Starting phenix.real_space_refine on Sat Apr 13 00:18:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhk_16058/04_2024/8bhk_16058_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhk_16058/04_2024/8bhk_16058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhk_16058/04_2024/8bhk_16058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhk_16058/04_2024/8bhk_16058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhk_16058/04_2024/8bhk_16058_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhk_16058/04_2024/8bhk_16058_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 85 5.16 5 Cl 5 4.86 5 C 8915 2.51 5 N 2270 2.21 5 O 2475 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 27165 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'DZP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'DZP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'DZP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'DZP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'DZP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.35, per 1000 atoms: 0.45 Number of scatterers: 27165 At special positions: 0 Unit cell: (93.09, 95.23, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 5 17.00 S 85 16.00 O 2475 8.00 N 2270 7.00 C 8915 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 20.69 Conformation dependent library (CDL) restraints added in 2.7 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 15 sheets defined 32.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.517A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 234 through 249 removed outlier: 4.207A pdb=" N SER A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TRP A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 279 removed outlier: 3.540A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 311 Processing helix chain 'A' and resid 318 through 417 removed outlier: 3.915A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 16 through 26 removed outlier: 3.517A pdb=" N ILE B 21 " --> pdb=" O ILE B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 234 through 249 removed outlier: 4.208A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TRP B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 279 removed outlier: 3.540A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 318 through 417 removed outlier: 3.915A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.516A pdb=" N ILE C 21 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 234 through 249 removed outlier: 4.208A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TRP C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 279 removed outlier: 3.540A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 311 Processing helix chain 'C' and resid 318 through 417 removed outlier: 3.915A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 16 through 26 removed outlier: 3.516A pdb=" N ILE D 21 " --> pdb=" O ILE D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 234 through 249 removed outlier: 4.207A pdb=" N SER D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TRP D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 279 removed outlier: 3.540A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 318 through 417 removed outlier: 3.915A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 16 through 26 removed outlier: 3.516A pdb=" N ILE E 21 " --> pdb=" O ILE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 234 through 249 removed outlier: 4.208A pdb=" N SER E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TRP E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 279 removed outlier: 3.541A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 311 Processing helix chain 'E' and resid 318 through 417 removed outlier: 3.914A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.942A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 137 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 111 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 