Starting phenix.real_space_refine on Tue Jun 24 02:05:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jqq_22441/06_2025/7jqq_22441.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jqq_22441/06_2025/7jqq_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_22441/06_2025/7jqq_22441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jqq_22441/06_2025/7jqq_22441.map" model { file = "/net/cci-nas-00/data/ceres_data/7jqq_22441/06_2025/7jqq_22441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jqq_22441/06_2025/7jqq_22441.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'GLU: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: {'TYR:plan': 1, 'GLU: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: {'TYR:plan': 1, 'GLU: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: {'TYR:plan': 1, 'GLU: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: {'TYR:plan': 1, 'GLU: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: 19.47, per 1000 atoms: 0.69 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: 7.59 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 15.05 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: 17.30 Time building geometry restraints manager: 9.67 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: 0.03 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: 2.770 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: 0.040 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.300 Process input model: 83.640 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.350 ------------------------------------------------------------------------------- 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 : 26.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.002 TRP B 94 HIS 0.006 0.002 HIS B 298 PHE 0.023 0.002 PHE C 230 TYR 0.021 0.002 TYR D 32 ARG 0.006 0.001 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.15434 ( 1059) hydrogen bonds : angle 6.72596 ( 2323) covalent geometry : bond 0.00395 (30472) covalent geometry : angle 0.87913 (44568) *********************** 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 : 1.863 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: 0.3824 time to fit residues: 125.3603 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 : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 50.0000 chunk 172 optimal weight: 50.0000 chunk 95 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 177 optimal weight: 40.0000 chunk 68 optimal weight: 7.9990 chunk 108 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 chunk 206 optimal weight: 50.0000 overall best weight: 12.1996 ------------------------------------------------------------------------------- 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 222 GLN B 268 HIS ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN D 158 ASN E 181 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.099738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.094396 restraints weight = 189455.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.094880 restraints weight = 243091.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.095056 restraints weight = 134588.530| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30472 Z= 0.222 Angle : 0.886 9.942 44568 Z= 0.444 Chirality : 0.045 0.278 5408 Planarity : 0.005 0.051 3128 Dihedral : 28.301 177.004 12284 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.20 % Allowed : 8.11 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.19), residues: 1625 helix: -0.90 (0.21), residues: 533 sheet: -2.10 (0.33), residues: 220 loop : -1.87 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 94 HIS 0.007 0.002 HIS B 298 PHE 0.019 0.002 PHE C 120 TYR 0.023 0.002 TYR C 55 ARG 0.006 0.001 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.09499 ( 1059) hydrogen bonds : angle 5.72090 ( 2323) covalent geometry : bond 0.00443 (30472) covalent geometry : angle 0.88613 (44568) *********************** 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 197 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.3821 (mmm) cc_final: 0.2774 (ptt) REVERT: E 101 TRP cc_start: 0.5369 (t60) cc_final: 0.4846 (t60) REVERT: E 261 LEU cc_start: 0.7705 (mt) cc_final: 0.7257 (mt) REVERT: E 262 MET cc_start: 0.7244 (tpp) cc_final: 0.6904 (tpt) outliers start: 3 outliers final: 1 residues processed: 197 average time/residue: 0.4348 time to fit residues: 140.1387 Evaluate side-chains 153 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 91 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 190 optimal weight: 40.0000 chunk 104 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 178 optimal weight: 50.0000 chunk 151 optimal weight: 30.0000 chunk 44 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 164 optimal weight: 40.0000 overall best weight: 9.5792 ------------------------------------------------------------------------------- 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 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 259 GLN B 268 HIS C 259 GLN C 296 ASN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4210 r_free = 0.4210 target = 0.100507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.095669 restraints weight = 190716.