Starting phenix.real_space_refine on Thu Feb 15 14:11:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0b_20986/02_2024/6v0b_20986.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0b_20986/02_2024/6v0b_20986.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0b_20986/02_2024/6v0b_20986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0b_20986/02_2024/6v0b_20986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0b_20986/02_2024/6v0b_20986.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0b_20986/02_2024/6v0b_20986.pdb" } 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= 0.001 sd= 0.009 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 8135 2.51 5 N 2075 2.21 5 O 2245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 36": "OD1" <-> "OD2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12485 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2497 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Chain: "B" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2497 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Chain: "C" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2497 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Chain: "D" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2497 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Chain: "E" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2497 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Time building chain proxies: 7.84, per 1000 atoms: 0.63 Number of scatterers: 12485 At special positions: 0 Unit cell: (92.0724, 92.0724, 117.283, 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 2245 8.00 N 2075 7.00 C 8135 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: 4.85 Conformation dependent library (CDL) restraints added in 2.5 seconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 25.2% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.594A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 207 removed outlier: 3.935A pdb=" N SER A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 removed outlier: 4.135A pdb=" N ILE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 253 removed outlier: 3.558A pdb=" N THR A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 264 removed outlier: 3.674A pdb=" N GLN A 264 " --> pdb=" O VAL A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 265 through 285 removed outlier: 4.374A pdb=" N ILE A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.592A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 removed outlier: 3.935A pdb=" N SER B 207 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 4.136A pdb=" N ILE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 253 removed outlier: 3.558A pdb=" N THR B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 264 removed outlier: 3.674A pdb=" N GLN B 264 " --> pdb=" O VAL B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 264' Processing helix chain 'B' and resid 265 through 285 removed outlier: 4.374A pdb=" N ILE B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 278 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.593A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 207 removed outlier: 3.934A pdb=" N SER C 207 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 220 removed outlier: 4.136A pdb=" N ILE C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 253 removed outlier: 3.558A pdb=" N THR C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 243 " --> pdb=" O MET C 239 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 264 removed outlier: 3.674A pdb=" N GLN C 264 " --> pdb=" O VAL C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 265 through 285 removed outlier: 4.373A pdb=" N ILE C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 278 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'D' and resid 62 through 67 removed outlier: 3.593A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 207 removed outlier: 3.934A pdb=" N SER D 207 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 220 removed outlier: 4.135A pdb=" N ILE D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 253 removed outlier: 3.558A pdb=" N THR D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 243 " --> pdb=" O MET D 239 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 264 removed outlier: 3.674A pdb=" N GLN D 264 " --> pdb=" O VAL D 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 265 through 285 removed outlier: 4.374A pdb=" N ILE D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 278 " --> pdb=" O PHE D 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 307 Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.594A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 207 removed outlier: 3.935A pdb=" N SER E 207 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 220 removed outlier: 4.136A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA E 217 " --> pdb=" O GLY E 213 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 253 removed outlier: 3.558A