Starting phenix.real_space_refine on Wed Feb 14 20:20:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/02_2024/8pvf_17964_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/02_2024/8pvf_17964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/02_2024/8pvf_17964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/02_2024/8pvf_17964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/02_2024/8pvf_17964_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvf_17964/02_2024/8pvf_17964_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 72 5.16 5 C 6372 2.51 5 N 1704 2.21 5 O 1984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 64": "OD1" <-> "OD2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 64": "OD1" <-> "OD2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "D TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 64": "OD1" <-> "OD2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 341": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10140 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2491 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 321} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2491 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 321} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2491 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 321} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2491 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 321} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.75, per 1000 atoms: 0.57 Number of scatterers: 10140 At special positions: 0 Unit cell: (95.0895, 84.9915, 96.7725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 8 15.00 O 1984 8.00 N 1704 7.00 C 6372 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: 3.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 12 sheets defined 30.3% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 27 through 38 removed outlier: 3.519A pdb=" N GLU A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 119 through 126 removed outlier: 4.012A pdb=" N LEU A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 168 through 183 Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.787A pdb=" N GLY A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 301 through 304 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 336 through 352 Processing helix chain 'B' and resid 27 through 38 removed outlier: 3.519A pdb=" N GLU B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 101 through 104 No H-bonds generated for 'chain 'B' and resid 101 through 104' Processing helix chain 'B' and resid 119 through 126 removed outlier: 4.012A pdb=" N LEU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 168 through 183 Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 231 through 238 removed outlier: 3.787A pdb=" N GLY B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 301 through 304 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 336 through 352 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.519A pdb=" N GLU C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 62 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 101 through 104 No H-bonds generated for 'chain 'C' and resid 101 through 104' Processing helix chain 'C' and resid 119 through 126 removed outlier: 4.012A pdb=" N LEU C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 168 through 183 Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 231 through 238 removed outlier: 3.787A pdb=" N GLY C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 237 " --> pdb=" O LYS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 301 through 304 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 336 through 352 Processing helix chain 'D' and resid 27 through 38 removed outlier: 3.519A pdb=" N GLU D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 101 through 104 No H-bonds generated for 'chain 'D' and resid 101 through 104' Processing helix chain 'D' and resid 119 through 126 removed outlier: 4.012A pdb=" N LEU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 168 through 183 Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 231 through 238 removed outlier: 3.787A pdb=" N GLY D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 237 " --> pdb=" O LYS D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 315 through 317 No H-bonds generated for 'chain 'D' and resid 315 through 317' Processing helix chain 'D' and resid 336 through 352 Processing sheet with id= A, first strand: chain 'A' and resid 162 through 164 removed outlier: 6.143A pdb=" N VAL A 133 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR A 43 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE A 22 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL A 45 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL A 87 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE A 47 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS A 89 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR A 247 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY A 189 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET A 249 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET A 191 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE A 251 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR A 193 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS A 266 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY A 189 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 264 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET A 191 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 262 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 193 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 260 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 322 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS A 327 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA A 320 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 292 through 295 removed outlier: 6.339A pdb=" N SER A 311 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR A 295 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 313 " --> pdb=" O THR A 295 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 162 through 164 removed outlier: 6.143A pdb=" N VAL B 133 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR B 43 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE B 22 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL B 45 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 87 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE B 47 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS B 89 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR B 247 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY B 189 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET B 249 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET B 191 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE B 251 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 193 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS B 266 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY B 189 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR B 264 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET B 191 " --> pdb=" O ASP B 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP B 262 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 193 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 260 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 322 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS B 327 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA B 320 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 292 through 295 removed outlier: 