139 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 109 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU A 141 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY A 107 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.759A pdb=" N MET A 48 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.446A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.942A pdb=" N THR B 42 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL B 173 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 44 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 137 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 111 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 139 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 109 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU B 141 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY B 107 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.760A pdb=" N MET B 48 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.447A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.942A pdb=" N THR C 42 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL C 173 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL C 44 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 137 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE C 111 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER C 139 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS C 109 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU C 141 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY C 107 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 182 through 184 removed outlier: 6.759A pdb=" N MET C 48 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.447A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.941A pdb=" N THR D 42 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VAL D 173 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL D 44 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR D 137 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D 111 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D 139 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS D 109 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU D 141 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY D 107 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 182 through 184 removed outlier: 6.759A pdb=" N MET D 48 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.447A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 170 through 174 removed outlier: 6.943A pdb=" N THR E 42 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL E 173 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL E 44 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR E 137 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE E 111 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER E 139 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS E 109 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU E 141 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY E 107 " --> pdb=" O GLU E 141 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.759A pdb=" N MET E 48 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.447A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1635 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: 9.81 Time building geometry restraints manager: 21.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 5 1.23 - 1.42: 6105 1.42 - 1.61: 7855 1.61 - 1.81: 155 Bond restraints: 27535 Sorted by residual: bond pdb=" N ASN D 14 " pdb=" H ASN D 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.45e+01 ... (remaining 27530 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.15: 472 107.15 - 113.86: 32015 113.86 - 120.57: 9532 120.57 - 127.28: 7291 127.28 - 134.00: 180 Bond angle restraints: 49490 Sorted by residual: angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 127.35 -5.65 1.80e+00 3.09e-01 9.84e+00 angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 