02 2.50e+03 pdb=" N3 C N 65 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C N 65 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C N 65 " 0.017 2.00e-02 2.50e+03 pdb=" C5 C N 65 " 0.017 2.00e-02 2.50e+03 pdb=" C6 C N 65 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C L 65 " -0.010 2.00e-02 2.50e+03 3.73e-02 3.14e+01 pdb=" N1 C L 65 " 0.016 2.00e-02 2.50e+03 pdb=" C2 C L 65 " 0.088 2.00e-02 2.50e+03 pdb=" O2 C L 65 " -0.061 2.00e-02 2.50e+03 pdb=" N3 C L 65 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C L 65 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C L 65 " -0.011 2.00e-02 2.50e+03 pdb=" C5 C L 65 " -0.020 2.00e-02 2.50e+03 pdb=" C6 C L 65 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C O 65 " -0.007 2.00e-02 2.50e+03 3.61e-02 2.92e+01 pdb=" N1 C O 65 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C O 65 " -0.081 2.00e-02 2.50e+03 pdb=" O2 C O 65 " 0.066 2.00e-02 2.50e+03 pdb=" N3 C O 65 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C O 65 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C O 65 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C O 65 " 0.020 2.00e-02 2.50e+03 pdb=" C6 C O 65 " 0.016 2.00e-02 2.50e+03 ... (remaining 3125 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 11 2.08 - 2.79: 7060 2.79 - 3.49: 42298 3.49 - 4.20: 81407 4.20 - 4.90: 112291 Nonbonded interactions: 243067 Sorted by model distance: nonbonded pdb=" OG SER B 31 " pdb=" O1B AGS B 401 " model vdw 1.379 3.040 nonbonded pdb=" CB SER A 31 " pdb="MG MG A 402 " model vdw 1.888 2.570 nonbonded pdb=" O1B AGS A 401 " pdb=" O3G AGS A 401 " model vdw 1.940 3.040 nonbonded pdb=" CB SER C 31 " pdb="MG MG C 402 " model vdw 1.962 2.570 nonbonded pdb=" O6 G N 6 " pdb=" O4 U N 113 " model vdw 2.031 2.432 ... (remaining 243062 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' and resid 4 through 330) selection = (chain 'B' and resid 4 through 330) selection = (chain 'C' and resid 4 through 330) selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.920 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.090 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 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 : 0.004 0.052 30472 Z= 0.203 Angle : 0.879 9.692 44568 Z= 0.449 Chirality : 0.044 0.243 5408 Planarity : 0.005 0.076 3128 Dihedral : 26.546 179.385 15569 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 26.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.31 (0.20), residues: 1625 helix: -0.81 (0.22), residues: 514 sheet: -2.23 (0.33), residues: 229 loop : -1.77 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 146 TYR 0.021 0.002 TYR D 32 PHE 0.023 0.002 PHE C 230 TRP 0.017 0.002 TRP B 94 HIS 0.006 0.002 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00395 (30472) covalent geometry : angle 0.87913 (44568) hydrogen bonds : bond 0.15434 ( 1059) hydrogen bonds : angle 6.72596 ( 2323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4556 (mm) cc_final: 0.4249 (mm) REVERT: A 141 MET cc_start: 0.3762 (mmm) cc_final: 0.2764 (ptt) REVERT: E 101 TRP cc_start: 0.5359 (t60) cc_final: 0.4841 (t60) REVERT: E 236 LYS cc_start: 0.4071 (mttp) cc_final: 0.3694 (tppt) REVERT: E 261 LEU cc_start: 0.7472 (mt) cc_final: 0.6905 (mt) REVERT: E 262 MET cc_start: 0.7101 (tpp) cc_final: 0.6525 (tpt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1649 time to fit residues: 54.2966 Evaluate side-chains 155 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 50.0000 chunk 194 optimal weight: 50.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 200 optimal weight: 50.0000 chunk 212 optimal weight: 50.0000 overall best weight: 19.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 222 GLN B 268 HIS ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN C 259 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.097878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.092431 restraints weight = 190294.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.093203 restraints weight = 225986.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.093345 restraints weight = 116058.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.093268 restraints weight = 103250.