6.339A pdb=" N SER B 311 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR B 295 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE B 313 " --> pdb=" O THR B 295 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 162 through 164 removed outlier: 6.143A pdb=" N VAL C 133 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR C 43 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE C 22 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL C 45 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL C 87 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE C 47 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS C 89 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR C 247 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY C 189 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET C 249 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET C 191 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE C 251 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 193 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS C 266 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY C 189 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR C 264 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET C 191 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP C 262 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR C 193 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 260 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C 322 " --> pdb=" O PHE C 325 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS C 327 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA C 320 " --> pdb=" O LYS C 327 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 292 through 295 removed outlier: 6.339A pdb=" N SER C 311 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR C 295 " --> pdb=" O SER C 311 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE C 313 " --> pdb=" O THR C 295 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 162 through 164 removed outlier: 6.143A pdb=" N VAL D 133 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR D 43 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE D 22 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL D 45 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL D 87 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE D 47 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS D 89 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 225 through 228 removed outlier: 9.310A pdb=" N THR D 247 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY D 189 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET D 249 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET D 191 " --> pdb=" O MET D 249 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE D 251 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR D 193 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS D 266 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY D 189 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR D 264 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET D 191 " --> pdb=" O ASP D 262 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP D 262 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR D 193 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL D 260 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN D 322 " --> pdb=" O PHE D 325 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS D 327 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA D 320 " --> pdb=" O LYS D 327 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 292 through 295 removed outlier: 6.339A pdb=" N SER D 311 " --> pdb=" O GLY D 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR D 295 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE D 313 " --> pdb=" O THR D 295 " (cutoff:3.500A) No H-bonds generated for sheet with id= L 292 hydrogen bonds defined for protein. 804 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: 3.27 Time building geometry restraints manager: 4.32 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: 2212 1.34 - 1.46: 2900 1.46 - 1.58: 5096 1.58 - 1.70: 16 1.70 - 1.82: 108 Bond restraints: 10332 Sorted by residual: bond pdb=" C1D NAD B 401 " pdb=" O4D NAD B 401 " ideal model delta sigma weight residual 1.376 1.433 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C1D NAD A 401 " pdb=" O4D NAD A 401 " ideal model delta sigma weight residual 1.376 1.433 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C1D NAD D 401 " pdb=" O4D NAD D 401 " ideal model delta sigma weight residual 1.376 1.433 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C1D NAD C 401 " pdb=" O4D NAD C 401 " ideal model delta sigma weight residual 1.376 1.433 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C ALA D 137 " pdb=" N PRO D 138 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.74e+00 ... (remaining 10327 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.24: 384 106.24 - 113.29: 4856 113.29 - 120.33: 5068 120.33 - 127.38: 3648 127.38 - 134.42: 108 Bond angle restraints: 14064 Sorted by residual: angle pdb=" CA ASP C 95 " pdb=" CB ASP C 95 " pdb=" CG ASP C 95 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.00e+00 1.00e+00 4.21e+01 angle pdb=" CA ASP B 95 " pdb=" CB ASP B 95 " pdb=" CG ASP B 95 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.00e+00 1.00e+00 4.18e+01 angle pdb=" CA ASP A 95 " pdb=" CB ASP A 95 " pdb=" CG ASP A 95 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.00e+00 1.00e+00 4.18e+01 angle pdb=" CA ASP D 95 " pdb=" CB ASP D 95 " pdb=" CG ASP D 95 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.00e+00 1.00e+00 4.18e+01 angle pdb=" C ASP A 262 " pdb=" CA ASP A 262 " pdb=" CB ASP A 262 " ideal model delta sigma weight residual 111.17 120.97 -9.80 1.54e+00 4.22e-01 4.05e+01 ... (remaining 14059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 5468 15.41 - 30.81: 676 30.81 - 46.21: 92 46.21 - 61.61: 44 61.61 - 77.01: 24 Dihedral angle restraints: 6304 sinusoidal: 2476 harmonic: 3828 Sorted by residual: dihedral pdb=" CA MET B 191 " pdb=" C MET B 191 " pdb=" N THR B 192 " pdb=" CA THR B 192 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA MET C 191 " pdb=" C MET C 191 " pdb=" N THR C 192 " pdb=" CA THR C 192 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA MET A 191 " pdb=" C MET A 191 " pdb=" N THR A 192 " pdb=" CA THR A 192 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 6301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 825 0.062 - 0.124: 511 0.124 - 0.186: 260 0.186 - 0.248: 36 0.248 - 0.310: 8 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CB ILE C 108 " pdb=" CA ILE C 108 " pdb=" CG1 ILE C 108 " pdb=" CG2 ILE C 108 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB ILE A 108 " pdb=" CA ILE A 108 " pdb=" CG1 ILE A 108 " pdb=" CG2 ILE A 108 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB ILE D 108 " pdb=" CA ILE D 108 " pdb=" CG1 ILE D 108 " pdb=" CG2 ILE D 108 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1637 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 252 " 0.172 9.50e-02 1.11e+02 8.18e-02 1.31e+01 pdb=" NE ARG C 252 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG C 252 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG C 252 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG C 252 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 252 " 0.172 9.50e-02 1.11e+02 8.18e-02 1.31e+01 pdb=" NE ARG D 252 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG D 252 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG D 252 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG D 252 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 252 " -0.172 9.50e-02 1.11e+02 8.18e-02 1.31e+01 pdb=" NE ARG B 252 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 252 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG B 252 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG B 252 " 0.011 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3856 2.91 - 3.41: 9676 3.41 - 3.91: 19020 3.91 - 4.40: 22206 4.40 - 4.90: 35102 Nonbonded interactions: 89860 Sorted by model distance: nonbonded pdb=" O ALA A 137 " pdb=" OG SER A 164 " model vdw 2.413 2.440 nonbonded pdb=" O ALA B 137 " pdb=" OG SER B 164 " model vdw 2.413 2.440 nonbonded pdb=" O ALA C 137 " pdb=" OG SER C 164 " model vdw 2.413 2.440 nonbonded pdb=" O ALA D 137 " pdb=" OG SER D 164 " model vdw 2.413 2.440 nonbonded pdb=" O SER B 136 " pdb=" OG SER B 136 " model vdw 2.493 2.440 ... (remaining 89855 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 4.030 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 31.020 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.010 0.057 10332 Z= 0.674 Angle : 1.803 9.801 14064 Z= 1.192 Chirality : 0.091 0.310 1640 Planarity : 0.011 0.091 1792 Dihedral : 14.887 77.012 3864 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.18 % Favored : 95.52 % Rotamer: Outliers : 1.12 % Allowed : 7.43 % Favored : 91.45 % Cbeta Deviations : 0.33 % 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: -1.16 (0.21), residues: 1340 helix: -0.96 (0.22), residues: 352 sheet: -1.41 (0.28), residues: 272 loop : -0.23 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.008 TRP B 101 HIS 0.008 0.004 HIS A 125 PHE 0.026 0.007 PHE D 304 TYR 0.040 0.008 TYR C 146 ARG 0.053 0.008 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 304 time to evaluate : 1.228 Fit side-chains REVERT: A 37 MET cc_start: 0.7451 (mmt) cc_final: 0.7128 (mpm) REVERT: A 43 THR cc_start: 0.7608 (t) cc_final: 0.7330 (m) REVERT: A 55 GLU cc_start: 0.6945 (mp0) cc_final: 0.6592 (mp0) REVERT: A 71 ASN cc_start: 0.7216 (t0) cc_final: 0.6593 (m-40) REVERT: A 75 GLU cc_start: 0.7628 (pt0) cc_final: 0.7360 (pt0) REVERT: A 89 LYS cc_start: 0.7003 (mtpt) cc_final: 0.6682 (mtpt) REVERT: A 120 GLU cc_start: 0.7692 (tt0) cc_final: 0.7109 (mp0) REVERT: A 131 LYS cc_start: 0.7686 (mmtp) cc_final: 0.7183 (mttm) REVERT: A 159 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6564 (ttmm) REVERT: A 160 PHE cc_start: 0.7491 (m-80) cc_final: 0.7260 (m-80) REVERT: A 183 LYS cc_start: 0.7221 (tptt) cc_final: 0.6942 (tptm) REVERT: A 247 THR cc_start: 0.8509 (t) cc_final: 0.8162 (p) REVERT: A 252 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7030 (mpp80) REVERT: A 282 GLU cc_start: 0.6790 (tt0) cc_final: 0.6441 (mt-10) REVERT: A 289 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7449 (ttmm) REVERT: A 308 LYS cc_start: 0.7991 (mttp) cc_final: 0.7762 (mttp) REVERT: A 327 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7766 (tppp) REVERT: B 37 MET cc_start: 0.7451 (mmt) cc_final: 0.7128 (mpm) REVERT: B 43 THR cc_start: 0.7606 (t) cc_final: 0.7330 (m) REVERT: B 55 GLU cc_start: 0.6947 (mp0) cc_final: 0.6594 (mp0) REVERT: B 71 ASN cc_start: 0.7218 (t0) cc_final: 0.6594 (m-40) REVERT: B 75 GLU cc_start: 0.7630 (pt0) cc_final: 0.7361 (pt0) REVERT: B 89 LYS cc_start: 0.7004 (mtpt) cc_final: 0.6683 (mtpt) REVERT: B 120 GLU cc_start: 0.7693 (tt0) cc_final: 0.7109 (mp0) REVERT: B 131 LYS cc_start: 0.7684 (mmtp) cc_final: 0.7180 (mttm) REVERT: B 159 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6565 (ttmm) REVERT: B 160 PHE cc_start: 0.7491 (m-80) cc_final: 0.7261 (m-80) REVERT: B 183 LYS cc_start: 0.7219 (tptt) cc_final: 0.6940 (tptm) REVERT: B 247 THR cc_start: 0.8509 (t) cc_final: 0.8161 (p) REVERT: B 252 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7030 (mpp80) REVERT: B 282 GLU cc_start: 0.6790 (tt0) cc_final: 0.6441 (mt-10) REVERT: B 289 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7451 (ttmm) REVERT: B 308 LYS cc_start: 0.7991 (mttp) cc_final: 0.7760 (mttp) REVERT: B 327 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7767 (tppp) REVERT: C 37 MET cc_start: 0.7452 (mmt) cc_final: 0.7128 (mpm) REVERT: C 43 THR cc_start: 0.7609 (t) cc_final: 0.7332 (m) REVERT: C 55 GLU cc_start: 0.6947 (mp0) cc_final: 0.6594 (mp0) REVERT: C 71 ASN cc_start: 0.7217 (t0) cc_final: 0.6593 (m-40) REVERT: C 75 GLU cc_start: 0.7630 (pt0) cc_final: 0.7360 (pt0) REVERT: C 89 LYS cc_start: 0.7005 (mtpt) cc_final: 0.6683 (mtpt) REVERT: C 120 GLU cc_start: 0.7693 (tt0) cc_final: 0.7109 (mp0) REVERT: C 131 LYS cc_start: 0.7685 (mmtp) cc_final: 0.7182 (mttm) REVERT: C 159 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6563 (ttmm) REVERT: C 160 PHE cc_start: 0.7492 (m-80) cc_final: 0.7260 (m-80) REVERT: C 183 LYS cc_start: 0.7221 (tptt) cc_final: 0.6941 (tptm) REVERT: C 247 THR cc_start: 0.8508 (t) cc_final: 0.8162 (p) REVERT: C 252 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7029 (mpp80) REVERT: C 282 GLU cc_start: 0.6792 (tt0) cc_final: 0.6442 (mt-10) REVERT: C 289 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7450 (ttmm) REVERT: C 308 LYS cc_start: 0.7993 (mttp) cc_final: 0.7762 (mttp) REVERT: C 327 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7769 (tppp) REVERT: D 37 MET cc_start: 0.7451 (mmt) cc_final: 0.7127 (mpm) REVERT: D 43 THR cc_start: 0.7607 (t) cc_final: 0.7330 (m) REVERT: D 55 GLU cc_start: 0.6947 (mp0) cc_final: 0.6593 (mp0) REVERT: D 71 ASN cc_start: 0.7218 (t0) cc_final: 0.6594 (m-40) REVERT: D 75 GLU cc_start: 0.7629 (pt0) cc_final: 0.7359 (pt0) REVERT: D 89 LYS cc_start: 0.7003 (mtpt) cc_final: 0.6681 (mtpt) REVERT: D 120 GLU cc_start: 0.7694 (tt0) cc_final: 0.7109 (mp0) REVERT: D 131 LYS cc_start: 0.7685 (mmtp) cc_final: 0.7182 (mttm) REVERT: D 159 LYS cc_start: 0.6957 (mmtt) cc_final: 0.6563 (ttmm) REVERT: D 160 PHE cc_start: 0.7492 (m-80) cc_final: 0.7261 (m-80) REVERT: D 183 LYS cc_start: 0.7223 (tptt) cc_final: 0.6944 (tptm) REVERT: D 247 THR cc_start: 0.8509 (t) cc_final: 0.8163 (p) REVERT: D 252 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7030 (mpp80) REVERT: D 282 GLU cc_start: 0.6790 (tt0) cc_final: 0.6439 (mt-10) REVERT: D 289 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7449 (ttmm) REVERT: D 308 LYS cc_start: 0.7992 (mttp) cc_final: 0.7762 (mttp) REVERT: D 327 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7766 (tppp) outliers start: 12 outliers final: 8 residues processed: 308 average time/residue: 1.4114 time to fit residues: 461.9358 Evaluate side-chains 232 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 224 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 261 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.0010 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 107 GLN A 195 HIS ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 107 GLN B 195 HIS ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 107 GLN C 195 HIS ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN D 107 GLN D 195 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10332 Z= 0.164 Angle : 0.518 5.823 14064 Z= 0.270 Chirality : 0.046 0.153 1640 Planarity : 0.004 0.034 1792 Dihedral : 8.810 71.778 1656 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.69 % Favored : 97.01 % Rotamer: Outliers : 1.12 % Allowed : 11.90 % Favored : 86.99 % 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: 0.35 (0.23), residues: 1340 helix: 1.10 (0.28), residues: 356 sheet: -1.03 (0.29), residues: 272 loop : 0.48 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 101 HIS 0.003 0.001 HIS A 67 PHE 0.009 0.001 PHE C 325 TYR 0.008 0.001 TYR A 332 ARG 0.002 0.000 ARG C 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 220 time to evaluate : 1.171 Fit side-chains REVERT: A 71 ASN cc_start: 