pdb=" N THR E 234 " --> pdb=" O GLU E 230 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL E 243 " --> pdb=" O MET E 239 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU E 253 " --> pdb=" O THR E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 264 removed outlier: 3.675A pdb=" N GLN E 264 " --> pdb=" O VAL E 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 261 through 264' Processing helix chain 'E' and resid 265 through 285 removed outlier: 4.374A pdb=" N ILE E 273 " --> pdb=" O GLY E 269 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E 278 " --> pdb=" O PHE E 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 27 removed outlier: 5.530A pdb=" N ILE A 23 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP A 36 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY A 25 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 34 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 35 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 108 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 37 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 27 removed outlier: 5.530A pdb=" N ILE A 23 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP A 36 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY A 25 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 34 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 14 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU A 131 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 194 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 167 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU A 131 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE B 23 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP B 36 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY B 25 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 34 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 35 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 108 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B 37 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE B 23 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP B 36 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY B 25 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 34 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL B 14 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU B 131 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 194 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 167 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU B 131 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE C 23 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP C 36 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY C 25 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS C 34 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 35 " --> pdb=" O GLY C 108 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY C 108 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 37 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE C 23 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP C 36 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY C 25 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS C 34 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL C 14 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 77 removed outlier: 3.779A pdb=" N GLU C 131 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG C 194 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 167 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 77 removed outlier: 3.779A pdb=" N GLU C 131 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE D 23 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP D 36 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY D 25 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS D 34 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 35 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY D 108 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY D 37 " --> pdb=" O PHE D 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE D 23 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP D 36 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY D 25 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS D 34 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL D 14 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 77 removed outlier: 3.779A pdb=" N GLU D 131 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 194 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER D 167 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 77 removed outlier: 3.779A pdb=" N GLU D 131 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE E 23 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP E 36 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY E 25 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS E 34 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 35 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY E 108 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY E 37 " --> pdb=" O PHE E 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE E 23 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP E 36 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY E 25 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS E 34 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL E 14 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU E 131 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG E 194 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER E 167 " --> pdb=" O ARG E 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU E 131 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1125 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: 3.91 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3952 1.34 - 1.46: 2919 1.46 - 1.58: 5904 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12825 Sorted by residual: bond pdb=" N CYS B 300 " pdb=" CA CYS B 300 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.32e-02 5.74e+03 6.55e+00 bond pdb=" N CYS E 300 " pdb=" CA CYS E 300 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.36e+00 bond pdb=" N CYS D 300 " pdb=" CA CYS D 300 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.34e+00 bond pdb=" N CYS A 300 " pdb=" CA CYS A 300 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.25e+00 bond pdb=" N CYS C 300 " pdb=" CA CYS C 300 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.24e+00 ... (remaining 12820 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.05: 458 107.05 - 113.83: 6890 113.83 - 120.61: 5253 120.61 - 127.38: 4706 127.38 - 134.16: 173 Bond angle restraints: 17480 Sorted by residual: angle pdb=" C PRO C 183 " pdb=" N ASN C 184 " pdb=" CA ASN C 184 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C PRO D 183 " pdb=" N ASN D 184 " pdb=" CA ASN D 184 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C PRO B 183 " pdb=" N ASN B 184 " pdb=" CA ASN B 184 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.26e+01 angle pdb=" C PRO E 183 " pdb=" N ASN E 184 " pdb=" CA ASN E 184 " ideal model delta sigma weight residual 121.54 130.58 -9.04 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C PRO A 183 " pdb=" N ASN A 184 " pdb=" CA ASN A 184 " ideal model delta sigma weight residual 121.54 130.55 -9.01 1.91e+00 2.74e-01 2.22e+01 ... (remaining 17475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 6291 14.11 - 28.22: 851 28.22 - 42.33: 272 42.33 - 56.44: 61 56.44 - 70.55: 25 Dihedral angle restraints: 7500 sinusoidal: 3010 harmonic: 4490 Sorted by residual: dihedral pdb=" CA ASN B 289 " pdb=" C ASN B 289 " pdb=" N GLY B 290 " pdb=" CA GLY B 290 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASN E 289 " pdb=" C ASN E 289 " pdb=" N GLY E 290 " pdb=" CA GLY E 290 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ASN A 289 " pdb=" C ASN A 289 " pdb=" N GLY A 290 " pdb=" CA GLY A 290 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 7497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1498 0.066 - 0.132: 374 0.132 - 0.198: 61 0.198 - 0.263: 2 0.263 - 0.329: 5 Chirality restraints: 1940 Sorted by residual: chirality pdb=" CG LEU E 214 " pdb=" CB LEU E 214 " pdb=" CD1 LEU E 214 " pdb=" CD2 LEU E 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CG LEU A 214 " pdb=" CB LEU A 214 " pdb=" CD1 LEU A 214 " pdb=" CD2 LEU A 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CG LEU D 214 " pdb=" CB LEU D 214 " pdb=" CD1 LEU D 214 " pdb=" CD2 LEU D 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1937 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 274 " 0.035 2.00e-02 2.50e+03 3.46e-02 2.09e+01 pdb=" CG PHE A 274 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE A 274 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 274 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 274 " 0.020 2.00e-02 2.50e+03 pdb=" CZ PHE A 274 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 274 " 0.035 2.00e-02 2.50e+03 3.46e-02 2.09e+01 pdb=" CG PHE C 274 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE C 274 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE C 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 274 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 274 " 0.020 2.00e-02 2.50e+03 pdb=" CZ PHE C 274 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 274 " 0.035 2.00e-02 2.50e+03 3.45e-02 2.09e+01 pdb=" CG PHE D 274 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE D 274 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 274 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 274 " 0.020 2.00e-02 2.50e+03 pdb=" CZ PHE D 274 " 0.000 2.00e-02 2.50e+03 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3323 2.80 - 3.32: 11440 3.32 - 3.85: 21011 3.85 - 4.37: 23553 4.37 - 4.90: 39449 Nonbonded interactions: 98776 Sorted by model distance: nonbonded pdb=" OG SER D 143 " pdb=" OG1 THR D 168 " model vdw 2.272 2.440 nonbonded pdb=" OG SER E 143 " pdb=" OG1 THR E 168 " model vdw 