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.093397 restraints weight = 78418.664| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 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 : 0.006 0.048 30472 Z= 0.289 Angle : 0.969 10.779 44568 Z= 0.483 Chirality : 0.048 0.278 5408 Planarity : 0.006 0.061 3128 Dihedral : 28.459 173.040 12284 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 26.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 0.27 % Allowed : 8.85 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.58 (0.19), residues: 1625 helix: -1.07 (0.21), residues: 528 sheet: -2.21 (0.33), residues: 220 loop : -1.98 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 330 TYR 0.027 0.002 TYR D 32 PHE 0.021 0.002 PHE C 230 TRP 0.022 0.003 TRP B 94 HIS 0.010 0.003 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00585 (30472) covalent geometry : angle 0.96911 (44568) hydrogen bonds : bond 0.10746 ( 1059) hydrogen bonds : angle 6.04825 ( 2323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 189 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: D 187 LEU cc_start: 0.7412 (tp) cc_final: 0.6958 (tt) REVERT: E 101 TRP cc_start: 0.5521 (t60) cc_final: 0.5118 (t60) outliers start: 4 outliers final: 2 residues processed: 193 average time/residue: 0.1570 time to fit residues: 49.6623 Evaluate side-chains 149 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 138 optimal weight: 20.0000 chunk 175 optimal weight: 50.0000 chunk 185 optimal weight: 40.0000 chunk 94 optimal weight: 30.0000 chunk 58 optimal weight: 50.0000 chunk 38 optimal weight: 30.0000 chunk 75 optimal weight: 8.9990 chunk 1 optimal weight: 40.0000 chunk 170 optimal weight: 50.0000 chunk 191 optimal weight: 50.0000 chunk 83 optimal weight: 5.9990 overall best weight: 18.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 268 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.096976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.091847 restraints weight = 189752.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.092399 restraints weight = 230973.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.092486 restraints weight = 120899.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.092591 restraints weight = 91469.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.092714 restraints weight = 74940.735| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 30472 Z= 0.286 Angle : 0.987 10.299 44568 Z= 0.495 Chirality : 0.050 0.270 5408 Planarity : 0.007 0.115 3128 Dihedral : 28.477 177.839 12284 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 27.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 0.27 % Allowed : 8.85 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.87 (0.19), residues: 1625 helix: -1.37 (0.21), residues: 534 sheet: -2.31 (0.36), residues: 184 loop : -2.18 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 148 TYR 0.027 0.003 TYR D 32 PHE 0.021 0.003 PHE E 249 TRP 0.016 0.002 TRP B 254 HIS 0.011 0.003 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00582 (30472) covalent geometry : angle 0.98687 (44568) hydrogen bonds : bond 0.10820 ( 1059) hydrogen bonds : angle 5.97686 ( 2323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 101 TRP cc_start: 0.5562 (t60) cc_final: 0.5237 (t60) REVERT: E 221 ASN cc_start: 0.6834 (m-40) cc_final: 0.6500 (t0) REVERT: E 236 LYS cc_start: 0.5298 (mttm) cc_final: 0.4223 (tppt) REVERT: E 261 LEU cc_start: 0.8080 (mt) cc_final: 0.7652 (mt) REVERT: E 262 MET cc_start: 0.7623 (tpp) cc_final: 0.7027 (tpt) REVERT: E 287 MET cc_start: 0.8151 (ppp) cc_final: 0.7857 (ppp) outliers start: 4 outliers final: 1 residues processed: 184 average time/residue: 0.1657 time to fit residues: 50.2855 Evaluate side-chains 139 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 0.0470 chunk 25 optimal weight: 30.0000 chunk 162 optimal weight: 50.0000 chunk 176 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 166 optimal weight: 40.0000 chunk 29 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 32 optimal weight: 40.0000 overall best weight: 8.