0.7160 (t0) cc_final: 0.6631 (m-40) REVERT: A 119 GLU cc_start: 0.6438 (tm-30) cc_final: 0.6032 (tm-30) REVERT: A 120 GLU cc_start: 0.7718 (tt0) cc_final: 0.7025 (mp0) REVERT: A 131 LYS cc_start: 0.7782 (mmtp) cc_final: 0.7302 (mttm) REVERT: A 140 LYS cc_start: 0.6929 (mmpt) cc_final: 0.6663 (mmmm) REVERT: A 159 LYS cc_start: 0.7005 (mmtt) cc_final: 0.6609 (mmtt) REVERT: A 247 THR cc_start: 0.8338 (t) cc_final: 0.8032 (p) REVERT: A 252 ARG cc_start: 0.7552 (mtt180) cc_final: 0.7199 (mpp80) REVERT: A 282 GLU cc_start: 0.6891 (tt0) cc_final: 0.6514 (mt-10) REVERT: A 289 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7347 (ttmm) REVERT: A 316 ASN cc_start: 0.8000 (m-40) cc_final: 0.7445 (m-40) REVERT: B 71 ASN cc_start: 0.7159 (t0) cc_final: 0.6630 (m-40) REVERT: B 119 GLU cc_start: 0.6439 (tm-30) cc_final: 0.6034 (tm-30) REVERT: B 120 GLU cc_start: 0.7718 (tt0) cc_final: 0.7025 (mp0) REVERT: B 131 LYS cc_start: 0.7782 (mmtp) cc_final: 0.7304 (mttm) REVERT: B 140 LYS cc_start: 0.6927 (mmpt) cc_final: 0.6663 (mmmm) REVERT: B 159 LYS cc_start: 0.7005 (mmtt) cc_final: 0.6609 (mmtt) REVERT: B 247 THR cc_start: 0.8338 (t) cc_final: 0.8031 (p) REVERT: B 252 ARG cc_start: 0.7553 (mtt180) cc_final: 0.7200 (mpp80) REVERT: B 282 GLU cc_start: 0.6889 (tt0) cc_final: 0.6515 (mt-10) REVERT: B 289 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7348 (ttmm) REVERT: B 316 ASN cc_start: 0.8000 (m-40) cc_final: 0.7446 (m-40) REVERT: C 71 ASN cc_start: 0.7162 (t0) cc_final: 0.6633 (m-40) REVERT: C 119 GLU cc_start: 0.6439 (tm-30) cc_final: 0.6035 (tm-30) REVERT: C 120 GLU cc_start: 0.7719 (tt0) cc_final: 0.7026 (mp0) REVERT: C 131 LYS cc_start: 0.7781 (mmtp) cc_final: 0.7303 (mttm) REVERT: C 140 LYS cc_start: 0.6928 (mmpt) cc_final: 0.6664 (mmmm) REVERT: C 159 LYS cc_start: 0.7004 (mmtt) cc_final: 0.6608 (mmtt) REVERT: C 247 THR cc_start: 0.8338 (t) cc_final: 0.8031 (p) REVERT: C 252 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7198 (mpp80) REVERT: C 282 GLU cc_start: 0.6890 (tt0) cc_final: 0.6515 (mt-10) REVERT: C 289 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7349 (ttmm) REVERT: C 316 ASN cc_start: 0.8000 (m-40) cc_final: 0.7446 (m-40) REVERT: D 71 ASN cc_start: 0.7159 (t0) cc_final: 0.6629 (m-40) REVERT: D 119 GLU cc_start: 0.6440 (tm-30) cc_final: 0.6034 (tm-30) REVERT: D 120 GLU cc_start: 0.7718 (tt0) cc_final: 0.7025 (mp0) REVERT: D 131 LYS cc_start: 0.7782 (mmtp) cc_final: 0.7304 (mttm) REVERT: D 140 LYS cc_start: 0.6927 (mmpt) cc_final: 0.6663 (mmmm) REVERT: D 159 LYS cc_start: 0.7005 (mmtt) cc_final: 0.6609 (mmtt) REVERT: D 247 THR cc_start: 0.8339 (t) cc_final: 0.8032 (p) REVERT: D 252 ARG cc_start: 0.7554 (mtt180) cc_final: 0.7201 (mpp80) REVERT: D 282 GLU cc_start: 0.6889 (tt0) cc_final: 0.6513 (mt-10) REVERT: D 289 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7346 (ttmm) REVERT: D 316 ASN cc_start: 0.8001 (m-40) cc_final: 0.7446 (m-40) outliers start: 12 outliers final: 4 residues processed: 224 average time/residue: 1.2861 time to fit residues: 308.3739 Evaluate side-chains 196 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 106 optimal weight: 0.0870 chunk 119 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 340 ASN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 340 ASN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 340 ASN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN D 340 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10332 Z= 0.287 Angle : 0.554 6.863 14064 Z= 0.285 Chirality : 0.048 0.146 1640 Planarity : 0.004 0.035 1792 Dihedral : 8.754 74.940 1644 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.69 % Favored : 97.01 % Rotamer: Outliers : 4.83 % Allowed : 12.64 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1340 helix: 0.98 (0.28), residues: 352 sheet: -1.06 (0.29), residues: 280 loop : 0.39 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 101 HIS 0.004 0.002 HIS C 67 PHE 0.009 0.002 PHE B 313 TYR 0.015 0.002 TYR B 146 ARG 0.003 0.001 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 216 time to evaluate : 1.221 Fit side-chains REVERT: A 71 ASN cc_start: 0.7254 (t0) cc_final: 0.6716 (m-40) REVERT: A 107 GLN cc_start: 0.7068 (mt0) cc_final: 0.6822 (mt0) REVERT: A 120 GLU cc_start: 0.7685 (tt0) cc_final: 0.6930 (mp0) REVERT: A 131 LYS cc_start: 0.7689 (mmtp) cc_final: 0.7247 (mttm) REVERT: A 140 LYS cc_start: 0.6684 (mmpt) cc_final: 0.6459 (mmmm) REVERT: A 159 LYS cc_start: 0.7139 (mmtt) cc_final: 0.6751 (mmtt) REVERT: A 247 THR cc_start: 0.8334 (t) cc_final: 0.8115 (m) REVERT: A 252 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7190 (mpp80) REVERT: A 282 GLU cc_start: 0.7042 (tt0) cc_final: 0.6611 (mt-10) REVERT: A 289 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7424 (ttmm) REVERT: A 316 ASN cc_start: 0.8007 (m-40) cc_final: 0.7356 (m110) REVERT: A 319 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7571 (tp) REVERT: A 342 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7187 (mt) REVERT: B 71 ASN cc_start: 0.7253 (t0) cc_final: 0.6715 (m-40) REVERT: B 107 GLN cc_start: 0.7070 (mt0) cc_final: 0.6824 (mt0) REVERT: B 120 GLU cc_start: 0.7684 (tt0) cc_final: 0.6930 (mp0) REVERT: B 131 LYS cc_start: 0.7691 (mmtp) cc_final: 0.7249 (mttm) REVERT: B 140 LYS cc_start: 0.6683 (mmpt) cc_final: 0.6458 (mmmm) REVERT: B 159 LYS cc_start: 0.7139 (mmtt) cc_final: 0.6752 (mmtt) REVERT: B 247 THR cc_start: 0.8336 (t) cc_final: 0.8116 (m) REVERT: B 252 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7189 (mpp80) REVERT: B 282 GLU cc_start: 0.7041 (tt0) cc_final: 0.6612 (mt-10) REVERT: B 289 LYS cc_start: 0.7932 (ttpt) cc_final: 0.7423 (ttmm) REVERT: B 316 ASN cc_start: 0.8008 (m-40) cc_final: 0.7356 (m110) REVERT: B 319 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7573 (tp) REVERT: B 342 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7189 (mt) REVERT: C 71 ASN cc_start: 0.7255 (t0) cc_final: 0.6717 (m-40) REVERT: C 107 GLN cc_start: 0.7067 (mt0) cc_final: 0.6821 (mt0) REVERT: C 120 GLU cc_start: 0.7685 (tt0) cc_final: 0.6931 (mp0) REVERT: C 131 LYS cc_start: 0.7689 (mmtp) cc_final: 0.7247 (mttm) REVERT: C 140 LYS cc_start: 0.6683 (mmpt) cc_final: 0.6459 (mmmm) REVERT: C 159 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6752 (mmtt) REVERT: C 247 THR cc_start: 0.8335 (t) cc_final: 0.8114 (m) REVERT: C 252 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7189 (mpp80) REVERT: C 282 GLU cc_start: 0.7041 (tt0) cc_final: 0.6612 (mt-10) REVERT: C 289 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7424 (ttmm) REVERT: C 316 ASN cc_start: 0.8008 (m-40) cc_final: 0.7357 (m110) REVERT: C 319 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7573 (tp) REVERT: C 342 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7187 (mt) REVERT: D 71 ASN cc_start: 0.7252 (t0) cc_final: 0.6715 (m-40) REVERT: D 107 GLN cc_start: 0.7069 (mt0) cc_final: 0.6822 (mt0) REVERT: D 120 GLU cc_start: 0.7685 (tt0) cc_final: 0.6931 (mp0) REVERT: D 131 LYS cc_start: 0.7688 (mmtp) cc_final: 0.7247 (mttm) REVERT: D 140 LYS cc_start: 0.6682 (mmpt) cc_final: 0.6457 (mmmm) REVERT: D 159 LYS cc_start: 0.7139 (mmtt) cc_final: 0.6751 (mmtt) REVERT: D 247 THR cc_start: 0.8336 (t) cc_final: 0.8116 (m) REVERT: D 252 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7190 (mpp80) REVERT: D 282 GLU cc_start: 0.7042 (tt0) cc_final: 0.6612 (mt-10) REVERT: D 289 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7423 (ttmm) REVERT: D 316 ASN cc_start: 0.8008 (m-40) cc_final: 0.7356 (m110) REVERT: D 319 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7573 (tp) REVERT: D 342 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7189 (mt) outliers start: 52 outliers final: 