Starting phenix.real_space_refine on Fri Sep 19 09:32:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6d_47556/09_2025/9e6d_47556_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6d_47556/09_2025/9e6d_47556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e6d_47556/09_2025/9e6d_47556_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6d_47556/09_2025/9e6d_47556_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e6d_47556/09_2025/9e6d_47556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6d_47556/09_2025/9e6d_47556.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.016 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 S 80 5.16 5 C 8055 2.51 5 N 1885 2.21 5 O 2300 1.98 5 H 12060 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24380 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4788 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "B" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4788 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "C" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4788 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "D" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4788 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "E" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4788 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 88 Unusual residues: {'LUM': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 88 Unusual residues: {'LUM': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 88 Unusual residues: {'LUM': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 88 Unusual residues: {'LUM': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 88 Unusual residues: {'LUM': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.26, per 1000 atoms: 0.22 Number of scatterers: 24380 At special positions: 0 Unit cell: (97.552, 95.408, 121.136, 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 80 16.00 O 2300 8.00 N 1885 7.00 C 8055 6.00 H 12060 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 150 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 150 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 150 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 150 " distance=2.02 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 145 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 150 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 145 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 77 " " NAG A 402 " - " ASN A 27 " " NAG A 403 " - " ASN A 180 " " NAG A 404 " - " ASN A 186 " " NAG A 405 " - " ASN A 17 " " NAG B 401 " - " ASN B 77 " " NAG B 402 " - " ASN B 27 " " NAG B 403 " - " ASN B 180 " " NAG B 404 " - " ASN B 186 " " NAG B 405 " - " ASN B 17 " " NAG C 401 " - " ASN C 77 " " NAG C 402 " - " ASN C 27 " " NAG C 403 " - " ASN C 180 " " NAG C 404 " - " ASN C 186 " " NAG C 405 " - " ASN C 17 " " NAG D 401 " - " ASN D 77 " " NAG D 402 " - " ASN D 27 " " NAG D 403 " - " ASN D 180 " " NAG D 404 " - " ASN D 186 " " NAG D 405 " - " ASN D 17 " " NAG E 401 " - " ASN E 77 " " NAG E 402 " - " ASN E 27 " " NAG E 403 " - " ASN E 180 " " NAG E 404 " - " ASN E 186 " " NAG E 405 " - " ASN E 17 " Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 780.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2810 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 20 sheets defined 36.0% alpha, 43.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 71 through 76 removed outlier: 4.223A pdb=" N ASN A 76 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 206 through 229 Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 230 through 234 removed outlier: 4.244A pdb=" N GLY A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 258 removed outlier: 3.594A pdb=" N THR A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 292 Processing helix chain 'B' and resid 3 through 15 Processing helix chain 'B' and resid 71 through 76 removed outlier: 4.229A pdb=" N ASN B 76 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 206 through 229 Proline residue: B 215 - end of helix Processing helix chain 'B' and resid 235 through 258 removed outlier: 3.597A pdb=" N THR B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 292 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 71 through 76 removed outlier: 4.220A pdb=" N ASN C 76 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 206 through 229 Proline residue: C 215 - end of helix Processing helix chain 'C' and resid 230 through 234 removed outlier: 4.308A pdb=" N GLY C 234 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 258 removed outlier: 3.596A pdb=" N THR C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 292 Processing helix chain 'D' and resid 3 through 15 Processing helix chain 'D' and resid 71 through 76 removed outlier: 4.212A pdb=" N ASN D 76 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 206 through 229 Proline residue: D 215 - end of helix Processing helix chain 'D' and resid 230 through 234 removed outlier: 4.250A pdb=" N GLY D 234 " --> pdb=" O PRO D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 258 removed outlier: 3.579A pdb=" N THR D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 292 Processing helix chain 'E' and resid 3 through 15 Processing helix chain 'E' and resid 71 through 76 removed outlier: 4.232A pdb=" N ASN E 76 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 206 through 229 Proline residue: E 215 - end of helix Processing helix chain 'E' and resid 235 through 258 removed outlier: 3.581A pdb=" N THR E 257 " --> pdb=" O GLN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 292 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 47 removed outlier: 6.017A pdb=" N LEU A 43 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ARG A 56 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 125 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 63 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.960A pdb=" N GLU A 110 " --> pdb=" O TRP A 122 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TRP