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 259 GLN B 268 HIS ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN C 296 ASN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN D 158 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.099528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.094815 restraints weight = 190123.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.095329 restraints weight = 203833.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.094504 restraints weight = 125327.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.094653 restraints weight = 125580.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.094732 restraints weight = 100854.573| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30472 Z= 0.194 Angle : 0.859 9.283 44568 Z= 0.432 Chirality : 0.045 0.303 5408 Planarity : 0.005 0.074 3128 Dihedral : 28.253 175.422 12284 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.59 (0.19), residues: 1625 helix: -1.11 (0.21), residues: 535 sheet: -2.12 (0.35), residues: 211 loop : -2.01 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 207 TYR 0.025 0.002 TYR D 109 PHE 0.045 0.002 PHE A 196 TRP 0.014 0.002 TRP D 101 HIS 0.005 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00389 (30472) covalent geometry : angle 0.85925 (44568) hydrogen bonds : bond 0.09113 ( 1059) hydrogen bonds : angle 5.55991 ( 2323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.4778 (m-80) cc_final: 0.4575 (m-80) REVERT: C 100 VAL cc_start: 0.7225 (m) cc_final: 0.6887 (m) REVERT: E 101 TRP cc_start: 0.5465 (t60) cc_final: 0.5193 (t60) REVERT: E 287 MET cc_start: 0.8122 (ppp) cc_final: 0.7871 (ppp) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1634 time to fit residues: 52.6588 Evaluate side-chains 145 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 218 optimal weight: 30.0000 chunk 176 optimal weight: 30.0000 chunk 115 optimal weight: 50.0000 chunk 113 optimal weight: 8.9990 chunk 35 optimal weight: 40.0000 chunk 22 optimal weight: 40.0000 chunk 52 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 97 optimal weight: 0.0870 chunk 69 optimal weight: 40.0000 overall best weight: 6.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.100791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.095113 restraints weight = 191368.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.094893 restraints weight = 194216.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.095411 restraints weight = 144240.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.095372 restraints weight = 103309.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.095538 restraints weight = 96064.528| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30472 Z= 0.177 Angle : 0.823 8.991 44568 Z= 0.414 Chirality : 0.043 0.274 5408 Planarity : 0.005 0.081 3128 Dihedral : 28.059 176.820 12284 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.49 % Favored : 91.45 % Rotamer: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.47 (0.19), residues: 1625 helix: -0.95 (0.21), residues: 548 sheet: -2.07 (0.33), residues: 230 loop : -1.97 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 207 TYR 0.020 0.002 TYR C 55 PHE 0.021 0.002 PHE C 120 TRP 0.015 0.002 TRP A 101 HIS 0.007 0.002 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00351 (30472) covalent geometry : angle 0.82328 (44568) hydrogen bonds : bond 0.08660 ( 1059) hydrogen bonds : angle 5.26989 ( 2323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.3859 (mmm) cc_final: 0.2696 (ptt) REVERT: D 130 ILE cc_start: 0.5533 (mp) cc_final: 0.5289 (mm) REVERT: E 7 TYR cc_start: 0.4114 (t80) cc_final: 0.3893 (t80) REVERT: E 261 LEU cc_start: 0.7275 (mt) cc_final: 0.7042 (mt) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.1737 time to fit residues: 58.9946 Evaluate side-chains 150 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 27 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 91 optimal weight: 30.0000 chunk 113 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 298 HIS ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.101926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.096242 restraints weight = 192447.