24 residues processed: 240 average time/residue: 1.2780 time to fit residues: 328.4953 Evaluate side-chains 220 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 201 GLN B 48 ASN B 201 GLN C 48 ASN C 201 GLN D 48 ASN D 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10332 Z= 0.179 Angle : 0.473 5.920 14064 Z= 0.244 Chirality : 0.045 0.145 1640 Planarity : 0.003 0.035 1792 Dihedral : 8.252 72.139 1644 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 4.83 % Allowed : 14.13 % Favored : 81.04 % 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: 0.44 (0.24), residues: 1340 helix: 1.06 (0.28), residues: 380 sheet: -0.57 (0.31), residues: 272 loop : 0.39 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 101 HIS 0.003 0.001 HIS A 67 PHE 0.011 0.001 PHE D 325 TYR 0.008 0.001 TYR A 146 ARG 0.001 0.000 ARG C 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 192 time to evaluate : 1.240 Fit side-chains REVERT: A 71 ASN cc_start: 0.7217 (t0) cc_final: 0.6735 (m-40) REVERT: A 107 GLN cc_start: 0.7022 (mt0) cc_final: 0.6771 (mt0) REVERT: A 119 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: A 120 GLU cc_start: 0.7773 (tt0) cc_final: 0.6973 (mp0) REVERT: A 131 LYS cc_start: 0.7628 (mmtp) cc_final: 0.7197 (mttm) REVERT: A 140 LYS cc_start: 0.6726 (mmpt) cc_final: 0.6273 (mmpt) REVERT: A 159 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6812 (mmtt) REVERT: A 191 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7574 (tmm) REVERT: A 247 THR cc_start: 0.8165 (t) cc_final: 0.7955 (p) REVERT: A 252 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7022 (mpp80) REVERT: A 282 GLU cc_start: 0.7103 (tt0) cc_final: 0.6684 (mt-10) REVERT: A 289 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7369 (ttmm) REVERT: A 316 ASN cc_start: 0.7989 (m-40) cc_final: 0.7344 (m110) REVERT: A 319 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7628 (tp) REVERT: B 71 ASN cc_start: 0.7216 (t0) cc_final: 0.6735 (m-40) REVERT: B 107 GLN cc_start: 0.7022 (mt0) cc_final: 0.6771 (mt0) REVERT: B 119 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: B 120 GLU cc_start: 0.7773 (tt0) cc_final: 0.6973 (mp0) REVERT: B 131 LYS cc_start: 0.7627 (mmtp) cc_final: 0.7195 (mttm) REVERT: B 140 LYS cc_start: 0.6724 (mmpt) cc_final: 0.6273 (mmpt) REVERT: B 159 LYS cc_start: 0.7172 (mmtt) cc_final: 0.6810 (mmtt) REVERT: B 191 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7573 (tmm) REVERT: B 247 THR cc_start: 0.8166 (t) cc_final: 0.7955 (p) REVERT: B 252 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7027 (mpp80) REVERT: B 282 GLU cc_start: 0.7104 (tt0) cc_final: 0.6684 (mt-10) REVERT: B 289 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7370 (ttmm) REVERT: B 316 ASN cc_start: 0.7989 (m-40) cc_final: 0.7342 (m110) REVERT: B 319 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7630 (tp) REVERT: C 71 ASN cc_start: 0.7218 (t0) cc_final: 0.6737 (m-40) REVERT: C 107 GLN cc_start: 0.7022 (mt0) cc_final: 0.6771 (mt0) REVERT: C 119 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6291 (tm-30) REVERT: C 120 GLU cc_start: 0.7773 (tt0) cc_final: 0.6973 (mp0) REVERT: C 131 LYS cc_start: 0.7626 (mmtp) cc_final: 0.7194 (mttm) REVERT: C 140 LYS cc_start: 0.6724 (mmpt) cc_final: 0.6274 (mmpt) REVERT: C 159 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6813 (mmtt) REVERT: C 191 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7572 (tmm) REVERT: C 247 THR cc_start: 0.8165 (t) cc_final: 0.7953 (p) REVERT: C 252 ARG cc_start: 0.7620 (mtt180) cc_final: 0.7026 (mpp80) REVERT: C 282 GLU cc_start: 0.7103 (tt0) cc_final: 0.6685 (mt-10) REVERT: C 289 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7370 (ttmm) REVERT: C 316 ASN cc_start: 0.7990 (m-40) cc_final: 0.7345 (m110) REVERT: C 319 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7630 (tp) REVERT: D 71 ASN cc_start: 0.7216 (t0) cc_final: 0.6734 (m-40) REVERT: D 107 GLN cc_start: 0.7023 (mt0) cc_final: 0.6772 (mt0) REVERT: D 119 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6290 (tm-30) REVERT: D 120 GLU cc_start: 0.7773 (tt0) cc_final: 0.6973 (mp0) REVERT: D 131 LYS cc_start: 0.7625 (mmtp) cc_final: 0.7193 (mttm) REVERT: D 140 LYS cc_start: 0.6723 (mmpt) cc_final: 0.6272 (mmpt) REVERT: D 159 LYS cc_start: 0.7171 (mmtt) cc_final: 0.6809 (mmtt) REVERT: D 191 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7572 (tmm) REVERT: D 247 THR cc_start: 0.8166 (t) cc_final: 0.7956 (p) REVERT: D 252 ARG cc_start: 0.7621 (mtt180) cc_final: 0.7029 (mpp80) REVERT: D 282 GLU cc_start: 0.7103 (tt0) cc_final: 0.6684 (mt-10) REVERT: D 289 LYS cc_start: 0.7876 (ttpt) cc_final: 0.7371 (ttmm) REVERT: D 316 ASN cc_start: 0.7990 (m-40) cc_final: 0.7344 (m110) REVERT: D 319 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7629 (tp) outliers start: 52 outliers final: 20 residues processed: 212 average time/residue: 1.2477 time to fit residues: 283.6312 Evaluate side-chains 220 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10332 Z= 0.317 Angle : 0.533 6.777 14064 Z= 0.275 Chirality : 0.048 0.143 1640 Planarity : 0.004 0.036 1792 Dihedral : 8.620 76.567 1644 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.28 % Favored : 96.42 % Rotamer: Outliers : 4.46 % Allowed : 14.13 % Favored : 81.41 % 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: 0.00 (0.24), residues: 1340 helix: 0.62 (0.28), residues: 376 sheet: -0.94 (0.30), residues: 300 loop : 0.29 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 214 HIS 0.003 0.001 HIS C 67 PHE 0.010 0.002 PHE C 304 TYR 0.013 0.002 TYR A 146 ARG 0.003 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 168 time to evaluate : 1.198 Fit side-chains REVERT: A 71 ASN cc_start: 0.7308 (t0) cc_final: 0.6797 (m-40) REVERT: A 119 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6149 (tm-30) REVERT: A 120 GLU cc_start: 0.7810 (tt0) cc_final: 0.7002 (mt-10) REVERT: A 140 LYS cc_start: 0.6726 (mmpt) cc_final: 0.6486 (mmmm) REVERT: A 159 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6824 (mmtt) REVERT: A 247 THR cc_start: 0.8260 (t) cc_final: 0.8059 (m) REVERT: A 252 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7183 (mpp80) REVERT: A 282 GLU cc_start: 0.7155 (tt0) cc_final: 0.6940 (tt0) REVERT: A 289 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7358 (ttmm) REVERT: A 316 ASN cc_start: 0.8017 (m-40) cc_final: 0.7393 (m110) REVERT: A 319 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7632 (tp) REVERT: A 342 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7212 (mt) REVERT: B 71 ASN cc_start: 0.7306 (t0) cc_final: 0.6796 (m-40) REVERT: B 119 GLU cc_start: 0.6664 (tm-30) cc_final: 0.6150 (tm-30) REVERT: B 120 GLU cc_start: 0.7811 (tt0) cc_final: 0.7003 (mt-10) REVERT: B 140 LYS cc_start: 0.6725 (mmpt) cc_final: 0.6485 (mmmm) REVERT: B 159 LYS cc_start: 0.7152 (mmtt) cc_final: 0.6804 (mmtt) REVERT: B 247 THR cc_start: 0.8261 (t) cc_final: 0.8060 (m) REVERT: B 252 ARG cc_start: 0.7629 (mtt180) cc_final: 0.7182 (mpp80) REVERT: B 282 GLU cc_start: 0.7157 (tt0) cc_final: 0.6942 (tt0) REVERT: B 289 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7360 (ttmm) REVERT: B 316 ASN cc_start: 0.8017 (m-40) cc_final: 0.7392 (m110) REVERT: B 319 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7634 (tp) REVERT: B 342 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7184 (mt) REVERT: C 71 ASN cc_start: 0.7308 (t0) cc_final: 0.6796 (m-40) REVERT: C 119 GLU cc_start: 0.6665 (tm-30) cc_final: 0.6150 (tm-30) REVERT: C 120 GLU cc_start: 0.7810 (tt0) cc_final: 0.7003 (mt-10) REVERT: C 140 LYS cc_start: 0.6726 (mmpt) cc_final: 0.6485 (mmmm) REVERT: C 159 LYS cc_start: 0.7174 (mmtt) cc_final: 0.6823 (mmtt) REVERT: C 247 THR cc_start: 