2.272 2.440 nonbonded pdb=" OG SER C 143 " pdb=" OG1 THR C 168 " model vdw 2.272 2.440 nonbonded pdb=" OG SER B 143 " pdb=" OG1 THR B 168 " model vdw 2.272 2.440 nonbonded pdb=" OG SER A 143 " pdb=" OG1 THR A 168 " model vdw 2.273 2.440 ... (remaining 98771 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.420 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: 2.440 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 37.340 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.006 0.060 12825 Z= 0.370 Angle : 0.981 9.117 17480 Z= 0.552 Chirality : 0.059 0.329 1940 Planarity : 0.007 0.051 2230 Dihedral : 15.045 70.555 4600 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.51 % Allowed : 10.22 % Favored : 89.27 % 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: -4.96 (0.18), residues: 1520 helix: -4.23 (0.15), residues: 345 sheet: -3.11 (0.22), residues: 395 loop : -2.89 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 160 HIS 0.006 0.003 HIS D 169 PHE 0.078 0.003 PHE D 274 TYR 0.024 0.003 TYR C 102 ARG 0.008 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.9030 (tp) cc_final: 0.8802 (tp) REVERT: A 131 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7906 (mm-30) REVERT: A 154 ASN cc_start: 0.7762 (m-40) cc_final: 0.7513 (t0) REVERT: A 239 MET cc_start: 0.9116 (mmm) cc_final: 0.8802 (mmm) REVERT: B 130 LEU cc_start: 0.9119 (tp) cc_final: 0.8845 (tp) REVERT: B 154 ASN cc_start: 0.7727 (m-40) cc_final: 0.7466 (m-40) REVERT: B 239 MET cc_start: 0.9159 (mmm) cc_final: 0.8528 (mpp) REVERT: C 154 ASN cc_start: 0.7940 (m-40) cc_final: 0.7577 (t0) REVERT: C 308 PHE cc_start: 0.5863 (m-80) cc_final: 0.5636 (m-10) REVERT: D 131 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8114 (mt-10) REVERT: D 239 MET cc_start: 0.9106 (mmm) cc_final: 0.8435 (mpp) REVERT: E 239 MET cc_start: 0.9082 (mmm) cc_final: 0.8704 (mmm) outliers start: 7 outliers final: 2 residues processed: 222 average time/residue: 0.2165 time to fit residues: 71.8398 Evaluate side-chains 150 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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: 0.5980 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 136 optimal weight: 0.9980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 80 ASN A 125 GLN ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 HIS A 264 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 125 GLN B 177 HIS B 264 GLN C 21 ASN C 80 ASN C 125 GLN C 177 HIS C 264 GLN D 21 ASN D 62 GLN ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS D 264 GLN E 80 ASN E 125 GLN E 177 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12825 Z= 0.252 Angle : 0.676 8.143 17480 Z= 0.361 Chirality : 0.045 0.153 1940 Planarity : 0.005 0.048 2230 Dihedral : 6.835 25.037 1680 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -4.29 (0.19), residues: 1520 helix: -3.16 (0.20), residues: 375 sheet: -2.86 (0.21), residues: 410 loop : -2.55 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 72 HIS 0.006 0.002 HIS C 177 PHE 0.024 0.002 PHE E 247 TYR 0.019 0.002 TYR C 270 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7739 (mm-30) REVERT: C 130 LEU cc_start: 0.8881 (tp) cc_final: 0.8336 (tp) REVERT: C 131 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7550 (mm-30) REVERT: D 131 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7780 (mt-10) REVERT: E 131 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7621 (mt-10) REVERT: E 239 MET cc_start: 0.8979 (mmm) cc_final: 0.8729 (mmm) REVERT: E 270 TYR cc_start: 0.8280 (m-80) cc_final: 0.8079 (m-80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2343 time to fit residues: 60.6159 Evaluate side-chains 118 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 147 optimal weight: 30.0000 chunk 121 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN C 21 ASN C 138 GLN ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN E 138 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12825 Z= 0.207 Angle : 0.628 8.740 17480 Z= 0.328 Chirality : 0.045 0.153 1940 Planarity : 0.004 0.042 2230 Dihedral : 6.449 22.041 1680 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: -3.81 (0.19), residues: 1520 helix: -2.44 (0.23), residues: 380 sheet: -2.61 (0.22), residues: 410 loop : -2.43 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.004 0.001 HIS E 177 PHE 0.028 0.002 PHE C 247 TYR 0.017 0.002 TYR B 270 ARG 0.002 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7840 (mt-10) REVERT: A 199 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7845 (mtm180) REVERT: A 265 MET cc_start: 0.5584 (mpp) cc_final: 0.5238 (mmm) REVERT: C 130 LEU cc_start: 0.8905 (tp) cc_final: 0.8286 (tp) REVERT: C 131 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7515 (mm-30) REVERT: C 199 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7047 (mtm180) REVERT: D 131 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7694 (mt-10) REVERT: D 270 TYR cc_start: 0.8182 (m-80) cc_final: 0.7979 (m-80) REVERT: E 131 