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.096103 restraints weight = 205752.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.096733 restraints weight = 155893.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.096628 restraints weight = 110321.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.096944 restraints weight = 103337.284| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30472 Z= 0.161 Angle : 0.793 8.757 44568 Z= 0.398 Chirality : 0.042 0.277 5408 Planarity : 0.005 0.076 3128 Dihedral : 27.903 177.074 12284 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.40 (0.19), residues: 1625 helix: -0.86 (0.21), residues: 553 sheet: -1.99 (0.34), residues: 218 loop : -1.98 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 207 TYR 0.035 0.002 TYR E 297 PHE 0.017 0.001 PHE C 120 TRP 0.016 0.002 TRP A 101 HIS 0.013 0.002 HIS D 298 Details of bonding type rmsd covalent geometry : bond 0.00317 (30472) covalent geometry : angle 0.79264 (44568) hydrogen bonds : bond 0.08178 ( 1059) hydrogen bonds : angle 5.04948 ( 2323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4259 (mm) cc_final: 0.3900 (mm) REVERT: A 141 MET cc_start: 0.3904 (mmm) cc_final: 0.2872 (ptt) REVERT: B 328 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8372 (ttmm) REVERT: D 130 ILE cc_start: 0.5399 (mp) cc_final: 0.5198 (mm) REVERT: E 7 TYR cc_start: 0.3996 (t80) cc_final: 0.3406 (t80) REVERT: E 236 LYS cc_start: 0.4517 (mttp) cc_final: 0.3554 (tppt) REVERT: E 261 LEU cc_start: 0.7217 (mt) cc_final: 0.6677 (mt) REVERT: E 262 MET cc_start: 0.7225 (tpt) cc_final: 0.6385 (tpt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1781 time to fit residues: 60.0374 Evaluate side-chains 157 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 0.0670 chunk 192 optimal weight: 50.0000 chunk 209 optimal weight: 20.0000 chunk 122 optimal weight: 50.0000 chunk 207 optimal weight: 50.0000 chunk 157 optimal weight: 9.9990 chunk 208 optimal weight: 40.0000 chunk 105 optimal weight: 4.9990 chunk 174 optimal weight: 50.0000 chunk 36 optimal weight: 40.0000 overall best weight: 11.0130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 164 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.100174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.095156 restraints weight = 189992.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.095734 restraints weight = 214872.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.095607 restraints weight = 119858.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.095604 restraints weight = 98976.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.095844 restraints weight = 88522.438| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30472 Z= 0.202 Angle : 0.834 9.546 44568 Z= 0.418 Chirality : 0.043 0.283 5408 Planarity : 0.005 0.070 3128 Dihedral : 27.970 175.958 12284 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.40 (0.19), residues: 1625 helix: -0.86 (0.21), residues: 543 sheet: -2.06 (0.35), residues: 208 loop : -1.96 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 53 TYR 0.022 0.002 TYR C 55 PHE 0.021 0.002 PHE C 120 TRP 0.014 0.002 TRP B 94 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00406 (30472) covalent geometry : angle 0.83443 (44568) hydrogen bonds : bond 0.08906 ( 1059) hydrogen bonds : angle 5.22160 ( 2323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4417 (mm) cc_final: 0.4129 (mm) REVERT: A 141 MET cc_start: 0.4056 (mmm) cc_final: 0.2873 (ptt) REVERT: A 306 PHE cc_start: 0.7732 (t80) cc_final: 0.7498 (t80) REVERT: B 55 TYR cc_start: 0.5137 (m-80) cc_final: 0.4779 (m-80) REVERT: B 134 VAL cc_start: 0.5934 (m) cc_final: 0.5610 (p) REVERT: D 130 ILE cc_start: 0.5695 (mp) cc_final: 0.5419 (mm) REVERT: E 7 TYR cc_start: 0.4615 (t80) cc_final: 0.4326 (t80) REVERT: E 261 LEU cc_start: 0.7194 (mt) cc_final: 0.6867 (mt) REVERT: E 262 MET cc_start: 0.7048 (tpt) cc_final: 0.6719 (tpt) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.1632 time to fit residues: 51.4869 Evaluate side-chains 150 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 93 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 191 optimal weight: 50.0000 chunk 72 optimal weight: 30.0000 chunk 135 optimal weight: 30.0000 chunk 25 optimal weight: 7.9990 chunk 103 optimal weight: 30.0000 chunk 175 optimal weight: 50.0000 chunk 22 optimal weight: 5.9990 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.100781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.094963 restraints weight = 192425.