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.095937 restraints weight = 237382.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.095303 restraints weight = 163508.988| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5790 moved from start: 0.1525 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= 0.195 Angle : 0.840 9.082 44568 Z= 0.422 Chirality : 0.044 0.332 5408 Planarity : 0.005 0.059 3128 Dihedral : 28.203 177.206 12284 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.20), residues: 1625 helix: -0.75 (0.22), residues: 527 sheet: -2.00 (0.34), residues: 217 loop : -1.76 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 101 HIS 0.006 0.002 HIS B 298 PHE 0.020 0.002 PHE C 120 TYR 0.020 0.002 TYR D 32 ARG 0.007 0.001 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.08974 ( 1059) hydrogen bonds : angle 5.44758 ( 2323) covalent geometry : bond 0.00390 (30472) covalent geometry : angle 0.83970 (44568) *********************** 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 200 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.950 Fit side-chains revert: symmetry clash REVERT: A 141 MET cc_start: 0.3579 (mmm) cc_final: 0.3033 (ptt) REVERT: E 101 TRP cc_start: 0.5431 (t60) cc_final: 0.4804 (t60) REVERT: E 261 LEU cc_start: 0.7263 (mt) cc_final: 0.7052 (mt) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.5296 time to fit residues: 174.3781 Evaluate side-chains 151 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 20.0000 chunk 161 optimal weight: 50.0000 chunk 67 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 178 optimal weight: 50.0000 chunk 18 optimal weight: 0.9990 chunk 120 optimal weight: 30.0000 chunk 138 optimal weight: 8.9990 chunk 103 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.101575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.095585 restraints weight = 193316.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.095522 restraints weight = 212236.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.096100 restraints weight = 162975.291| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30472 Z= 0.170 Angle : 0.803 8.884 44568 Z= 0.403 Chirality : 0.043 0.283 5408 Planarity : 0.005 0.064 3128 Dihedral : 28.031 177.742 12284 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.20), residues: 1625 helix: -0.77 (0.22), residues: 531 sheet: -1.89 (0.34), residues: 217 loop : -1.74 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 101 HIS 0.008 0.001 HIS B 298 PHE 0.035 0.002 PHE A 196 TYR 0.026 0.002 TYR E 297 ARG 0.006 0.001 ARG E 207 Details of bonding type rmsd hydrogen bonds : bond 0.08351 ( 1059) hydrogen bonds : angle 5.24926 ( 2323) covalent geometry : bond 0.00336 (30472) covalent geometry : angle 0.80347 (44568) *********************** 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 205 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4096 (mm) cc_final: 0.3800 (mm) REVERT: B 290 ILE cc_start: 0.8187 (mp) cc_final: 0.7669 (mp) REVERT: B 328 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8186 (ttmm) REVERT: D 205 PHE cc_start: 0.6766 (m-10) cc_final: 0.6518 (m-10) REVERT: E 7 TYR cc_start: 0.3857 (t80) cc_final: 0.3567 (t80) REVERT: E 236 LYS cc_start: 0.4765 (mttm) cc_final: 0.3878 (tppt) REVERT: E 261 LEU cc_start: 0.7599 (mt) cc_final: 0.7106 (mt) REVERT: E 262 MET cc_start: 0.7282 (tpp) cc_final: 0.6769 (tpt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3696 time to fit residues: 122.2984 Evaluate side-chains 161 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 173 optimal weight: 50.0000 chunk 226 optimal weight: 40.0000 chunk 138 optimal weight: 2.9990 chunk 177 optimal weight: 40.0000 chunk 145 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 115 optimal weight: 40.0000 chunk 219 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 30.0000 chunk 53 optimal weight: 0.0060 overall best weight: 6.8006 ------------------------------------------------------------------------------- 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 ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** 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 = 0.4231 r_free = 0.4231 target = 0.101691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.096005 restraints weight = 192721.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.095532 restraints weight = 197545.