Starting phenix.real_space_refine on Thu Feb 15 16:39:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v03_20968/02_2024/6v03_20968_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v03_20968/02_2024/6v03_20968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v03_20968/02_2024/6v03_20968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v03_20968/02_2024/6v03_20968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v03_20968/02_2024/6v03_20968_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v03_20968/02_2024/6v03_20968_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 8371 2.51 5 N 2146 2.21 5 O 2261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 36": "OD1" <-> "OD2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ASP 263": "OD1" <-> "OD2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ASP 176": "OD1" <-> "OD2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 263": "OD1" <-> "OD2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 36": "OD1" <-> "OD2" Residue "D ARG 48": "NH1" <-> "NH2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D ASP 293": "OD1" <-> "OD2" Residue "E ASP 13": "OD1" <-> "OD2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E ASP 294": "OD1" <-> "OD2" Residue "E PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12808 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2513 Chain: "B" Number of atoms: 2553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2516 Chain: "C" Number of atoms: 2553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2516 Chain: "D" Number of atoms: 2553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2516 Chain: "E" Number of atoms: 2553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2516 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'3CN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'3CN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'3CN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'3CN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'3CN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" N ATRP A 160 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 160 " occ=0.50 residue: pdb=" N AHIS A 169 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 169 " occ=0.50 residue: pdb=" N APHE A 282 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 282 " occ=0.50 residue: pdb=" N AHIS B 169 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 169 " occ=0.50 residue: pdb=" N APHE B 282 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 282 " occ=0.50 residue: pdb=" N AHIS C 169 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 169 " occ=0.50 residue: pdb=" N APHE C 282 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 282 " occ=0.50 residue: pdb=" N AHIS D 169 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 169 " occ=0.50 residue: pdb=" N APHE D 282 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 282 " occ=0.50 residue: pdb=" N AHIS E 169 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 169 " occ=0.50 residue: pdb=" N APHE E 282 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE E 282 " occ=0.50 Time building chain proxies: 12.67, per 1000 atoms: 0.99 Number of scatterers: 12808 At special positions: 0 Unit cell: (88.7841, 89.8802, 124.955, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 2261 8.00 N 2146 7.00 C 8371 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 - 3.50 Amino acid : False - 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: 5.17 Conformation dependent library (CDL) restraints added in 4.6 seconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 17 sheets defined 23.9% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 220 through 223 Processing helix chain 'A' and resid 228 through 231 No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.936A pdb=" N LEU A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 284 removed outlier: 3.956A pdb=" N MET A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 269 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N APHE A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.852A pdb=" N ILE A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.780A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 220 