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.095437 restraints weight = 223264.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.095664 restraints weight = 145550.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.095666 restraints weight = 103560.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.095822 restraints weight = 97857.691| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30472 Z= 0.177 Angle : 0.810 9.230 44568 Z= 0.406 Chirality : 0.042 0.276 5408 Planarity : 0.005 0.074 3128 Dihedral : 27.931 177.156 12284 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.35 (0.20), residues: 1625 helix: -0.79 (0.21), residues: 543 sheet: -2.00 (0.34), residues: 221 loop : -1.94 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 53 TYR 0.025 0.002 TYR B 166 PHE 0.021 0.002 PHE D 205 TRP 0.014 0.002 TRP D 94 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00353 (30472) covalent geometry : angle 0.81018 (44568) hydrogen bonds : bond 0.08438 ( 1059) hydrogen bonds : angle 5.13809 ( 2323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4297 (mm) cc_final: 0.4072 (mm) REVERT: A 141 MET cc_start: 0.3933 (mmm) cc_final: 0.2766 (ptt) REVERT: A 306 PHE cc_start: 0.7805 (t80) cc_final: 0.7557 (t80) REVERT: B 55 TYR cc_start: 0.5156 (m-80) cc_final: 0.4776 (m-80) REVERT: D 10 GLN cc_start: 0.5781 (tt0) cc_final: 0.5552 (tt0) REVERT: D 130 ILE cc_start: 0.5710 (mp) cc_final: 0.5454 (mm) REVERT: E 7 TYR cc_start: 0.4293 (t80) cc_final: 0.3603 (t80) REVERT: E 261 LEU cc_start: 0.7411 (mt) cc_final: 0.6995 (mt) REVERT: E 262 MET cc_start: 0.7135 (tpt) cc_final: 0.6851 (tpt) REVERT: E 307 MET cc_start: 0.6797 (mmm) cc_final: 0.6563 (mmm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1740 time to fit residues: 57.7213 Evaluate side-chains 153 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 58 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 226 optimal weight: 40.0000 chunk 81 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 188 optimal weight: 40.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.100879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.094742 restraints weight = 187991.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.095079 restraints weight = 189926.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.095454 restraints weight = 126216.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.095301 restraints weight = 99662.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.095553 restraints weight = 93144.185| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30472 Z= 0.175 Angle : 0.803 9.150 44568 Z= 0.402 Chirality : 0.042 0.274 5408 Planarity : 0.005 0.071 3128 Dihedral : 27.879 177.735 12284 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.07 % Allowed : 0.61 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.27 (0.20), residues: 1625 helix: -0.71 (0.22), residues: 535 sheet: -2.01 (0.34), residues: 221 loop : -1.89 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 53 TYR 0.019 0.002 TYR E 55 PHE 0.024 0.002 PHE C 249 TRP 0.011 0.002 TRP B 94 HIS 0.004 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00349 (30472) covalent geometry : angle 0.80310 (44568) hydrogen bonds : bond 0.08443 ( 1059) hydrogen bonds : angle 5.09501 ( 2323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.7798 (t80) cc_final: 0.7558 (t80) REVERT: B 55 TYR cc_start: 0.5095 (m-80) cc_final: 0.4760 (m-80) REVERT: D 10 GLN cc_start: 0.5878 (tt0) cc_final: 0.5644 (tt0) REVERT: D 130 ILE cc_start: 0.5817 (mp) cc_final: 0.5532 (mm) REVERT: E 7 TYR cc_start: 0.4379 (t80) cc_final: 0.4173 (t80) REVERT: E 261 LEU cc_start: 0.7210 (mt) cc_final: 0.6931 (mt) REVERT: E 262 MET cc_start: 0.7180 (tpt) cc_final: 0.6911 (tpt) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.1694 time to fit residues: 54.9893 Evaluate side-chains 156 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 106 optimal weight: 4.9990 chunk 181 optimal weight: 50.0000 chunk 69 optimal weight: 6.9990 chunk 198 optimal weight: 30.0000 chunk 211 optimal weight: 50.0000 chunk 96 optimal weight: 50.0000 chunk 193 optimal weight: 50.0000 chunk 138 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 108 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.101062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.095474 restraints weight = 189696.