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.096114 restraints weight = 159354.874| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30472 Z= 0.171 Angle : 0.797 8.851 44568 Z= 0.399 Chirality : 0.042 0.273 5408 Planarity : 0.005 0.057 3128 Dihedral : 27.978 177.592 12284 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.25 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.20), residues: 1625 helix: -0.60 (0.22), residues: 532 sheet: -1.88 (0.33), residues: 239 loop : -1.71 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 101 HIS 0.004 0.001 HIS B 298 PHE 0.021 0.001 PHE C 120 TYR 0.040 0.002 TYR D 55 ARG 0.017 0.001 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.08358 ( 1059) hydrogen bonds : angle 5.17976 ( 2323) covalent geometry : bond 0.00339 (30472) covalent geometry : angle 0.79665 (44568) *********************** 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 201 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4106 (mm) cc_final: 0.3808 (mm) REVERT: E 236 LYS cc_start: 0.4735 (mttm) cc_final: 0.4248 (tppt) REVERT: E 262 MET cc_start: 0.7306 (tpp) cc_final: 0.6890 (tpt) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.3764 time to fit residues: 123.2651 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 : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 163 optimal weight: 40.0000 chunk 126 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 161 optimal weight: 50.0000 chunk 99 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** 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** E 247 ASN ** E 274 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 = 0.4235 r_free = 0.4235 target = 0.101906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.096446 restraints weight = 192597.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.096312 restraints weight = 194442.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.096766 restraints weight = 149268.157| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30472 Z= 0.165 Angle : 0.787 8.768 44568 Z= 0.394 Chirality : 0.041 0.275 5408 Planarity : 0.005 0.055 3128 Dihedral : 27.882 177.483 12284 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.20), residues: 1625 helix: -0.67 (0.22), residues: 553 sheet: -1.82 (0.33), residues: 239 loop : -1.85 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 101 HIS 0.004 0.001 HIS B 298 PHE 0.019 0.002 PHE C 120 TYR 0.040 0.002 TYR B 276 ARG 0.007 0.001 ARG E 207 Details of bonding type rmsd hydrogen bonds : bond 0.08170 ( 1059) hydrogen bonds : angle 5.05652 ( 2323) covalent geometry : bond 0.00328 (30472) covalent geometry : angle 0.78697 (44568) *********************** 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 208 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4165 (mm) cc_final: 0.3854 (mm) REVERT: B 134 VAL cc_start: 0.5580 (m) cc_final: 0.5012 (p) REVERT: B 328 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8221 (ttmm) REVERT: D 201 ARG cc_start: 0.5971 (ttt180) cc_final: 0.5464 (tpp80) REVERT: E 261 LEU cc_start: 0.7643 (mt) cc_final: 0.7201 (mt) outliers start: 1 outliers final: 1 residues processed: 208 average time/residue: 0.3625 time to fit residues: 123.6180 Evaluate side-chains 160 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 205 optimal weight: 50.0000 chunk 192 optimal weight: 50.0000 chunk 113 optimal weight: 40.0000 chunk 222 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 215 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 183 optimal weight: 40.0000 chunk 226 optimal weight: 30.0000 overall best weight: 12.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 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 = 0.4206 r_free = 0.4206 target = 0.100279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.094361 restraints weight = 190806.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.094267 restraints weight = 215850.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.094754 restraints weight = 164091.874| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30472 Z= 0.210 Angle : 0.840 9.479 44568 Z= 0.421 Chirality : 0.044 0.314 5408 Planarity : 0.005 0.071 3128 Dihedral : 27.965 177.022 12284 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.19), residues: 1625 helix: -0.78 (0.21), residues: 553 sheet: -1.99 (0.33), residues: 233 loop : -1.93 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 101 HIS 0.007 0.002 HIS B 298 PHE 0.021 0.002 PHE C 120 TYR 0.032 0.002 TYR B 276 ARG 0.008 0.001 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.08981 ( 1059) hydrogen bonds : angle 5.28073 ( 2323) covalent geometry : bond 0.00421 (30472) covalent geometry : angle 0.84015 (44568) *********************** 