through 223 Processing helix chain 'B' and resid 228 through 247 removed outlier: 4.106A pdb=" N GLN B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 281 removed outlier: 3.511A pdb=" N MET B 265 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.684A pdb=" N GLY B 312 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 69 removed outlier: 3.713A pdb=" N ILE C 63 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU C 64 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE C 67 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 156 No H-bonds generated for 'chain 'C' and resid 154 through 156' Processing helix chain 'C' and resid 176 through 178 No H-bonds generated for 'chain 'C' and resid 176 through 178' Processing helix chain 'C' and resid 210 through 217 Processing helix chain 'C' and resid 220 through 223 Processing helix chain 'C' and resid 228 through 247 removed outlier: 3.671A pdb=" N LEU C 232 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLN C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 240 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 287 removed outlier: 3.655A pdb=" N APHE C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLN C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.665A pdb=" N ALA C 310 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 69 removed outlier: 3.713A pdb=" N ASN D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 210 through 217 Processing helix chain 'D' and resid 220 through 223 Processing helix chain 'D' and resid 228 through 231 No H-bonds generated for 'chain 'D' and resid 228 through 231' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.964A pdb=" N LEU D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 281 removed outlier: 3.626A pdb=" N ILE D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 309 through 312 No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'E' and resid 63 through 69 removed outlier: 3.933A pdb=" N ASN E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 203 No H-bonds generated for 'chain 'E' and resid 201 through 203' Processing helix chain 'E' and resid 210 through 219 removed outlier: 3.668A pdb=" N ALA E 217 " --> pdb=" O GLY E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 228 through 231 No H-bonds generated for 'chain 'E' and resid 228 through 231' Processing helix chain 'E' and resid 233 through 236 No H-bonds generated for 'chain 'E' and resid 233 through 236' Processing helix chain 'E' and resid 239 through 242 No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 244 through 247 No H-bonds generated for 'chain 'E' and resid 244 through 247' Processing helix chain 'E' and resid 261 through 282 Processing helix chain 'E' and resid 307 through 312 removed outlier: 3.943A pdb=" N ALA E 310 " --> pdb=" O GLY E 307 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY E 312 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 143 through 147 removed outlier: 6.956A pdb=" N VAL A 16 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLN A 146 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 18 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= D, first strand: chain 'A' and resid 167 through 174 Processing sheet with id= E, first strand: chain 'B' and resid 144 through 147 removed outlier: 7.028A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= G, first strand: chain 'B' and resid 167 through 174 Processing sheet with id= H, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= I, first strand: chain 'C' and resid 143 through 147 removed outlier: 6.459A pdb=" N VAL C 16 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN C 146 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 18 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR C 33 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 101 " --> pdb=" O MET C 93 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.627A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 160 through 162 Processing sheet with id= L, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.699A pdb=" N TYR D 38 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE D 20 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL D 40 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE D 18 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLN D 42 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL D 16 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR D 44 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL D 14 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN D 139 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL D 16 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ARG D 141 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 12.577A pdb=" N ILE D 18 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N SER D 143 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 12.039A pdb=" N ILE D 20 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N ILE D 145 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 12.488A pdb=" N LYS D 22 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N VAL D 147 " --> pdb=" O LYS D 22 " (cutoff:3.500A) removed outlier: 13.766A pdb=" N TYR D 24 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 76 through 78 removed outlier: 4.134A pdb=" N ASP D 196 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 172 through 174 Processing sheet with id= O, first strand: chain 'E' and resid 145 through 147 removed outlier: 6.511A pdb=" N ILE E 18 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= Q, first strand: chain 'E' and resid 168 through 171 393 hydrogen bonds defined for protein. 1091 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.20: 10 1.20 - 1.35: 4077 1.35 - 1.50: 3990 1.50 - 1.66: 5056 1.66 - 1.81: 50 Bond restraints: 13183 Sorted by residual: bond pdb=" CB 3CN B 402 " pdb=" CC 3CN B 402 " ideal model delta sigma weight residual 1.521 1.045 0.476 2.00e-02 2.50e+03 5.66e+02 bond pdb=" CB 3CN C 402 " pdb=" CC 3CN C 402 " ideal model delta sigma weight residual 1.521 1.045 0.476 2.00e-02 2.50e+03 5.66e+02 bond pdb=" CB 3CN E 402 " pdb=" CC 3CN E 402 " ideal model delta sigma weight residual 1.521 1.045 0.476 2.00e-02 2.50e+03 5.66e+02 bond pdb=" CB 3CN A 402 " pdb=" CC 3CN A 402 " ideal model delta sigma weight residual 1.521 1.046 0.475 2.00e-02 2.50e+03 5.64e+02 bond pdb=" CB 3CN D 402 " pdb=" CC 3CN D 402 " ideal model delta sigma weight residual 1.521 1.046 0.475 2.00e-02 2.50e+03 5.64e+02 ... (remaining 13178 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.80: 429 106.80 - 113.61: 7062 113.61 - 120.41: 5101 120.41 - 127.21: 5212 127.21 - 134.02: 180 Bond angle restraints: 17984 Sorted by residual: angle pdb=" N ASN B 60 " pdb=" CA ASN B 60 " pdb=" C ASN B 60 " ideal model delta sigma weight residual 111.02 115.41 -4.39 1.22e+00 6.72e-01 1.29e+01 angle pdb=" N ILE E 209 " pdb=" CA ILE E 209 " pdb=" C ILE E 209 " ideal model delta sigma weight residual 111.81 108.90 2.91 8.60e-01 1.35e+00 1.14e+01 angle pdb=" N ASN A 60 " pdb=" CA ASN A 60 " pdb=" C ASN A 60 " ideal model delta sigma weight residual 111.02 115.05 -4.03 1.22e+00 6.72e-01 1.09e+01 angle pdb=" C GLU B 59 " pdb=" N ASN B 60 " pdb=" CA ASN B 60 " ideal model delta sigma weight residual 120.79 125.22 -4.43 1.39e+00 5.18e-01 1.01e+01 angle pdb=" CA 3CN A 402 " pdb=" CB 3CN A 402 " pdb=" CC 3CN A 402 " ideal model delta sigma weight residual 112.40 102.98 9.42 3.00e+00 1.11e-01 9.87e+00 ... (remaining 17979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 7028 17.81 - 35.61: 552 35.61 - 53.42: 114 53.42 - 71.23: 16 71.23 - 89.03: 5 Dihedral angle restraints: 7715 sinusoidal: 3110 harmonic: 4605 Sorted by residual: dihedral pdb=" CA ASN D 137 " pdb=" C ASN D 137 " pdb=" N GLN D 138 " pdb=" CA GLN D 138 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ASN A 137 " pdb=" C ASN A 137 " pdb=" N GLN A 138 " pdb=" CA GLN A 138 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU A 118 " pdb=" C LEU A 118 " pdb=" N PHE A 119 " pdb=" CA PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 7712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1027 0.030 - 0.061: 599 0.061 - 0.091: 203 0.091 - 0.121: 125 0.121 - 0.151: 21 Chirality restraints: 1975 Sorted by residual: chirality pdb=" CA VAL C 291 " pdb=" N VAL C 291 " pdb=" C VAL C 291 " pdb=" CB VAL C 291 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ILE C 195 " pdb=" N ILE C 195 " pdb=" C ILE C 195 " pdb=" CB ILE C 195 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE B 195 " pdb=" N ILE B 195 " pdb=" C ILE B 195 " pdb=" CB ILE B 195 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1972 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 54 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO D 55 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 55 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 55 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 54 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO B 55 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 54 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO C 55 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.017 5.00e-02 4.00e+02 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2234 2.77 - 3.30: 11648 3.30 - 3.83: 20076 3.83 - 4.37: 24789 4.37 - 4.90: 43134 Nonbonded interactions: 101881 Sorted by model distance: nonbonded pdb=" OH TYR A 148 " pdb=" OD2 ASP B 176 " model vdw 2.234 2.440 nonbonded pdb=" OD2 ASP D 122 " pdb=" NH1 ARG D 199 " model vdw 2.236 2.520 nonbonded pdb=" O GLU B 150 " pdb=" ND2 ASN B 154 " model vdw 2.254 2.520 nonbonded pdb=" OD1 ASP A 115 " pdb=" NH1 ARG A 117 " model vdw 2.294 2.520 nonbonded pdb=" O ARG D 299 " pdb=" NH1 ARG D 299 " model vdw 2.301 2.520 ... (remaining 101876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 317 \ or resid 401 through 402)) selection = (chain 'B' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 317 \ or resid 401 through 402)) selection = (chain 'C' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 317 \ or resid 401 through 402)) selection = (chain 'D' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 317 \ or resid 401 through 402)) selection = (chain 'E' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 317 \ or resid 401 through 402)) } 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=0.50 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.410 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 44.640 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.476 13183 Z= 1.014 Angle : 0.670 9.480 17984 Z= 0.352 Chirality : 0.047 0.151 1975 Planarity : 0.003 0.032 2296 Dihedral : 13.488 89.035 4755 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.79 % Allowed : 4.21 % Favored : 95.00 % 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: -4.30 (0.18), residues: 1572 helix: -3.03 (0.19), residues: 415 sheet: -1.93 (0.21), residues: 519 loop : -3.39 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 224 HIS 0.006 0.001 HIS B 177 PHE 0.017 0.001 PHE D 142 TYR 0.007 0.001 TYR A 245 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.535 Fit side-chains revert: symmetry clash REVERT: C 86 ASP cc_start: 0.7753 (t70) cc_final: 0.7489 (t70) REVERT: C 258 TYR cc_start: 0.8711 (p90) cc_final: 0.7962 (p90) REVERT: D 36 ASP cc_start: 0.8028 (t0) cc_final: 0.7728 (t0) REVERT: E 216 ILE cc_start: 0.7802 (mm) cc_final: 0.7496 (mt) REVERT: E 231 ARG cc_start: 0.7194 (mtp-110) cc_final: 0.6965 (mtp85) REVERT: E 247 PHE cc_start: 0.7463 (t80) cc_final: 0.7228 (t80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2700 time to fit residues: 60.1715 Evaluate side-chains 131 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 69 ASN ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN B 62 GLN B 124 GLN B 169 HIS B ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 284 HIS D 62 GLN D 124 GLN D 138 GLN ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS E 60 ASN E 62 GLN E 69 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13183 Z= 0.252 Angle : 0.576 7.827 17984 Z= 0.294 Chirality : 0.047 0.153 1975 Planarity : 0.004 0.034 2296 Dihedral : 5.168 32.756 1755 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.64 % Allowed : 8.79 % Favored : 89.57 % 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: -3.18 (0.20), residues: 1572 helix: -2.06 (0.23), residues: 405 sheet: -1.31 (0.22), residues: 526 loop : -2.73 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 224 HIS 0.006 0.001 HIS B 177 PHE 0.030 0.001 PHE E 228 TYR 0.008 0.001 TYR A 270 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.538 Fit side-chains REVERT: C 86 ASP cc_start: 0.7745 (t70) cc_final: 