127.34 -5.64 1.80e+00 3.09e-01 9.81e+00 angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 127.33 -5.63 1.80e+00 3.09e-01 9.80e+00 angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 127.33 -5.63 1.80e+00 3.09e-01 9.78e+00 angle pdb=" C MET C 115 " pdb=" N THR C 116 " pdb=" CA THR C 116 " ideal model delta sigma weight residual 121.70 127.32 -5.62 1.80e+00 3.09e-01 9.73e+00 ... (remaining 49485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.52: 12915 29.52 - 59.04: 210 59.04 - 88.56: 30 88.56 - 118.08: 15 118.08 - 147.60: 15 Dihedral angle restraints: 13185 sinusoidal: 7055 harmonic: 6130 Sorted by residual: dihedral pdb=" C18 DZP D 502 " pdb=" C17 DZP D 502 " pdb=" N15 DZP D 502 " pdb=" C5 DZP D 502 " ideal model delta sinusoidal sigma weight residual 73.87 -73.73 147.60 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C18 DZP E 502 " pdb=" C17 DZP E 502 " pdb=" N15 DZP E 502 " pdb=" C5 DZP E 502 " ideal model delta sinusoidal sigma weight residual 73.87 -73.73 147.60 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C18 DZP B 502 " pdb=" C17 DZP B 502 " pdb=" N15 DZP B 502 " pdb=" C5 DZP B 502 " ideal model delta sinusoidal sigma weight residual 73.87 -73.69 147.56 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 13182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1267 0.024 - 0.048: 571 0.048 - 0.073: 171 0.073 - 0.097: 68 0.097 - 0.121: 83 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE B 41 " pdb=" N ILE B 41 " pdb=" C ILE B 41 " pdb=" CB ILE B 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE D 41 " pdb=" N ILE D 41 " pdb=" C ILE D 41 " pdb=" CB ILE D 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 2157 not shown) Planarity restraints: 3995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 DZP C 502 " -0.110 2.00e-02 2.50e+03 8.69e-02 1.13e+02 pdb=" C18 DZP C 502 " 0.009 2.00e-02 2.50e+03 pdb=" C20 DZP C 502 " -0.109 2.00e-02 2.50e+03 pdb=" C6 DZP C 502 " 0.101 2.00e-02 2.50e+03 pdb=" N2 DZP C 502 " 0.002 2.00e-02 2.50e+03 pdb=" O1 DZP C 502 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 DZP B 502 " -0.110 2.00e-02 2.50e+03 8.69e-02 1.13e+02 pdb=" C18 DZP B 502 " 0.009 2.00e-02 2.50e+03 pdb=" C20 DZP B 502 " -0.109 2.00e-02 2.50e+03 pdb=" C6 DZP B 502 " 0.101 2.00e-02 2.50e+03 pdb=" N2 DZP B 502 " 0.002 2.00e-02 2.50e+03 pdb=" O1 DZP B 502 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 DZP E 502 " -0.110 2.00e-02 2.50e+03 8.68e-02 1.13e+02 pdb=" C18 DZP E 502 " 0.009 2.00e-02 2.50e+03 pdb=" C20 DZP E 502 " -0.109 2.00e-02 2.50e+03 pdb=" C6 DZP E 502 " 0.100 2.00e-02 2.50e+03 pdb=" N2 DZP E 502 " 0.003 2.00e-02 2.50e+03 pdb=" O1 DZP E 502 " 0.106 2.00e-02 2.50e+03 ... (remaining 3992 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 6269 2.32 - 2.89: 60586 2.89 - 3.46: 63763 3.46 - 4.03: 91582 4.03 - 4.60: 139005 Nonbonded interactions: 361205 Sorted by model distance: nonbonded pdb=" H GLY B 54 " pdb=" O THR B 64 " model vdw 1.748 1.850 nonbonded pdb=" H GLY E 54 " pdb=" O THR E 64 " model vdw 1.748 1.850 nonbonded pdb=" H GLY D 54 " pdb=" O THR D 64 " model vdw 1.749 1.850 nonbonded pdb=" H GLY A 54 " pdb=" O THR A 64 " model vdw 1.749 1.850 nonbonded pdb=" H GLY C 54 " pdb=" O THR C 64 " model vdw 1.749 1.850 ... (remaining 361200 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.400 Extract box with map and model: 4.680 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 83.920 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.002 0.026 14120 Z= 0.109 Angle : 0.365 5.647 19215 Z= 0.179 Chirality : 0.037 0.121 2160 Planarity : 0.005 0.087 2390 Dihedral : 13.091 147.602 5175 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.20 % Allowed : 1.48 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.80 (0.21), residues: 1670 helix: 3.12 (0.22), residues: 570 sheet: -0.10 (0.24), residues: 450 loop : 0.53 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 414 HIS 0.002 0.001 HIS B 195 PHE 0.004 