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.095282 restraints weight = 180688.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.095796 restraints weight = 145927.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.095784 restraints weight = 103809.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.095962 restraints weight = 103034.714| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30472 Z= 0.172 Angle : 0.799 9.123 44568 Z= 0.400 Chirality : 0.042 0.274 5408 Planarity : 0.005 0.087 3128 Dihedral : 27.825 178.368 12284 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.07 % Allowed : 0.54 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.33 (0.20), residues: 1625 helix: -0.76 (0.21), residues: 548 sheet: -1.99 (0.34), residues: 222 loop : -1.96 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 53 TYR 0.022 0.002 TYR B 129 PHE 0.022 0.002 PHE C 167 TRP 0.034 0.002 TRP A 101 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00342 (30472) covalent geometry : angle 0.79877 (44568) hydrogen bonds : bond 0.08321 ( 1059) hydrogen bonds : angle 5.07927 ( 2323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4272 (mm) cc_final: 0.4022 (mm) REVERT: A 306 PHE cc_start: 0.7766 (t80) cc_final: 0.7547 (t80) REVERT: B 55 TYR cc_start: 0.5165 (m-80) cc_final: 0.4839 (m-80) REVERT: D 10 GLN cc_start: 0.5823 (tt0) cc_final: 0.5597 (tt0) REVERT: D 130 ILE cc_start: 0.5714 (mp) cc_final: 0.5449 (mm) REVERT: D 207 ARG cc_start: 0.4939 (mtt-85) cc_final: 0.4361 (mpp-170) REVERT: D 259 GLN cc_start: 0.7152 (pm20) cc_final: 0.6888 (pm20) REVERT: E 7 TYR cc_start: 0.4274 (t80) cc_final: 0.3728 (t80) REVERT: E 236 LYS cc_start: 0.4126 (mttp) cc_final: 0.3801 (tppt) REVERT: E 261 LEU cc_start: 0.7250 (mt) cc_final: 0.6650 (mt) REVERT: E 262 MET cc_start: 0.7116 (tpt) cc_final: 0.6301 (tpt) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1670 time to fit residues: 51.8058 Evaluate side-chains 154 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 107 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 167 optimal weight: 50.0000 chunk 125 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 211 optimal weight: 50.0000 chunk 56 optimal weight: 0.0370 chunk 0 optimal weight: 50.0000 chunk 204 optimal weight: 50.0000 chunk 74 optimal weight: 6.9990 overall best weight: 5.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.102302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.096412 restraints weight = 188200.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.096523 restraints weight = 184218.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.096987 restraints weight = 139263.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.096914 restraints weight = 106039.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.096949 restraints weight = 106177.659| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30472 Z= 0.156 Angle : 0.771 8.628 44568 Z= 0.385 Chirality : 0.041 0.271 5408 Planarity : 0.005 0.076 3128 Dihedral : 27.667 179.218 12284 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.21 (0.20), residues: 1625 helix: -0.66 (0.21), residues: 552 sheet: -1.86 (0.35), residues: 210 loop : -1.90 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 201 TYR 0.024 0.001 TYR B 129 PHE 0.020 0.002 PHE C 167 TRP 0.024 0.002 TRP A 101 HIS 0.003 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00310 (30472) covalent geometry : angle 0.77073 (44568) hydrogen bonds : bond 0.07945 ( 1059) hydrogen bonds : angle 4.92410 ( 2323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3304.69 seconds wall clock time: 58 minutes 45.81 seconds (3525.81 seconds total)