0.7535 (t70) REVERT: C 247 PHE cc_start: 0.7545 (t80) cc_final: 0.7181 (t80) REVERT: C 258 TYR cc_start: 0.8718 (p90) cc_final: 0.7937 (p90) REVERT: D 36 ASP cc_start: 0.8039 (t0) cc_final: 0.7788 (t0) REVERT: E 216 ILE cc_start: 0.7740 (mm) cc_final: 0.7474 (mt) REVERT: E 247 PHE cc_start: 0.7449 (t80) cc_final: 0.7197 (t80) outliers start: 12 outliers final: 7 residues processed: 141 average time/residue: 0.2751 time to fit residues: 54.7717 Evaluate side-chains 137 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain E residue 196 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 284 HIS ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 13183 Z= 0.387 Angle : 0.630 7.121 17984 Z= 0.324 Chirality : 0.049 0.149 1975 Planarity : 0.004 0.032 2296 Dihedral : 5.424 31.555 1755 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.86 % Allowed : 11.29 % Favored : 86.86 % 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: -2.96 (0.20), residues: 1572 helix: -1.86 (0.24), residues: 422 sheet: -1.11 (0.23), residues: 523 loop : -2.67 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 43 HIS 0.007 0.002 HIS B 177 PHE 0.018 0.002 PHE D 228 TYR 0.011 0.001 TYR B 148 ARG 0.004 0.000 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.570 Fit side-chains REVERT: C 86 ASP cc_start: 0.7660 (t70) cc_final: 0.7458 (t70) REVERT: C 258 TYR cc_start: 0.8706 (p90) cc_final: 0.7944 (p90) REVERT: D 36 ASP cc_start: 0.8105 (t0) cc_final: 0.7871 (t0) REVERT: E 247 PHE cc_start: 0.7433 (t80) cc_final: 0.7216 (t80) outliers start: 15 outliers final: 10 residues processed: 138 average time/residue: 0.2770 time to fit residues: 54.7109 Evaluate side-chains 135 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 196 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 20.0000 chunk 102 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 62 GLN ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 138 GLN D 151 ASN E 138 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13183 Z= 0.147 Angle : 0.526 8.150 17984 Z= 0.265 Chirality : 0.045 0.152 1975 Planarity : 0.003 0.031 2296 Dihedral : 4.682 20.459 1755 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.93 % Allowed : 11.93 % Favored : 86.14 % 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: -2.30 (0.21), residues: 1572 helix: -1.49 (0.24), residues: 418 sheet: -0.58 (0.24), residues: 519 loop : -2.28 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 224 HIS 0.005 0.001 HIS B 177 PHE 0.019 0.001 PHE D 228 TYR 0.009 0.001 TYR A 38 ARG 0.003 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.436 Fit side-chains REVERT: C 247 PHE cc_start: 0.7446 (t80) cc_final: 0.7076 (t80) REVERT: C 258 TYR cc_start: 0.8658 (p90) cc_final: 0.7833 (p90) REVERT: D 36 ASP cc_start: 0.8019 (t0) cc_final: 0.7754 (t0) REVERT: D 38 TYR cc_start: 0.8732 (m-80) cc_final: 0.8501 (m-80) REVERT: D 258 TYR cc_start: 0.8434 (p90) cc_final: 0.7847 (p90) REVERT: E 247 PHE cc_start: 0.7399 (t80) cc_final: 0.7170 (t80) outliers start: 16 outliers final: 14 residues processed: 159 average time/residue: 0.2438 time to fit residues: 57.1184 Evaluate side-chains 153 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 196 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 4.9990 chunk 82 optimal weight: 0.0070 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 59 optimal weight: 8.9990 chunk 123 optimal weight: 0.0470 chunk 100 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 13183 Z= 0.143 Angle : 0.516 7.809 17984 Z= 0.260 Chirality : 0.045 0.160 1975 Planarity : 0.003 0.030 2296 Dihedral : 4.452 18.031 1755 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.93 % Allowed : 12.79 % Favored : 85.29 % 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: -1.92 (0.21), residues: 1572 helix: -1.28 (0.25), residues: 424 sheet: -0.28 (0.24), residues: 519 loop : -2.04 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 224 HIS 0.005 0.001 HIS B 177 PHE 0.016 0.001 PHE D 228 TYR 0.009 0.001 TYR C 38 ARG 0.002 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.531 Fit side-chains REVERT: B 245 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.6606 (t80) REVERT: C 247 PHE cc_start: 0.7411 (t80) cc_final: 0.7053 (t80) REVERT: C 258 TYR cc_start: 0.8649 (p90) cc_final: 0.7854 (p90) REVERT: D 36 ASP cc_start: 0.7988 (t0) cc_final: 0.7707 (t0) REVERT: D 38 TYR cc_start: 0.8706 (m-80) cc_final: 0.8483 (m-80) REVERT: D 258 TYR cc_start: 0.8397 (p90) cc_final: 0.7863 (p90) REVERT: E 247 PHE cc_start: 0.7367 (t80) cc_final: 0.7144 (t80) outliers start: 16 outliers final: 13 residues processed: 152 average time/residue: 0.2282 time to fit residues: 52.3102 Evaluate side-chains 152 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 196 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13183 Z= 0.212 Angle : 0.535 7.205 17984 Z= 0.271 Chirality : 0.046 0.172 1975 Planarity : 0.003 0.028 2296 Dihedral : 4.559 19.872 1755 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.14 % Allowed : 13.21 % Favored : 84.64 % 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: -1.77 (0.22), residues: 1572 helix: -1.13 (0.25), residues: 424 sheet: -0.23 (0.24), residues: 521 loop : -1.93 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 224 HIS 0.006 0.001 HIS B 177 PHE 0.013 0.001 PHE D 228 TYR 0.009 0.001 TYR C 38 ARG 0.002 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.453 Fit side-chains REVERT: B 245 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6646 (t80) REVERT: C 247 PHE cc_start: 0.7398 (t80) cc_final: 0.7052 (t80) REVERT: C 258 TYR cc_start: 0.8679 (p90) cc_final: 0.7933 (p90) REVERT: D 36 ASP cc_start: 0.8007 (t0) cc_final: 0.7735 (t0) REVERT: D 38 TYR cc_start: 0.8745 (m-80) cc_final: 0.8509 (m-80) REVERT: D 258 TYR cc_start: 0.8397 (p90) cc_final: 0.7928 (p90) REVERT: E 247 PHE cc_start: 0.7392 (t80) cc_final: 0.7168 (t80) outliers start: 19 outliers final: 15 residues processed: 151 average time/residue: 0.2784 time to fit residues: 61.3454 Evaluate side-chains 157 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 196 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 124 GLN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 13183 Z= 0.446 Angle : 0.655 7.237 17984 Z= 0.338 Chirality : 0.050 0.254 1975 Planarity : 0.004 0.028 2296 Dihedral : 5.293 27.350 1755 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.14 % Allowed : 14.07 % Favored : 83.79 % 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: -2.01 (0.21), residues: 1572 helix: -1.25 (0.25), residues: 424 sheet: -0.38 (0.24), residues: 510 loop : -2.10 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 43 HIS 0.008 0.002 HIS B 177 PHE 0.020 0.002 PHE C 106 TYR 0.013 0.002 TYR B 148 ARG 0.004 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.464 Fit side-chains REVERT: C 258 TYR cc_start: 0.8652 (p90) cc_final: 0.7955 (p90) REVERT: D 36 ASP cc_start: 0.8113 (t0) cc_final: 0.7885 (t0) REVERT: D 38 TYR cc_start: 0.8736 (m-80) cc_final: 0.8528 (m-80) REVERT: E 216 ILE cc_start: 0.7747 (mm) cc_final: 0.7488 (mt) REVERT: E 247 PHE cc_start: 0.7392 (t80) cc_final: 0.7172 (t80) outliers start: 19 outliers final: 16 residues processed: 145 average time/residue: 0.2828 time to fit residues: 59.1206 Evaluate side-chains 149 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 196 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 124 GLN B 138 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 284 HIS E 138 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13183 Z= 0.173 Angle : 0.533 7.363 17984 Z= 0.271 Chirality : 0.046 0.190 1975 Planarity : 0.003 0.028 2296 Dihedral : 4.656 19.668 1755 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.00 % Allowed : 14.43 % Favored : 83.57 % 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: -1.60 (0.22), residues: 1572 helix: -0.94 (0.26), residues: 419 sheet: -0.16 (0.24), residues: 515 loop : -1.81 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 224 HIS 0.005 0.001 HIS B 177 PHE 0.013 0.001 PHE D 228 TYR 0.012 0.001 TYR A 203 ARG 0.002 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.486 Fit side-chains REVERT: C 114 MET cc_start: 0.8202 (mtt) cc_final: 0.7995 (mtt) REVERT: C 247 PHE cc_start: 0.7431 (t80) cc_final: 0.7075 (t80) REVERT: C 258 TYR cc_start: 0.8556 (p90) cc_final: 0.7857 (p90) REVERT: D 36 ASP cc_start: 0.8048 (t0) cc_final: 0.7788 (t0) REVERT: D 38 TYR cc_start: 0.8690 (m-80) cc_final: 0.8447 (m-80) REVERT: D 258 TYR cc_start: 0.8349 (p90) cc_final: 0.7861 (p90) REVERT: E 247 PHE cc_start: 0.7361 (t80) cc_final: 0.7149 (t80) outliers start: 17 outliers final: 16 residues processed: 153 average time/residue: 0.2685 time to fit residues: 60.1955 Evaluate side-chains 159 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 196 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 0.0000 chunk 41 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN D 124 GLN E 285 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13183 Z= 0.227 Angle : 0.543 7.275 17984 Z= 0.276 Chirality : 0.047 0.222 1975 Planarity : 0.003 0.028 2296 Dihedral : 4.676 20.557 1755 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.07 % Allowed : 14.57 % Favored : 83.36 % 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: -1.50 (0.22), residues: 1572 helix: -0.90 (0.25), residues: 419 sheet: -0.07 (0.25), residues: 515 loop : -1.76 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 224 HIS 0.006 0.001 HIS B 177 PHE 0.012 0.001 PHE D 228 TYR 0.012 0.001 TYR A 203 ARG 0.002 0.000 ARG D 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.480 Fit side-chains REVERT: C 247 PHE cc_start: 0.7398 (t80) cc_final: 0.7048 (t80) REVERT: C 258 TYR cc_start: 0.8583 (p90) cc_final: 0.7847 (p90) REVERT: D 36 ASP cc_start: 0.8055 (t0) cc_final: 0.7798 (t0) REVERT: D 38 TYR cc_start: 0.8716 (m-80) cc_final: 0.8474 (m-80) REVERT: D 258 TYR cc_start: 0.8344 (p90) cc_final: 0.7857 (p90) REVERT: E 247 PHE cc_start: 0.7364 (t80) cc_final: 0.7152 (t80) outliers start: 18 outliers final: 17 residues processed: 153 average time/residue: 0.2737 time to fit residues: 60.6356 Evaluate side-chains 159 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 196 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 12 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 chunk 126 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 13183 Z= 0.230 Angle : 0.778 59.138 17984 Z= 0.445 Chirality : 0.048 0.483 1975 Planarity : 0.003 0.028 2296 Dihedral : 4.694 21.829 1755 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 2.07 % Allowed : 14.57 % Favored : 83.36 % 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: -1.49 (0.22), residues: 1572 helix: -0.89 (0.26), residues: 419 sheet: -0.07 (0.25), residues: 515 loop : -1.75 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 224 HIS 0.005 0.001 HIS B 177 PHE 0.031 0.001 PHE B 308 TYR 0.011 0.001 TYR A 203 ARG 0.002 0.000 ARG D 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.457 Fit side-chains REVERT: B 245 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6634 (t80) REVERT: C 247 PHE cc_start: 0.7397 (t80) cc_final: 0.7047 (t80) REVERT: C 258 TYR cc_start: 0.8583 (p90) cc_final: 0.7846 (p90) REVERT: D 36 ASP cc_start: 0.8053 (t0) cc_final: 0.7793 (t0) REVERT: D 38 TYR cc_start: 0.8708 (m-80) cc_final: 0.8471 (m-80) REVERT: D 258 TYR cc_start: 0.8342 (p90) cc_final: 0.7855 (p90) REVERT: E 247 PHE cc_start: 0.7363 (t80) cc_final: 0.7153 (t80) outliers start: 18 outliers final: 16 residues processed: 151 average time/residue: 0.2817 time to fit residues: 61.7612 Evaluate side-chains 159 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 196 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 119 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.174069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.133817 restraints weight = 83981.823| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.78 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 13183 Z= 0.218 Angle : 0.777 59.199 17984 Z= 0.441 Chirality : 0.046 0.209 1975 Planarity : 0.003 0.028 2296 Dihedral : 4.680 20.510 1755 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 2.07 % Allowed : 14.71 % Favored : 83.21 % 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: -1.49 (0.22), residues: 1572 helix: -0.88 (0.26), residues: 419 sheet: -0.06 (0.25), residues: 515 loop : -1.75 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 206 HIS 0.005 0.001 HIS B 177 PHE 0.030 0.001 PHE B 308 TYR 0.010 0.001 TYR A 203 ARG 0.002 0.000 ARG C 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.51 seconds wall clock time: 47 minutes 48.78 seconds (2868.78 seconds total)