0.001 PHE B 149 TYR 0.005 0.001 TYR E 132 ARG 0.002 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 250 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TRP cc_start: 0.7557 (m-90) cc_final: 0.7228 (m-90) REVERT: A 180 LYS cc_start: 0.6782 (mttt) cc_final: 0.6202 (tttt) REVERT: B 111 PHE cc_start: 0.5833 (p90) cc_final: 0.4395 (p90) REVERT: B 180 LYS cc_start: 0.6808 (mttt) cc_final: 0.6118 (tttt) REVERT: C 111 PHE cc_start: 0.5831 (p90) cc_final: 0.4501 (p90) REVERT: C 180 LYS cc_start: 0.6991 (mttt) cc_final: 0.6477 (tttt) REVERT: C 200 THR cc_start: 0.8787 (p) cc_final: 0.8444 (m) REVERT: D 125 TRP cc_start: 0.7767 (m-90) cc_final: 0.7373 (m-90) REVERT: D 180 LYS cc_start: 0.6920 (mttt) cc_final: 0.6294 (tttt) REVERT: E 58 ASP cc_start: 0.7989 (m-30) cc_final: 0.7708 (m-30) REVERT: E 111 PHE cc_start: 0.5702 (p90) cc_final: 0.4150 (p90) REVERT: E 125 TRP cc_start: 0.7675 (m-90) cc_final: 0.7414 (m-90) REVERT: E 180 LYS cc_start: 0.6736 (mttt) cc_final: 0.6056 (tttt) outliers start: 3 outliers final: 0 residues processed: 253 average time/residue: 0.7876 time to fit residues: 264.5061 Evaluate side-chains 179 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 ASN E 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 14120 Z= 0.366 Angle : 0.575 5.542 19215 Z= 0.308 Chirality : 0.043 0.170 2160 Planarity : 0.005 0.036 2390 Dihedral : 17.206 150.104 2040 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.54 % Allowed : 3.49 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.89 (0.20), residues: 1670 helix: 2.49 (0.20), residues: 535 sheet: -0.22 (0.23), residues: 485 loop : -0.31 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 414 HIS 0.006 0.002 HIS A 105 PHE 0.010 0.001 PHE A 103 TYR 0.014 0.002 TYR D 132 ARG 0.006 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.6968 (mttt) cc_final: 0.6264 (tttt) REVERT: A 280 LEU cc_start: 0.8149 (tp) cc_final: 0.7781 (mp) REVERT: A 400 ILE cc_start: 0.7344 (mm) cc_final: 0.6632 (pt) REVERT: B 66 ASP cc_start: 0.8443 (t0) cc_final: 0.8181 (t0) REVERT: B 111 PHE cc_start: 0.6141 (p90) cc_final: 0.4577 (p90) REVERT: B 180 LYS cc_start: 0.7117 (mttt) cc_final: 0.6327 (tttt) REVERT: B 239 MET cc_start: 0.8508 (mmp) cc_final: 0.7981 (mmp) REVERT: C 66 ASP cc_start: 0.8454 (t0) cc_final: 0.8228 (t0) REVERT: C 180 LYS cc_start: 0.7098 (mttt) cc_final: 0.6358 (tttt) REVERT: C 245 GLN cc_start: 0.7941 (mt0) cc_final: 0.7527 (mm-40) REVERT: D 180 LYS cc_start: 0.7164 (mttt) cc_final: 0.6398 (tttt) REVERT: D 400 ILE cc_start: 0.7555 (mm) cc_final: 0.6904 (pt) REVERT: E 111 PHE cc_start: 0.6216 (p90) cc_final: 0.4483 (p90) REVERT: E 180 LYS cc_start: 0.6963 (mttt) cc_final: 0.6117 (tttt) REVERT: E 280 LEU cc_start: 0.8062 (tp) cc_final: 0.7729 (mp) REVERT: E 400 ILE cc_start: 0.7573 (mm) cc_final: 0.6815 (pt) outliers start: 8 outliers final: 5 residues processed: 181 average time/residue: 0.6953 time to fit residues: 175.9434 Evaluate side-chains 148 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 ASN E 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14120 Z= 0.269 Angle : 0.482 4.932 19215 Z= 0.254 Chirality : 0.040 0.153 2160 Planarity : 0.004 0.041 2390 Dihedral : 17.283 150.887 2040 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.60 % Allowed : 5.30 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.99 (0.21), residues: 1670 helix: 2.80 (0.21), residues: 535 sheet: -0.40 (0.23), residues: 470 loop : -0.25 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 414 HIS 0.003 0.001 HIS B 105 PHE 0.023 0.001 PHE A 111 TYR 0.010 0.001 TYR B 417 ARG 0.007 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.6999 (mttt) cc_final: 0.6312 (tttt) REVERT: A 280 LEU cc_start: 0.8083 (tp) cc_final: 0.7748 (mp) REVERT: B 111 PHE cc_start: 0.6365 (p90) cc_final: 0.4703 (p90) REVERT: B 180 LYS cc_start: 0.6986 (mttt) cc_final: 0.6208 (tttt) REVERT: B 239 MET cc_start: 0.8598 (mmp) cc_final: 0.8289 (mmp) REVERT: B 280 LEU cc_start: 0.7926 (tp) cc_final: 