0.8260 (t) cc_final: 0.8058 (m) REVERT: C 252 ARG cc_start: 0.7631 (mtt180) cc_final: 0.7184 (mpp80) REVERT: C 282 GLU cc_start: 0.7155 (tt0) cc_final: 0.6940 (tt0) REVERT: C 289 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7360 (ttmm) REVERT: C 316 ASN cc_start: 0.8016 (m-40) cc_final: 0.7392 (m110) REVERT: C 319 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7634 (tp) REVERT: C 342 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7210 (mt) REVERT: D 71 ASN cc_start: 0.7306 (t0) cc_final: 0.6796 (m-40) REVERT: D 119 GLU cc_start: 0.6666 (tm-30) cc_final: 0.6150 (tm-30) REVERT: D 120 GLU cc_start: 0.7810 (tt0) cc_final: 0.7003 (mt-10) REVERT: D 140 LYS cc_start: 0.6724 (mmpt) cc_final: 0.6484 (mmmm) REVERT: D 159 LYS cc_start: 0.7151 (mmtt) cc_final: 0.6804 (mmtt) REVERT: D 247 THR cc_start: 0.8261 (t) cc_final: 0.8059 (m) REVERT: D 252 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7183 (mpp80) REVERT: D 282 GLU cc_start: 0.7156 (tt0) cc_final: 0.6940 (tt0) REVERT: D 289 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7360 (ttmm) REVERT: D 316 ASN cc_start: 0.8018 (m-40) cc_final: 0.7393 (m110) REVERT: D 319 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7636 (tp) REVERT: D 342 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7186 (mt) outliers start: 48 outliers final: 28 residues processed: 192 average time/residue: 1.2237 time to fit residues: 252.3502 Evaluate side-chains 200 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN C 48 ASN C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10332 Z= 0.161 Angle : 0.452 5.784 14064 Z= 0.233 Chirality : 0.045 0.146 1640 Planarity : 0.003 0.035 1792 Dihedral : 8.077 73.300 1644 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.69 % Favored : 97.01 % Rotamer: Outliers : 4.65 % Allowed : 14.87 % Favored : 80.48 % 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: 0.44 (0.24), residues: 1340 helix: 0.99 (0.28), residues: 380 sheet: -0.47 (0.31), residues: 272 loop : 0.39 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 101 HIS 0.003 0.001 HIS D 67 PHE 0.009 0.001 PHE B 325 TYR 0.006 0.001 TYR A 332 ARG 0.001 0.000 ARG C 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 168 time to evaluate : 1.169 Fit side-chains REVERT: A 71 ASN cc_start: 0.7365 (t0) cc_final: 0.6882 (m-40) REVERT: A 119 GLU cc_start: 0.6601 (tm-30) cc_final: 0.6206 (tm-30) REVERT: A 120 GLU cc_start: 0.7790 (tt0) cc_final: 0.7031 (mt-10) REVERT: A 140 LYS cc_start: 0.6742 (mmpt) cc_final: 0.6297 (mmpt) REVERT: A 159 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6779 (mmtt) REVERT: A 191 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7667 (tmm) REVERT: A 252 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7146 (mpp80) REVERT: A 282 GLU cc_start: 0.7216 (tt0) cc_final: 0.6815 (mt-10) REVERT: A 289 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7370 (ttmm) REVERT: A 316 ASN cc_start: 0.8015 (m-40) cc_final: 0.7389 (m110) REVERT: A 319 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7710 (tp) REVERT: B 71 ASN cc_start: 0.7363 (t0) cc_final: 0.6881 (m-40) REVERT: B 119 GLU cc_start: 0.6604 (tm-30) cc_final: 0.6209 (tm-30) REVERT: B 120 GLU cc_start: 0.7790 (tt0) cc_final: 0.7031 (mt-10) REVERT: B 140 LYS cc_start: 0.6740 (mmpt) cc_final: 0.6297 (mmpt) REVERT: B 159 LYS cc_start: 0.7142 (mmtt) cc_final: 0.6778 (mmtt) REVERT: B 191 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7667 (tmm) REVERT: B 252 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7145 (mpp80) REVERT: B 282 GLU cc_start: 0.7218 (tt0) cc_final: 0.6815 (mt-10) REVERT: B 289 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7369 (ttmm) REVERT: B 316 ASN cc_start: 0.8013 (m-40) cc_final: 0.7387 (m110) REVERT: B 319 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7706 (tp) REVERT: C 71 ASN cc_start: 0.7364 (t0) cc_final: 0.6881 (m-40) REVERT: C 119 GLU cc_start: 0.6602 (tm-30) cc_final: 0.6207 (tm-30) REVERT: C 120 GLU cc_start: 0.7789 (tt0) cc_final: 0.7030 (mt-10) REVERT: C 140 LYS cc_start: 0.6740 (mmpt) cc_final: 0.6297 (mmpt) REVERT: C 159 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6779 (mmtt) REVERT: C 191 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7665 (tmm) REVERT: C 252 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7145 (mpp80) REVERT: C 282 GLU cc_start: 0.7216 (tt0) cc_final: 0.6815 (mt-10) REVERT: C 289 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7369 (ttmm) REVERT: C 316 ASN cc_start: 0.8014 (m-40) cc_final: 0.7388 (m110) REVERT: C 319 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7712 (tp) REVERT: D 71 ASN cc_start: 0.7363 (t0) cc_final: 0.6880 (m-40) REVERT: D 119 GLU cc_start: 0.6605 (tm-30) cc_final: 0.6209 (tm-30) REVERT: D 120 GLU cc_start: 0.7789 (tt0) cc_final: 0.7030 (mt-10) REVERT: D 140 LYS cc_start: 0.6738 (mmpt) cc_final: 0.6296 (mmpt) REVERT: D 159 LYS cc_start: 0.7142 (mmtt) cc_final: 0.6777 (mmtt) REVERT: D 191 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7665 (tmm) REVERT: D 252 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7147 (mpp80) REVERT: D 282 GLU cc_start: 0.7217 (tt0) cc_final: 0.6815 (mt-10) REVERT: D 289 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7369 (ttmm) REVERT: D 316 ASN cc_start: 0.8012 (m-40) cc_final: 0.7387 (m110) REVERT: D 319 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7704 (tp) outliers start: 50 outliers final: 28 residues processed: 194 average time/residue: 1.2266 time to fit residues: 255.5649 Evaluate side-chains 204 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 127 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 58 optimal weight: 0.0020 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN D 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10332 Z= 0.119 Angle : 0.425 5.193 14064 Z= 0.219 Chirality : 0.044 0.144 1640 Planarity : 0.003 0.034 1792 Dihedral : 7.423 65.816 1644 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.72 % Rotamer: Outliers : 3.90 % Allowed : 16.17 % Favored : 79.93 % 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: 0.80 (0.25), residues: 1340 helix: 1.35 (0.29), residues: 380 sheet: -0.17 (0.31), residues: 272 loop : 0.53 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 101 HIS 0.003 0.001 HIS B 67 PHE 0.008 0.001 PHE B 325 TYR 0.005 0.001 TYR B 332 ARG 0.001 0.000 ARG B 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 190 time to evaluate : 1.264 Fit side-chains REVERT: A 71 ASN cc_start: 0.7302 (t0) cc_final: 0.6879 (m-40) REVERT: A 89 LYS cc_start: 0.7001 (mttt) cc_final: 0.6090 (mmtp) REVERT: A 119 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: A 120 GLU cc_start: 0.7742 (tt0) cc_final: 0.7019 (mp0) REVERT: A 140 LYS cc_start: 0.6791 (mmpt) cc_final: 0.6526 (mmmm) REVERT: A 159 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6778 (mmtt) REVERT: A 252 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7117 (mpp80) REVERT: A 282 GLU cc_start: 0.7356 (tt0) cc_final: 0.6893 (mt-10) REVERT: A 289 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7349 (ttmm) REVERT: A 316 ASN cc_start: 0.8039 (m-40) cc_final: 0.7390 (m110) REVERT: A 319 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7755 (tp) REVERT: B 71 ASN cc_start: 0.7301 (t0) cc_final: 0.6877 (m-40) REVERT: B 119 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: B 120 GLU cc_start: 0.7742 (tt0) cc_final: 0.7022 (mp0) REVERT: B 140 LYS cc_start: 0.6791 (mmpt) cc_final: 0.6526 (mmmm) REVERT: B 159 LYS cc_start: 0.7130 (mmtt) cc_final: 0.6778 (mmtt) REVERT: B 252 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7117 (mpp80) REVERT: B 282 GLU cc_start: 0.7359 (tt0) cc_final: 0.6895 (mt-10) REVERT: B 289 