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 192 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 2.034 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.4486 (mm) cc_final: 0.4252 (mm) REVERT: A 288 MET cc_start: 0.5361 (tpp) cc_final: 0.5160 (tpp) REVERT: B 55 TYR cc_start: 0.5469 (m-80) cc_final: 0.4953 (m-80) REVERT: D 201 ARG cc_start: 0.6446 (ttt180) cc_final: 0.5830 (tpp80) REVERT: D 277 THR cc_start: 0.8467 (m) cc_final: 0.8027 (p) REVERT: D 288 MET cc_start: 0.5190 (mmp) cc_final: 0.4883 (mmp) REVERT: E 261 LEU cc_start: 0.7834 (mt) cc_final: 0.7368 (mt) REVERT: E 262 MET cc_start: 0.7475 (tpp) cc_final: 0.7254 (tpt) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.3695 time to fit residues: 116.2065 Evaluate side-chains 148 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 116 optimal weight: 9.9990 chunk 187 optimal weight: 30.0000 chunk 218 optimal weight: 30.0000 chunk 160 optimal weight: 50.0000 chunk 173 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 chunk 146 optimal weight: 40.0000 chunk 84 optimal weight: 30.0000 chunk 128 optimal weight: 40.0000 chunk 156 optimal weight: 5.9990 chunk 162 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 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 268 HIS ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN C 139 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.097160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.092701 restraints weight = 190094.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.092853 restraints weight = 214301.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.092150 restraints weight = 130263.974| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 30472 Z= 0.291 Angle : 0.981 10.919 44568 Z= 0.490 Chirality : 0.049 0.289 5408 Planarity : 0.007 0.071 3128 Dihedral : 28.240 178.049 12284 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 28.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.19), residues: 1625 helix: -1.12 (0.21), residues: 537 sheet: -2.43 (0.35), residues: 189 loop : -2.17 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 94 HIS 0.011 0.003 HIS B 298 PHE 0.034 0.003 PHE C 145 TYR 0.043 0.003 TYR B 276 ARG 0.016 0.001 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.10699 ( 1059) hydrogen bonds : angle 5.74581 ( 2323) covalent geometry : bond 0.00592 (30472) covalent geometry : angle 0.98055 (44568) *********************** 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 174 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.5338 (tpp) cc_final: 0.5087 (tpp) REVERT: B 55 TYR cc_start: 0.5366 (m-80) cc_final: 0.4974 (m-80) REVERT: D 130 ILE cc_start: 0.5350 (mp) cc_final: 0.5035 (mm) REVERT: D 201 ARG cc_start: 0.6318 (ttt180) cc_final: 0.5621 (tpp80) REVERT: E 217 MET cc_start: 0.6265 (mpp) cc_final: 0.6026 (mpp) REVERT: E 261 LEU cc_start: 0.7770 (mt) cc_final: 0.7388 (mt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3745 time to fit residues: 106.9874 Evaluate side-chains 142 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 24 optimal weight: 40.0000 chunk 38 optimal weight: 40.0000 chunk 181 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 chunk 55 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 206 optimal weight: 50.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- 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 ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E 274 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 = 0.4189 r_free = 0.4189 target = 0.099132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.094366 restraints weight = 189583.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.094798 restraints weight = 223477.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.094562 restraints weight = 115116.509| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30472 Z= 0.206 Angle : 0.869 10.612 44568 Z= 0.435 Chirality : 0.045 0.279 5408 Planarity : 0.005 0.078 3128 Dihedral : 28.094 178.545 12284 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.19), residues: 1625 helix: -1.04 (0.21), residues: 545 sheet: -2.09 (0.35), residues: 206 loop : -2.09 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 101 HIS 0.006 0.002 HIS E 298 PHE 0.026 0.002 PHE C 230 TYR 0.038 0.002 TYR B 276 ARG 0.007 0.001 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.09016 ( 1059) hydrogen bonds : angle 5.49217 ( 2323) covalent geometry : bond 0.00412 (30472) covalent geometry : angle 0.86860 (44568) *********************** 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 183 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.5121 (tpp) cc_final: 0.4894 (tpp) REVERT: B 55 TYR cc_start: 0.5211 (m-80) cc_final: 0.4860 (m-80) REVERT: D 130 ILE cc_start: 0.4755 (mp) cc_final: 0.4399 (mm) REVERT: D 201 ARG cc_start: 0.6370 (ttt180) cc_final: 0.5771 (tpp80) REVERT: D 329 MET cc_start: 0.7933 (tmm) cc_final: 0.6621 (tmm) REVERT: E 236 LYS cc_start: 0.4364 (mttp) cc_final: 0.3919 (tppt) REVERT: E 261 LEU cc_start: 0.7560 (mt) cc_final: 0.6959 (mt) REVERT: E 262 MET cc_start: 0.7274 (tpp) cc_final: 0.6505 (tpt) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3989 time to fit residues: 120.9673 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 : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 132 optimal weight: 30.0000 chunk 161 optimal weight: 50.0000 chunk 26 optimal weight: 3.9990 chunk 110 optimal weight: 40.0000 chunk 11 optimal weight: 40.0000 chunk 203 optimal weight: 50.0000 chunk 51 optimal weight: 20.0000 chunk 32 optimal weight: 50.0000 chunk 144 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 overall best weight: 12.7996 ------------------------------------------------------------------------------- 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 ** 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** ** E 274 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 = 0.4182 r_free = 0.4182 target = 0.098638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.093506 restraints weight = 189649.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.093717 restraints weight = 233827.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.093852 restraints weight = 144184.768| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.3003 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= 0.223 Angle : 0.883 10.692 44568 Z= 0.442 Chirality : 0.045 0.276 5408 Planarity : 0.006 0.095 3128 Dihedral : 28.083 178.526 12284 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.19), residues: 1625 helix: -1.02 (0.21), residues: 545 sheet: -2.14 (0.35), residues: 207 loop : -2.12 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 94 HIS 0.018 0.002 HIS D 298 PHE 0.027 0.002 PHE C 230 TYR 0.046 0.002 TYR B 276 ARG 0.016 0.001 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.09369 ( 1059) hydrogen bonds : angle 5.52465 ( 2323) covalent geometry : bond 0.00450 (30472) covalent geometry : angle 0.88338 (44568) ********************** 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 172 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 TYR cc_start: 0.5344 (m-80) cc_final: 0.4980 (m-80) REVERT: B 288 MET cc_start: 0.6228 (tmm) cc_final: 0.5920 (tmm) REVERT: D 201 ARG cc_start: 0.6472 (ttt180) cc_final: 0.5819 (tpp80) REVERT: D 329 MET cc_start: 0.7875 (tmm) cc_final: 0.6489 (tmm) REVERT: E 217 MET cc_start: 0.6226 (mpp) cc_final: 0.6021 (mpp) REVERT: E 236 LYS cc_start: 0.4384 (mttp) cc_final: 0.3928 (tppt) REVERT: E 261 LEU cc_start: 0.7727 (mt) cc_final: 0.7160 (mt) REVERT: E 262 MET cc_start: 0.7354 (tpp) cc_final: 0.6679 (tpt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3594 time to fit residues: 104.3487 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 : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 185 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 170 optimal weight: 50.0000 chunk 214 optimal weight: 50.0000 chunk 205 optimal weight: 40.0000 chunk 26 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 163 optimal weight: 40.0000 chunk 139 optimal weight: 5.9990 overall best weight: 10.3994 ------------------------------------------------------------------------------- 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 ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 D 107 ASN ** E 274 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 = 0.4197 r_free = 0.4197 target = 0.099328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.093279 restraints weight = 188794.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.093571 restraints weight = 182717.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.093831 restraints weight = 132325.561| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.3144 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= 0.198 Angle : 0.849 10.491 44568 Z= 0.425 Chirality : 0.044 0.275 5408 Planarity : 0.006 0.098 3128 Dihedral : 27.993 178.884 12284 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.20), residues: 1625 helix: -0.90 (0.22), residues: 546 sheet: -2.10 (0.34), residues: 219 loop : -2.09 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 94 HIS 0.005 0.002 HIS B 298 PHE 0.025 0.002 PHE A 306 TYR 0.040 0.002 TYR B 276 ARG 0.013 0.001 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.08863 ( 1059) hydrogen bonds : angle 5.42317 ( 2323) covalent geometry : bond 0.00397 (30472) covalent geometry : angle 0.84938 (44568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7094.74 seconds wall clock time: 127 minutes 30.53 seconds (7650.53 seconds total)