0.7456 (mp) REVERT: C 180 LYS cc_start: 0.7110 (mttt) cc_final: 0.6314 (tttt) REVERT: C 245 GLN cc_start: 0.7931 (mt0) cc_final: 0.7474 (mm-40) REVERT: D 180 LYS cc_start: 0.7149 (mttt) cc_final: 0.6403 (tttt) REVERT: D 400 ILE cc_start: 0.7551 (mm) cc_final: 0.6853 (pt) REVERT: E 61 MET cc_start: 0.7903 (mmm) cc_final: 0.7303 (mmt) REVERT: E 111 PHE cc_start: 0.6200 (p90) cc_final: 0.4523 (p90) REVERT: E 180 LYS cc_start: 0.6988 (mttt) cc_final: 0.6164 (tttt) REVERT: E 280 LEU cc_start: 0.7747 (tp) cc_final: 0.7490 (mp) outliers start: 9 outliers final: 8 residues processed: 163 average time/residue: 0.5809 time to fit residues: 139.0620 Evaluate side-chains 147 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN C 167 ASN E 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14120 Z= 0.191 Angle : 0.446 4.287 19215 Z= 0.231 Chirality : 0.039 0.146 2160 Planarity : 0.004 0.045 2390 Dihedral : 17.037 151.789 2040 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.60 % Allowed : 6.98 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.15 (0.21), residues: 1670 helix: 3.01 (0.22), residues: 535 sheet: -0.34 (0.23), residues: 470 loop : -0.22 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 414 HIS 0.003 0.001 HIS B 105 PHE 0.020 0.001 PHE A 111 TYR 0.010 0.001 TYR C 417 ARG 0.007 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.6903 (mttt) cc_final: 0.6218 (tttt) REVERT: A 245 GLN cc_start: 0.7920 (mt0) cc_final: 0.7438 (mm-40) REVERT: B 180 LYS cc_start: 0.6973 (mttt) cc_final: 0.6196 (tttt) REVERT: B 239 MET cc_start: 0.8715 (mmp) cc_final: 0.8260 (mmm) REVERT: C 14 ASN cc_start: 0.3297 (m-40) cc_final: 0.2999 (m-40) REVERT: C 180 LYS cc_start: 0.7075 (mttt) cc_final: 0.6344 (tttp) REVERT: C 245 GLN cc_start: 0.7988 (mt0) cc_final: 0.7547 (mm-40) REVERT: D 239 MET cc_start: 0.8560 (mmp) cc_final: 0.8133 (mmp) REVERT: D 400 ILE cc_start: 0.7513 (mm) cc_final: 0.6917 (pt) REVERT: E 111 PHE cc_start: 0.6238 (p90) cc_final: 0.4491 (p90) REVERT: E 180 LYS cc_start: 0.6970 (mttt) cc_final: 0.6148 (tttt) outliers start: 9 outliers final: 9 residues processed: 145 average time/residue: 0.5357 time to fit residues: 116.5769 Evaluate side-chains 141 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN E 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14120 Z= 0.211 Angle : 0.444 4.102 19215 Z= 0.230 Chirality : 0.039 0.146 2160 Planarity : 0.004 0.036 2390 Dihedral : 17.065 152.111 2040 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.01 % Allowed : 7.25 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.25 (0.21), residues: 1670 helix: 3.06 (0.22), residues: 535 sheet: -0.44 (0.23), residues: 440 loop : -0.01 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 414 HIS 0.003 0.001 HIS A 105 PHE 0.018 0.001 PHE D 111 TYR 0.008 0.001 TYR A 132 ARG 0.004 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.6913 (mttt) cc_final: 0.6228 (tttt) REVERT: A 245 GLN cc_start: 0.7957 (mt0) cc_final: 0.7444 (mm-40) REVERT: B 180 LYS cc_start: 0.6984 (mttt) cc_final: 0.6153 (tttt) REVERT: B 239 MET cc_start: 0.8768 (mmp) cc_final: 0.8332 (mmm) REVERT: B 245 GLN cc_start: 0.8016 (mt0) cc_final: 0.7422 (mm-40) REVERT: C 14 ASN cc_start: 0.3617 (m-40) cc_final: 0.3318 (m-40) REVERT: C 180 LYS cc_start: 0.7086 (mttt) cc_final: 0.6313 (tttt) REVERT: C 245 GLN cc_start: 0.7982 (mt0) cc_final: 0.7523 (mm-40) REVERT: D 239 MET cc_start: 0.8634 (mmp) cc_final: 0.8173 (mmp) REVERT: D 400 ILE cc_start: 0.7509 (mm) cc_final: 0.6906 (pt) REVERT: E 111 PHE cc_start: 0.6260 (p90) cc_final: 0.4509 (p90) REVERT: E 180 LYS cc_start: 0.6967 (mttt) cc_final: 0.6151 (tttt) outliers start: 15 outliers final: 15 residues processed: 144 average time/residue: 0.5267 time to fit residues: 114.3876 Evaluate side-chains 144 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN E 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14120 Z= 0.193 Angle : 0.431 3.859 19215 Z= 0.222 Chirality : 0.039 0.144 2160 Planarity : 0.004 0.036 2390 Dihedral : 16.988 152.778 2040 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.07 % Allowed : 7.58 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.31 (0.21), residues: 1670 helix: 3.16 (0.22), residues: 535 sheet: -0.43 (0.23), residues: 440 loop : -0.01 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 414 HIS 0.003 0.001 HIS B 105 PHE 0.017 0.001 PHE D 111 TYR 0.008 0.001 TYR C 417 ARG 0.004 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.7059 (mttt) cc_final: 0.6335 (tttt) REVERT: A 245 GLN cc_start: 0.7815 (mt0) cc_final: 0.7346 (mm-40) REVERT: B 180 LYS cc_start: 0.6989 (mttt) cc_final: 0.6148 (tttt) REVERT: B 239 MET cc_start: 0.8857 (mmp) cc_final: 0.8377 (mmm) REVERT: B 245 GLN cc_start: 0.7986 (mt0) cc_final: 0.7416 (mm-40) REVERT: C 14 ASN cc_start: 0.3602 (m-40) cc_final: 0.3316 (m-40) REVERT: C 245 GLN cc_start: 0.7946 (mt0) cc_final: 0.7380 (mm-40) REVERT: D 239 MET cc_start: 0.8729 (mmp) cc_final: 0.8282 (mmp) REVERT: D 400 ILE cc_start: 0.7484 (mm) cc_final: 0.6879 (pt) REVERT: E 111 PHE cc_start: 0.6267 (p90) cc_final: 0.4519 (p90) REVERT: E 180 LYS cc_start: 0.6995 (mttt) cc_final: 0.6212 (tttt) outliers start: 16 outliers final: 14 residues processed: 154 average time/residue: 0.5763 time to fit residues: 133.9886 Evaluate side-chains 143 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 3.9990 chunk 17 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 0.0050 chunk 134 optimal weight: 0.6980 chunk 89 optimal weight: 0.3980 chunk 159 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.6294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN E 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 14120 Z= 0.135 Angle : 0.403 3.731 19215 Z= 0.204 Chirality : 0.038 0.136 2160 Planarity : 0.003 0.035 2390 Dihedral : 16.785 154.120 2040 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.81 % Allowed : 7.92 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.21), residues: 1670 helix: 3.30 (0.22), residues: 540 sheet: -0.39 (0.23), residues: 435 loop : 0.14 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 414 HIS 0.002 0.001 HIS B 105 PHE 0.018 0.001 PHE D 111 TYR 0.008 0.001 TYR A 417 ARG 0.003 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.7065 (mttt) cc_final: 0.6354 (tttt) REVERT: A 239 MET cc_start: 0.8344 (mmp) cc_final: 0.8116 (mmp) REVERT: A 245 GLN cc_start: 0.7720 (mt0) cc_final: 0.7346 (mm-40) REVERT: B 180 LYS cc_start: 0.6959 (mttt) cc_final: 0.6125 (tttt) REVERT: B 239 MET cc_start: 0.8823 (mmp) cc_final: 0.8328 (mmm) REVERT: B 245 GLN cc_start: 0.7816 (mt0) cc_final: 0.7415 (mm-40) REVERT: C 245 GLN cc_start: 0.7815 (mt0) cc_final: 0.7310 (mm-40) REVERT: D 239 MET cc_start: 0.8778 (mmp) cc_final: 0.8313 (mmp) REVERT: D 400 ILE cc_start: 0.7461 (mm) cc_final: 0.6930 (pt) REVERT: E 111 PHE cc_start: 0.6252 (p90) cc_final: 0.4506 (p90) REVERT: E 180 LYS cc_start: 0.7007 (mttt) cc_final: 0.6301 (tttt) outliers start: 12 outliers final: 12 residues processed: 147 average time/residue: 0.5248 time to fit residues: 118.4006 Evaluate side-chains 140 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.0870 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 101 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 251 ASN E 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14120 Z= 0.123 Angle : 0.402 5.184 19215 Z= 0.201 Chirality : 0.038 0.134 2160 Planarity : 0.003 0.034 2390 Dihedral : 16.678 155.231 2040 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.47 % Allowed : 8.59 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.21), residues: 1670 helix: 3.28 (0.22), residues: 550 sheet: -0.29 (0.24), residues: 410 loop : -0.01 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 414 HIS 0.002 0.001 HIS B 105 PHE 0.018 0.001 PHE D 111 TYR 0.008 0.001 TYR C 417 ARG 0.003 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.7058 (mttt) cc_final: 0.6361 (tttt) REVERT: A 239 MET cc_start: 0.8349 (mmp) cc_final: 