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7350 (ttmm) REVERT: B 316 ASN cc_start: 0.8036 (m-40) cc_final: 0.7384 (m110) REVERT: B 319 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7762 (tp) REVERT: C 71 ASN cc_start: 0.7300 (t0) cc_final: 0.6877 (m-40) REVERT: C 89 LYS cc_start: 0.6999 (mttt) cc_final: 0.6088 (mmtp) REVERT: C 119 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6491 (tm-30) REVERT: C 120 GLU cc_start: 0.7742 (tt0) cc_final: 0.7021 (mp0) REVERT: C 140 LYS cc_start: 0.6790 (mmpt) cc_final: 0.6526 (mmmm) REVERT: C 159 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6778 (mmtt) REVERT: C 252 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7117 (mpp80) REVERT: C 282 GLU cc_start: 0.7357 (tt0) cc_final: 0.6894 (mt-10) REVERT: C 289 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7349 (ttmm) REVERT: C 316 ASN cc_start: 0.8038 (m-40) cc_final: 0.7390 (m110) REVERT: C 319 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7756 (tp) REVERT: D 71 ASN cc_start: 0.7301 (t0) cc_final: 0.6877 (m-40) REVERT: D 119 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: D 120 GLU cc_start: 0.7742 (tt0) cc_final: 0.7020 (mp0) REVERT: D 140 LYS cc_start: 0.6790 (mmpt) cc_final: 0.6527 (mmmm) REVERT: D 159 LYS cc_start: 0.7129 (mmtt) cc_final: 0.6776 (mmtt) REVERT: D 252 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7119 (mpp80) REVERT: D 282 GLU cc_start: 0.7356 (tt0) cc_final: 0.6892 (mt-10) REVERT: D 289 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7349 (ttmm) REVERT: D 316 ASN cc_start: 0.8036 (m-40) cc_final: 0.7384 (m110) REVERT: D 319 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7763 (tp) outliers start: 42 outliers final: 20 residues processed: 212 average time/residue: 1.1673 time to fit residues: 266.9231 Evaluate side-chains 200 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 319 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.0370 chunk 111 optimal weight: 1.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10332 Z= 0.249 Angle : 0.503 6.503 14064 Z= 0.253 Chirality : 0.046 0.143 1640 Planarity : 0.004 0.034 1792 Dihedral : 7.928 68.996 1644 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.28 % Favored : 96.42 % Rotamer: Outliers : 4.83 % Allowed : 15.99 % Favored : 79.18 % 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: 0.44 (0.24), residues: 1340 helix: 0.89 (0.27), residues: 380 sheet: -0.43 (0.31), residues: 272 loop : 0.44 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 331 HIS 0.003 0.001 HIS A 67 PHE 0.014 0.002 PHE B 325 TYR 0.010 0.001 TYR D 146 ARG 0.002 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 164 time to evaluate : 1.251 Fit side-chains REVERT: A 71 ASN cc_start: 0.7350 (t0) cc_final: 0.6893 (m-40) REVERT: A 119 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6445 (tm-30) REVERT: A 120 GLU cc_start: 0.7715 (tt0) cc_final: 0.6991 (mt-10) REVERT: A 140 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6295 (mmpt) REVERT: A 159 LYS cc_start: 0.7161 (mmtt) cc_final: 0.6796 (mmtt) REVERT: A 191 MET cc_start: 0.7921 (pp-130) cc_final: 0.7706 (pp-130) REVERT: A 252 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7160 (mpp80) REVERT: A 282 GLU cc_start: 0.7220 (tt0) cc_final: 0.6803 (mt-10) REVERT: A 289 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7401 (ttmm) REVERT: A 315 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7528 (tttt) REVERT: A 316 ASN cc_start: 0.8076 (m-40) cc_final: 0.7450 (m110) REVERT: A 319 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7635 (tp) REVERT: B 71 ASN cc_start: 0.7349 (t0) cc_final: 0.6893 (m-40) REVERT: B 119 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6438 (tm-30) REVERT: B 120 GLU cc_start: 0.7713 (tt0) cc_final: 0.6991 (mt-10) REVERT: B 140 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.6300 (mmpt) REVERT: B 159 LYS cc_start: 0.7141 (mmtt) cc_final: 0.6781 (mmtt) REVERT: B 191 MET cc_start: 0.7918 (pp-130) cc_final: 0.7706 (pp-130) REVERT: B 252 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7159 (mpp80) REVERT: B 282 GLU cc_start: 0.7221 (tt0) cc_final: 0.6804 (mt-10) REVERT: B 289 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7402 (ttmm) REVERT: B 315 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7520 (tttt) REVERT: B 316 ASN cc_start: 0.8074 (m-40) cc_final: 0.7446 (m110) REVERT: B 319 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7649 (tp) REVERT: C 71 ASN cc_start: 0.7349 (t0) cc_final: 0.6892 (m-40) REVERT: C 119 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6439 (tm-30) REVERT: C 120 GLU cc_start: 0.7713 (tt0) cc_final: 0.6991 (mt-10) REVERT: C 140 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.6294 (mmpt) REVERT: C 159 LYS cc_start: 0.7160 (mmtt) cc_final: 0.6795 (mmtt) REVERT: C 191 MET cc_start: 0.7918 (pp-130) cc_final: 0.7705 (pp-130) REVERT: C 252 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7159 (mpp80) REVERT: C 282 GLU cc_start: 0.7219 (tt0) cc_final: 0.6803 (mt-10) REVERT: C 289 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7401 (ttmm) REVERT: C 315 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7503 (tttt) REVERT: C 316 ASN cc_start: 0.8075 (m-40) cc_final: 0.7448 (m110) REVERT: C 319 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7635 (tp) REVERT: D 71 ASN cc_start: 0.7349 (t0) cc_final: 0.6892 (m-40) REVERT: D 119 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6446 (tm-30) REVERT: D 120 GLU cc_start: 0.7714 (tt0) cc_final: 0.6992 (mt-10) REVERT: D 140 LYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6294 (mmpt) REVERT: D 159 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6778 (mmtt) REVERT: D 191 MET cc_start: 0.7918 (pp-130) cc_final: 0.7705 (pp-130) REVERT: D 252 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7159 (mpp80) REVERT: D 282 GLU cc_start: 0.7218 (tt0) cc_final: 0.6802 (mt-10) REVERT: D 289 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7401 (ttmm) REVERT: D 315 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7521 (tttt) REVERT: D 316 ASN cc_start: 0.8076 (m-40) cc_final: 0.7450 (m110) REVERT: D 319 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7652 (tp) outliers start: 52 outliers final: 24 residues processed: 192 average time/residue: 1.2454 time to fit residues: 256.9410 Evaluate side-chains 196 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 121 optimal weight: 0.0040 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 125 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 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 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10332 Z= 0.151 Angle : 0.457 6.889 14064 Z= 0.231 Chirality : 0.045 0.143 1640 Planarity : 0.003 0.034 1792 Dihedral : 7.574 65.456 1644 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.69 % Favored : 97.01 % Rotamer: Outliers : 4.46 % Allowed : 17.10 % Favored : 78.44 % 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: 0.54 (0.24), residues: 1340 helix: 1.15 (0.28), residues: 380 sheet: -0.68 (0.30), residues: 292 loop : 0.57 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 101 HIS 0.003 0.001 HIS A 67 PHE 0.011 0.001 PHE B 325 TYR 0.006 0.001 TYR A 332 ARG 0.002 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 168 time to evaluate : 1.160 Fit side-chains REVERT: A 71 ASN cc_start: 0.7350 (t0) cc_final: 0.6899 (m-40) REVERT: A 119 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: A 120 GLU cc_start: 0.7703 (tt0) cc_final: 0.7016 (mt-10) REVERT: A 140 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6543 (mmmm) REVERT: A 159 LYS cc_start: 0.7225 (mmtt) cc_final: 0.6878 (mmtt) REVERT: A 252 