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7623 (mt-10) REVERT: E 239 MET cc_start: 0.8963 (mmm) cc_final: 0.8754 (mmm) REVERT: E 270 TYR cc_start: 0.8381 (m-80) cc_final: 0.8168 (m-80) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2392 time to fit residues: 59.5545 Evaluate side-chains 119 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.5980 chunk 102 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 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 21 ASN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12825 Z= 0.191 Angle : 0.617 8.359 17480 Z= 0.318 Chirality : 0.045 0.152 1940 Planarity : 0.004 0.041 2230 Dihedral : 6.135 20.670 1680 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: -3.60 (0.19), residues: 1520 helix: -2.01 (0.24), residues: 380 sheet: -2.25 (0.23), residues: 410 loop : -2.63 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.012 0.002 HIS B 177 PHE 0.026 0.001 PHE E 247 TYR 0.020 0.002 TYR A 270 ARG 0.002 0.000 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.5483 (mpp) cc_final: 0.5209 (mmm) REVERT: C 130 LEU cc_start: 0.8987 (tp) cc_final: 0.8354 (tp) REVERT: C 131 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7535 (mm-30) REVERT: C 199 ARG cc_start: 0.7932 (mtm180) cc_final: 0.6966 (mtm180) REVERT: D 131 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7638 (mt-10) REVERT: D 270 TYR cc_start: 0.8384 (m-80) cc_final: 0.8086 (m-80) REVERT: E 131 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7649 (mt-10) REVERT: E 270 TYR cc_start: 0.8392 (m-80) cc_final: 0.8017 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2360 time to fit residues: 57.9761 Evaluate side-chains 116 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12825 Z= 0.347 Angle : 0.721 8.232 17480 Z= 0.379 Chirality : 0.047 0.152 1940 Planarity : 0.006 0.069 2230 Dihedral : 6.525 22.611 1680 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: -3.41 (0.20), residues: 1520 helix: -1.64 (0.26), residues: 350 sheet: -2.25 (0.23), residues: 425 loop : -2.54 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 72 HIS 0.014 0.003 HIS C 177 PHE 0.036 0.002 PHE A 274 TYR 0.024 0.002 TYR E 102 ARG 0.003 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8109 (mt-10) REVERT: C 127 VAL cc_start: 0.9225 (t) cc_final: 0.8892 (p) REVERT: C 130 LEU cc_start: 0.9184 (tp) cc_final: 0.8480 (tp) REVERT: C 131 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7521 (mm-30) REVERT: D 131 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7611 (mt-10) REVERT: D 270 TYR cc_start: 0.8496 (m-80) cc_final: 0.8207 (m-80) REVERT: E 131 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7607 (mt-10) REVERT: E 270 TYR cc_start: 0.8532 (m-80) cc_final: 0.8199 (m-80) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2319 time to fit residues: 51.7116 Evaluate side-chains 110 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 0.0030 chunk 35 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12825 Z= 0.294 Angle : 0.686 8.209 17480 Z= 0.359 Chirality : 0.046 0.155 1940 Planarity : 0.005 0.053 2230 Dihedral : 6.448 22.576 1680 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: -3.33 (0.20), residues: 1520 helix: -1.47 (0.26), residues: 350 sheet: -2.18 (0.23), residues: 410 loop : -2.57 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 72 HIS 0.014 0.003 HIS C 177 PHE 0.036 0.002 PHE C 274 TYR 0.020 0.002 TYR D 102 ARG 0.003 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7677 (mt-10) REVERT: C 131 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7283 (mm-30) REVERT: D 131 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7597 (mt-10) REVERT: D 239 MET cc_start: 0.9163 (mmt) cc_final: 0.8939 (mmt) REVERT: D 270 TYR cc_start: 0.8492 (m-80) cc_final: 0.8153 (m-80) REVERT: E 131 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7614 (mt-10) REVERT: E 265 MET cc_start: 0.4208 (mmt) cc_final: 0.3931 (mmt) REVERT: E 270 TYR cc_start: 0.8573 (m-80) cc_final: 0.8138 (m-80) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2475 time to fit residues: 55.7008 Evaluate side-chains 109 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 89 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12825 Z= 0.230 Angle : 0.652 8.339 17480 Z= 0.339 Chirality : 0.046 0.148 1940 Planarity : 0.004 0.044 2230 Dihedral : 6.263 21.907 1680 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: -3.07 (0.20), residues: 1520 helix: -0.85 (0.29), residues: 320 sheet: -2.09 (0.24), residues: 410 loop : -2.54 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 161 HIS 0.013 0.002 HIS B 177 PHE 0.039 0.002 PHE D 274 TYR 0.024 0.002 TYR C 270 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7834 (mt-10) REVERT: B 131 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7659 (mt-10) REVERT: C 131 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7287 (mm-30) REVERT: D 131 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7534 (mt-10) REVERT: E 131 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7590 (mt-10) REVERT: E 265 MET cc_start: 0.4147 (mmt) cc_final: 0.3886 (mmt) REVERT: E 270 TYR cc_start: 0.8627 (m-80) cc_final: 0.8382 (m-80) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2235 time to fit residues: 50.0398 Evaluate side-chains 115 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 28 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12825 Z= 0.226 Angle : 0.642 8.108 17480 Z= 0.331 Chirality : 0.046 0.148 1940 Planarity : 0.004 0.042 2230 Dihedral : 6.194 21.423 1680 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -2.98 (0.20), residues: 1520 helix: -0.77 (0.30), residues: 320 sheet: -2.00 (0.24), residues: 410 loop : -2.51 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 206 HIS 0.011 0.002 HIS C 177 PHE 0.025 0.002 PHE D 247 TYR 0.021 0.002 TYR A 270 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 148 TYR cc_start: 0.5275 (m-80) cc_final: 0.5072 (m-10) REVERT: B 127 VAL cc_start: 0.9186 (t) cc_final: 0.8863 (p) REVERT: B 131 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 265 MET cc_start: 0.3716 (mmt) cc_final: 0.3491 (mmt) REVERT: C 131 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7283 (mm-30) REVERT: D 131 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7485 (mt-10) REVERT: E 131 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7577 (mt-10) REVERT: E 239 MET cc_start: 0.8767 (mmm) cc_final: 0.8563 (mmm) REVERT: E 270 TYR cc_start: 0.8579 (m-80) cc_final: 0.8273 (m-80) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2288 time to fit residues: 51.1187 Evaluate side-chains 117 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12825 Z= 0.371 Angle : 0.754 8.142 17480 Z= 0.396 Chirality : 0.048 0.157 1940 Planarity : 0.006 0.076 2230 Dihedral : 6.585 22.456 1680 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -3.07 (0.21), residues: 1520 helix: -0.82 (0.30), residues: 305 sheet: -2.16 (0.24), residues: 425 loop : -2.46 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 72 HIS 0.014 0.003 HIS C 177 PHE 0.041 0.003 PHE C 274 TYR 0.026 0.002 TYR D 102 ARG 0.004 0.001 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7757 (mt-10) REVERT: C 130 LEU cc_start: 0.8893 (tp) cc_final: 0.8503 (tt) REVERT: C 131 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7422 (mm-30) REVERT: D 131 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7557 (mt-10) REVERT: E 131 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7999 (mt-10) REVERT: E 270 TYR cc_start: 0.8697 (m-80) cc_final: 0.8412 (m-80) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2267 time to fit residues: 50.9524 Evaluate side-chains 111 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 0.0870 chunk 137 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 overall best weight: 0.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12825 Z= 0.170 Angle : 0.635 9.546 17480 Z= 0.323 Chirality : 0.047 0.144 1940 Planarity : 0.004 0.040 2230 Dihedral : 6.000 20.777 1680 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -2.89 (0.21), residues: 1520 helix: -0.61 (0.30), residues: 320 sheet: -2.08 (0.23), residues: 430 loop : -2.40 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 161 HIS 0.008 0.001 HIS C 177 PHE 0.046 0.002 PHE A 274 TYR 0.024 0.002 TYR D 270 ARG 0.002 0.000 ARG A 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.8680 (tt) cc_final: 0.8078 (mp) REVERT: A 148 TYR cc_start: 0.5158 (m-80) cc_final: 0.4837 (m-10) REVERT: B 131 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7543 (mt-10) REVERT: C 265 MET cc_start: 0.3456 (mmt) cc_final: 0.3222 (mmt) REVERT: E 77 GLU cc_start: 0.7814 (pt0) cc_final: 0.7546 (pp20) REVERT: E 128 LEU cc_start: 0.8507 (tt) cc_final: 0.7878 (mp) REVERT: E 131 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7775 (mt-10) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2321 time to fit residues: 56.3772 Evaluate side-chains 121 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 15 optimal weight: 0.0980 chunk 21 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN E 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.106316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.085007 restraints weight = 44158.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.087547 restraints weight = 27308.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.089156 restraints weight = 19971.890| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12825 Z= 0.392 Angle : 0.771 9.758 17480 Z= 0.401 Chirality : 0.048 0.158 1940 Planarity : 0.006 0.089 2230 Dihedral : 6.514 23.496 1680 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -3.03 (0.21), residues: 1520 helix: -0.88 (0.30), residues: 305 sheet: -2.19 (0.23), residues: 430 loop : -2.35 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 161 HIS 0.013 0.003 HIS C 177 PHE 0.031 0.002 PHE B 208 TYR 0.026 0.002 TYR C 102 ARG 0.004 0.001 ARG D 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.57 seconds wall clock time: 42 minutes 0.61 seconds (2520.61 seconds total)