0.8096 (mmp) REVERT: A 245 GLN cc_start: 0.7685 (mt0) cc_final: 0.7326 (mm-40) REVERT: B 180 LYS cc_start: 0.6843 (mttt) cc_final: 0.6022 (tttt) REVERT: B 245 GLN cc_start: 0.7959 (mt0) cc_final: 0.7386 (mm-40) REVERT: C 245 GLN cc_start: 0.7807 (mt0) cc_final: 0.7342 (mm-40) REVERT: D 239 MET cc_start: 0.8759 (mmp) cc_final: 0.8304 (mmp) REVERT: D 400 ILE cc_start: 0.7435 (mm) cc_final: 0.6941 (pt) REVERT: E 111 PHE cc_start: 0.6187 (p90) cc_final: 0.4441 (p90) REVERT: E 180 LYS cc_start: 0.6976 (mttt) cc_final: 0.6269 (tttt) outliers start: 7 outliers final: 7 residues processed: 138 average time/residue: 0.6119 time to fit residues: 129.3995 Evaluate side-chains 135 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 148 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 0.0060 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN C 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14120 Z= 0.161 Angle : 0.413 5.490 19215 Z= 0.209 Chirality : 0.038 0.138 2160 Planarity : 0.004 0.035 2390 Dihedral : 16.780 154.434 2040 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.67 % Allowed : 8.86 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.52 (0.21), residues: 1670 helix: 3.38 (0.22), residues: 545 sheet: -0.38 (0.23), residues: 440 loop : 0.07 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 414 HIS 0.003 0.001 HIS B 105 PHE 0.019 0.001 PHE D 111 TYR 0.007 0.001 TYR C 417 ARG 0.002 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.7069 (mttt) cc_final: 0.6345 (tttt) REVERT: A 239 MET cc_start: 0.8370 (mmp) cc_final: 0.8125 (mmp) REVERT: A 245 GLN cc_start: 0.7686 (mt0) cc_final: 0.7334 (mm-40) REVERT: B 180 LYS cc_start: 0.6963 (mttt) cc_final: 0.6113 (tttt) REVERT: B 245 GLN cc_start: 0.7978 (mt0) cc_final: 0.7369 (mm-40) REVERT: C 245 GLN cc_start: 0.7848 (mt0) cc_final: 0.7356 (mm-40) REVERT: D 239 MET cc_start: 0.8725 (mmp) cc_final: 0.8269 (mmp) REVERT: D 400 ILE cc_start: 0.7436 (mm) cc_final: 0.6956 (pt) REVERT: E 111 PHE cc_start: 0.6209 (p90) cc_final: 0.4465 (p90) REVERT: E 180 LYS cc_start: 0.6985 (mttt) cc_final: 0.6271 (tttt) outliers start: 10 outliers final: 10 residues processed: 140 average time/residue: 0.5688 time to fit residues: 120.2973 Evaluate side-chains 136 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN E 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14120 Z= 0.282 Angle : 0.476 4.992 19215 Z= 0.250 Chirality : 0.040 0.148 2160 Planarity : 0.004 0.037 2390 Dihedral : 17.186 151.392 2040 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.01 % Allowed : 8.66 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.20 (0.21), residues: 1670 helix: 2.97 (0.22), residues: 550 sheet: -0.49 (0.23), residues: 440 loop : -0.06 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 414 HIS 0.004 0.001 HIS D 105 PHE 0.017 0.001 PHE D 111 TYR 0.012 0.001 TYR A 132 ARG 0.003 0.000 ARG B 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.7111 (mttt) cc_final: 0.6384 (tttt) REVERT: A 239 MET cc_start: 0.8412 (mmp) cc_final: 0.8162 (mmp) REVERT: A 245 GLN cc_start: 0.7757 (mt0) cc_final: 0.7265 (mm-40) REVERT: A 411 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6631 (mp) REVERT: B 66 ASP cc_start: 0.8406 (t0) cc_final: 0.8140 (t0) REVERT: B 180 LYS cc_start: 0.7037 (mttt) cc_final: 0.6175 (tttt) REVERT: B 245 GLN cc_start: 0.8051 (mt0) cc_final: 0.7459 (mm-40) REVERT: C 245 GLN cc_start: 0.7977 (mt0) cc_final: 0.7377 (mm-40) REVERT: D 239 MET cc_start: 0.8730 (mmp) cc_final: 0.8253 (mmp) REVERT: D 400 ILE cc_start: 0.7449 (mm) cc_final: 0.6947 (pt) REVERT: E 180 LYS cc_start: 0.7060 (mttt) cc_final: 0.6284 (tttt) outliers start: 15 outliers final: 13 residues processed: 141 average time/residue: 0.4898 time to fit residues: 105.9520 Evaluate side-chains 140 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.1524 > 50: distance: 107 - 117: 14.824 distance: 117 - 118: 4.752 distance: 117 - 124: 31.170 distance: 118 - 119: 20.671 distance: 118 - 121: 