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7132 (mpp80) REVERT: A 282 GLU cc_start: 0.7345 (tt0) cc_final: 0.6926 (mt-10) REVERT: A 289 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7431 (ttmm) REVERT: A 316 ASN cc_start: 0.8035 (m-40) cc_final: 0.7413 (m110) REVERT: A 319 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7702 (tp) REVERT: B 71 ASN cc_start: 0.7349 (t0) cc_final: 0.6898 (m-40) REVERT: B 119 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: B 120 GLU cc_start: 0.7701 (tt0) cc_final: 0.7017 (mt-10) REVERT: B 140 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6542 (mmmm) REVERT: B 159 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6777 (mmtt) REVERT: B 252 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7131 (mpp80) REVERT: B 282 GLU cc_start: 0.7348 (tt0) cc_final: 0.6926 (mt-10) REVERT: B 289 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7423 (ttmm) REVERT: B 316 ASN cc_start: 0.8034 (m-40) cc_final: 0.7411 (m110) REVERT: B 319 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7717 (tp) REVERT: C 71 ASN cc_start: 0.7350 (t0) cc_final: 0.6899 (m-40) REVERT: C 119 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6535 (tm-30) REVERT: C 120 GLU cc_start: 0.7700 (tt0) cc_final: 0.7016 (mt-10) REVERT: C 140 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6543 (mmmm) REVERT: C 159 LYS cc_start: 0.7225 (mmtt) cc_final: 0.6876 (mmtt) REVERT: C 252 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7132 (mpp80) REVERT: C 282 GLU cc_start: 0.7344 (tt0) cc_final: 0.6924 (mt-10) REVERT: C 289 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7424 (ttmm) REVERT: C 315 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7391 (tttt) REVERT: C 316 ASN cc_start: 0.8023 (m-40) cc_final: 0.7412 (m110) REVERT: C 319 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7704 (tp) REVERT: D 71 ASN cc_start: 0.7350 (t0) cc_final: 0.6898 (m-40) REVERT: D 119 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: D 120 GLU cc_start: 0.7703 (tt0) cc_final: 0.7017 (mt-10) REVERT: D 140 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6543 (mmmm) REVERT: D 159 LYS cc_start: 0.7134 (mmtt) cc_final: 0.6787 (mmtt) REVERT: D 252 ARG cc_start: 0.7647 (mtt180) cc_final: 0.7134 (mpp80) REVERT: D 282 GLU cc_start: 0.7346 (tt0) cc_final: 0.6925 (mt-10) REVERT: D 289 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7424 (ttmm) REVERT: D 316 ASN cc_start: 0.8034 (m-40) cc_final: 0.7413 (m110) REVERT: D 319 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7717 (tp) outliers start: 48 outliers final: 28 residues processed: 188 average time/residue: 1.2661 time to fit residues: 255.3876 Evaluate side-chains 205 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 0.0050 chunk 104 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 111 optimal weight: 0.0670 chunk 32 optimal weight: 3.9990 overall best weight: 0.9934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10332 Z= 0.196 Angle : 0.481 7.073 14064 Z= 0.244 Chirality : 0.045 0.142 1640 Planarity : 0.004 0.034 1792 Dihedral : 7.710 66.214 1644 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.88 % Favored : 95.82 % Rotamer: Outliers : 3.81 % Allowed : 17.75 % Favored : 78.44 % 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: 0.44 (0.24), residues: 1340 helix: 1.01 (0.28), residues: 380 sheet: -0.69 (0.30), residues: 292 loop : 0.53 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 101 HIS 0.003 0.001 HIS B 67 PHE 0.013 0.002 PHE A 325 TYR 0.008 0.001 TYR A 146 ARG 0.003 0.000 ARG D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 1.227 Fit side-chains REVERT: A 71 ASN cc_start: 0.7371 (t0) cc_final: 0.6915 (m-40) REVERT: A 119 GLU cc_start: 0.6894 (tm-30) cc_final: 0.6505 (tm-30) REVERT: A 120 GLU cc_start: 0.7702 (tt0) cc_final: 0.7009 (mt-10) REVERT: A 140 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6502 (mmmm) REVERT: A 159 LYS cc_start: 0.7202 (mmtt) cc_final: 0.6851 (mmtt) REVERT: A 252 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7117 (mpp80) REVERT: A 282 GLU cc_start: 0.7363 (tt0) cc_final: 0.6932 (mt-10) REVERT: A 289 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7418 (ttmm) REVERT: A 316 ASN cc_start: 0.8070 (m-40) cc_final: 0.7426 (m110) REVERT: A 319 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7693 (tp) REVERT: B 71 ASN cc_start: 0.7369 (t0) cc_final: 0.6914 (m-40) REVERT: B 119 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6492 (tm-30) REVERT: B 120 GLU cc_start: 0.7700 (tt0) cc_final: 0.7008 (mt-10) REVERT: B 140 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6501 (mmmm) REVERT: B 159 LYS cc_start: 0.7120 (mmtt) cc_final: 0.6854 (mmtt) REVERT: B 252 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7116 (mpp80) REVERT: B 282 GLU cc_start: 0.7364 (tt0) cc_final: 0.6932 (mt-10) REVERT: B 289 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7421 (ttmm) REVERT: B 316 ASN cc_start: 0.8069 (m-40) cc_final: 0.7429 (m110) REVERT: B 319 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7693 (tp) REVERT: C 71 ASN cc_start: 0.7372 (t0) cc_final: 0.6916 (m-40) REVERT: C 119 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6491 (tm-30) REVERT: C 120 GLU cc_start: 0.7699 (tt0) cc_final: 0.7009 (mt-10) REVERT: C 140 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6502 (mmmm) REVERT: C 159 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6892 (mmtt) REVERT: C 252 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7117 (mpp80) REVERT: C 282 GLU cc_start: 0.7359 (tt0) cc_final: 0.6928 (mt-10) REVERT: C 289 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7418 (ttmm) REVERT: C 315 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7434 (tttt) REVERT: C 316 ASN cc_start: 0.8066 (m-40) cc_final: 0.7432 (m110) REVERT: C 319 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7697 (tp) REVERT: D 71 ASN cc_start: 0.7371 (t0) cc_final: 0.6914 (m-40) REVERT: D 119 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6505 (tm-30) REVERT: D 120 GLU cc_start: 0.7702 (tt0) cc_final: 0.7009 (mt-10) REVERT: D 140 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6501 (mmmm) REVERT: D 159 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6866 (mmtt) REVERT: D 252 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7119 (mpp80) REVERT: D 282 GLU cc_start: 0.7362 (tt0) cc_final: 0.6930 (mt-10) REVERT: D 289 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7429 (ttmm) REVERT: D 316 ASN cc_start: 0.8068 (m-40) cc_final: 0.7428 (m110) REVERT: D 319 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7699 (tp) outliers start: 41 outliers final: 28 residues processed: 177 average time/residue: 1.2799 time to fit residues: 242.8948 Evaluate side-chains 193 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.096882 restraints weight = 12214.668| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.63 r_work: 0.2891 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10332 Z= 0.309 Angle : 0.547 8.473 14064 Z= 0.278 Chirality : 0.048 0.144 1640 Planarity : 0.004 0.035 1792 Dihedral : 8.269 71.611 1644 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.58 % Favored : 96.12 % Rotamer: Outliers : 4.55 % Allowed : 17.01 % Favored : 78.44 % 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: -0.17 (0.23), residues: 1340 helix: 0.37 (0.26), residues: 400 sheet: -0.82 (0.30), residues: 292 loop : 0.11 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 331 HIS 0.003 0.001 HIS B 67 PHE 0.013 0.002 PHE A 325 TYR 0.013 0.002 TYR D 146 ARG 0.004 0.001 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4715.36 seconds wall clock time: 84 minutes 23.04 seconds (5063.04 seconds total)