19.936 distance: 118 - 125: 10.087 distance: 119 - 120: 27.198 distance: 119 - 133: 20.072 distance: 121 - 122: 22.369 distance: 121 - 123: 16.565 distance: 121 - 126: 31.390 distance: 122 - 127: 29.808 distance: 122 - 128: 27.171 distance: 122 - 129: 30.905 distance: 123 - 130: 29.371 distance: 123 - 131: 24.514 distance: 123 - 132: 37.500 distance: 133 - 134: 32.208 distance: 133 - 147: 40.179 distance: 134 - 135: 25.457 distance: 134 - 137: 40.110 distance: 134 - 148: 34.770 distance: 135 - 136: 26.835 distance: 135 - 157: 25.391 distance: 137 - 138: 43.505 distance: 137 - 149: 37.576 distance: 137 - 150: 36.139 distance: 138 - 139: 38.737 distance: 138 - 140: 27.166 distance: 139 - 141: 29.421 distance: 139 - 151: 22.222 distance: 140 - 142: 12.509 distance: 140 - 143: 18.675 distance: 141 - 142: 23.029 distance: 141 - 152: 20.148 distance: 142 - 144: 26.354 distance: 143 - 145: 22.608 distance: 143 - 153: 9.409 distance: 144 - 146: 5.044 distance: 144 - 154: 14.743 distance: 145 - 146: 23.928 distance: 146 - 156: 14.431 distance: 157 - 158: 15.765 distance: 157 - 164: 4.538 distance: 158 - 165: 31.674 distance: 159 - 160: 19.762 distance: 159 - 171: 48.811 distance: 161 - 162: 15.158 distance: 161 - 163: 30.118 distance: 161 - 166: 35.212 distance: 162 - 167: 17.991 distance: 163 - 168: 11.835 distance: 163 - 169: 21.143 distance: 163 - 170: 43.914 distance: 171 - 172: 16.246 distance: 171 - 179: 29.059 distance: 172 - 173: 24.630 distance: 172 - 175: 19.407 distance: 172 - 180: 25.427 distance: 173 - 174: 19.545 distance: 173 - 185: 28.959 distance: 175 - 176: 34.351 distance: 175 - 181: 4.414 distance: 175 - 182: 42.603 distance: 176 - 177: 14.709 distance: 176 - 178: 20.186 distance: 178 - 183: 13.230 distance: 178 - 184: 18.222 distance: 185 - 186: 34.336 distance: 185 - 189: 27.459 distance: 186 - 187: 40.619 distance: 186 - 190: 30.717 distance: 186 - 191: 17.584 distance: 187 - 188: 13.424 distance: 187 - 192: 31.974 distance: 192 - 193: 15.155 distance: 192 - 198: 4.169 distance: 193 - 194: 23.754 distance: 193 - 196: 10.442 distance: 193 - 199: 10.842 distance: 194 - 195: 21.134 distance: 194 - 203: 9.335 distance: 196 - 197: 27.872 distance: 196 - 200: 28.128 distance: 196 - 201: 43.050 distance: 197 - 202: 16.303 distance: 203 - 204: 4.587 distance: 203 - 210: 21.635 distance: 204 - 205: 9.041 distance: 204 - 207: 8.037 distance: 204 - 211: 6.662 distance: 205 - 206: 19.994 distance: 205 - 217: 6.563 distance: 207 - 208: 10.438 distance: 207 - 209: 9.261 distance: 207 - 212: 9.457 distance: 208 - 213: 19.530 distance: 209 - 214: 14.608 distance: 209 - 215: 14.420 distance: 209 - 216: 18.447 distance: 217 - 218: 11.168 distance: 217 - 226: 12.443 distance: 218 - 219: 6.303 distance: 218 - 221: 22.816 distance: 218 - 227: 8.716 distance: 219 - 220: 10.913 distance: 219 - 239: 15.097 distance: 221 - 222: 25.562 distance: 221 - 228: 8.271 distance: 221 - 229: 14.522 distance: 222 - 223: 29.017 distance: 222 - 230: 6.325 distance: 222 - 231: 12.757 distance: 223 - 224: 12.502 distance: 223 - 232: 8.125 distance: 223 - 233: 7.737 distance: 224 - 225: 14.423 distance: 224 - 235: 12.632 distance: 225 - 236: 13.593 distance: 225 - 237: 7.633 distance: 225 - 238: 10.527 distance: 239 - 240: 8.238 distance: 239 - 245: 14.598 distance: 240 - 241: 14.149 distance: 240 - 243: 26.654 distance: 240 - 246: 19.396 distance: 241 - 242: 10.418 distance: 241 - 250: 28.927 distance: 243 - 244: 16.985 distance: 243 - 247: 24.732 distance: 243 - 248: 21.114 distance: 244 - 249: 9.523 distance: 250 - 251: 17.494 distance: 250 - 257: 25.687 distance: 251 - 252: 39.468 distance: 251 - 254: 18.112 distance: 251 - 258: 18.598 distance: 252 - 253: 9.603 distance: 252 - 266: 24.751 distance: 254 - 255: 7.726 distance: 254 - 256: 21.232 distance: 254 - 259: 19.186 distance: 255 - 260: 17.932 distance: 255 - 261: 7.366 distance: 255 - 262: 16.868 distance: 256 - 263: 27.909 distance: 256 - 264: 23.944 distance: 256 - 265: 10.738