A 122 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TRP A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 63 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 125 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR A 39 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE A 64 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP A 33 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ALA A 36 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A 164 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 38 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR A 166 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU A 40 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 168 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.531A pdb=" N CYS A 150 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER A 193 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.531A pdb=" N CYS A 150 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER A 193 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 47 removed outlier: 6.010A pdb=" N LEU B 43 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG B 56 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP B 63 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 84 removed outlier: 7.020A pdb=" N GLU B 110 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TRP B 122 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP B 118 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP B 63 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR B 39 " --> pdb=" O TYR B 58 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE B 64 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 33 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA B 36 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU B 164 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 38 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR B 166 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU B 40 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASP B 168 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.514A pdb=" N LYS B 94 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS B 150 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER B 193 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 200 " --> pdb=" O ASN B 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.514A pdb=" N LYS B 94 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS B 150 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER B 193 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 42 through 47 removed outlier: 6.016A pdb=" N LEU C 43 " --> pdb=" O ARG C 56 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ARG C 56 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 125 " --> pdb=" O TYR C 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 84 removed outlier: 6.918A pdb=" N GLU C 110 " --> pdb=" O TRP C 122 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TRP C 122 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TRP C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 125 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR C 39 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE C 64 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP C 33 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ALA C 36 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU C 164 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU C 38 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR C 166 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU C 40 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASP C 168 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 183 " --> pdb=" O TYR C 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.505A pdb=" N LYS C 94 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS C 150 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER C 193 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR C 200 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.505A pdb=" N LYS C 94 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS C 150 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER C 193 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 42 through 47 removed outlier: 5.965A pdb=" N LEU D 43 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ARG D 56 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG D 125 " --> pdb=" O TYR D 57 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.931A pdb=" N GLU D 110 " --> pdb=" O TRP D 122 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TRP D 122 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG D 125 " --> pdb=" O TYR D 57 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR D 39 " --> pdb=" O TYR D 58 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE D 64 " --> pdb=" O ASP D 33 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP D 33 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA D 36 " --> pdb=" O LYS D 162 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU D 164 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU D 38 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR D 166 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU D 40 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP D 168 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.556A pdb=" N CYS D 150 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER D 193 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D 200 " --> pdb=" O ASN D 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.556A pdb=" N CYS D 150 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER D 193 " --> pdb=" O VAL D 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 47 removed outlier: 5.983A pdb=" N LEU E 43 " --> pdb=" O ARG E 56 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ARG E 56 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 125 " --> pdb=" O TYR E 57 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP E 63 " --> pdb=" O ILE E 119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 80 through 84 removed outlier: 7.025A pdb=" N GLU E 110 " --> pdb=" O TRP E 122 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TRP E 122 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TRP E 118 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP E 63 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 125 " --> pdb=" O TYR E 57 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR E 39 " --> pdb=" O TYR E 58 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE E 64 " --> pdb=" O ASP E 33 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP E 33 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA E 36 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU E 164 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU E 38 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR E 166 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU E 40 " --> pdb=" O TYR E 166 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASP E 168 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 94 removed outlier: 3.544A pdb=" N CYS E 150 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER E 193 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR E 200 " --> pdb=" O ASN E 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 93 through 94 removed outlier: 3.544A pdb=" N CYS E 150 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER E 193 " --> pdb=" O VAL E 151 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2034 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: 6.84 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 12060 1.03 - 1.22: 0 1.22 - 1.42: 5119 1.42 - 1.62: 7361 1.62 - 1.82: 140 Bond restraints: 24680 Sorted by residual: bond pdb=" CG MET C 269 " pdb=" HG2 MET C 269 " ideal model delta sigma weight residual 0.970 0.938 0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" N THR B 1 " pdb=" CA THR B 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.47e+00 bond pdb=" N THR C 1 " pdb=" CA THR C 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.47e+00 bond pdb=" N THR A 1 " pdb=" CA THR A 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.43e+00 bond pdb=" N THR E 1 " pdb=" CA THR E 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.42e+00 ... (remaining 24675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 42838 1.90 - 3.81: 1527 3.81 - 5.71: 204 5.71 - 7.62: 22 7.62 - 9.52: 9 Bond angle restraints: 44600 Sorted by residual: angle pdb=" CB MET E 273 " pdb=" CG MET E 273 " pdb=" SD MET E 273 " ideal model delta sigma weight residual 112.70 122.22 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB MET C 273 " pdb=" CG MET C 273 " pdb=" SD MET C 273 " ideal model delta sigma weight residual 112.70 122.02 -9.32 3.00e+00 1.11e-01 9.65e+00 angle pdb=" CB MET B 273 " pdb=" CG MET B 273 " pdb=" SD MET B 273 " ideal model delta sigma weight residual 112.70 121.91 -9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" CB MET D 273 " pdb=" CG MET D 273 " pdb=" SD MET D 273 " ideal model delta sigma weight residual 112.70 121.91 -9.21 3.00e+00 1.11e-01 9.42e+00 angle pdb=" CA MET C 277 " pdb=" CB MET C 277 " pdb=" CG MET C 277 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.00e+00 ... (remaining 44595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.42: 10439 14.42 - 28.83: 999 28.83 - 43.25: 342 43.25 - 57.66: 154 57.66 - 72.08: 26 Dihedral angle restraints: 11960 sinusoidal: 6705 harmonic: 5255 Sorted by residual: dihedral pdb=" CA ASP D 74 " pdb=" CB ASP D 74 " pdb=" CG ASP D 74 " pdb=" OD1 ASP D 74 " ideal model delta sinusoidal sigma weight residual -30.00 -87.31 57.31 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP E 74 " pdb=" CB ASP E 74 " pdb=" CG ASP E 74 " pdb=" OD1 ASP E 74 " ideal model delta sinusoidal sigma weight residual -30.00 -87.20 57.20 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP A 74 " pdb=" CB ASP A 74 " pdb=" CG ASP A 74 " pdb=" OD1 ASP A 74 " ideal model delta sinusoidal sigma weight residual -30.00 -87.18 57.18 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 11957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1612 0.054 - 0.108: 398 0.108 - 0.162: 75 0.162 - 0.216: 5 0.216 - 0.270: 5 Chirality restraints: 2095 Sorted by residual: chirality pdb=" CB ILE A 133 " pdb=" CA ILE A 133 " pdb=" CG1 ILE A 133 " pdb=" CG2 ILE A 133 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE B 133 " pdb=" CA ILE B 133 " pdb=" CG1 ILE B 133 " pdb=" CG2 ILE B 133 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE C 133 " pdb=" CA ILE C 133 " pdb=" CG1 ILE C 133 " pdb=" CG2 ILE C 133 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 2092 not shown) Planarity restraints: 3445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 LUM B 406 " -0.010 2.00e-02 2.50e+03 2.54e-02 2.90e+01 pdb=" C2 LUM B 406 " -0.010 2.00e-02 2.50e+03 pdb=" C4 LUM B 406 " 0.005 2.00e-02 2.50e+03 pdb=" C4A LUM B 406 " -0.002 2.00e-02 2.50e+03 pdb=" C5A LUM B 406 " 0.014 2.00e-02 2.50e+03 pdb=" C6 LUM B 406 " 0.015 2.00e-02 2.50e+03 pdb=" C7 LUM B 406 " 0.008 2.00e-02 2.50e+03 pdb=" C7M LUM B 406 " -0.083 2.00e-02 2.50e+03 pdb=" C8 LUM B 406 " 0.004 2.00e-02 2.50e+03 pdb=" C8M LUM B 406 " 0.048 2.00e-02 2.50e+03 pdb=" C9 LUM B 406 " 0.003 2.00e-02 2.50e+03 pdb=" C9A LUM B 406 " 0.008 2.00e-02 2.50e+03 pdb=" N1 LUM B 406 " -0.016 2.00e-02 2.50e+03 pdb=" N10 LUM B 406 " -0.008 2.00e-02 2.50e+03 pdb=" N3 LUM B 406 " 0.000 2.00e-02 2.50e+03 pdb=" N5 LUM B 406 " 0.010 2.00e-02 2.50e+03 pdb=" O2 LUM B 406 " -0.015 2.00e-02 2.50e+03 pdb=" O4 LUM B 406 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 LUM E 406 " 0.017 2.00e-02 2.50e+03 2.33e-02 2.43e+01 pdb=" C2 LUM E 406 " 0.005 2.00e-02 2.50e+03 pdb=" C4 LUM E 406 " -0.003 2.00e-02 2.50e+03 pdb=" C4A LUM E 406 " 0.008 2.00e-02 2.50e+03 pdb=" C5A LUM E 406 " -0.009 2.00e-02 2.50e+03 pdb=" C6 LUM E 406 " -0.012 2.00e-02 2.50e+03 pdb=" C7 LUM E 406 " -0.011 2.00e-02 2.50e+03 pdb=" C7M LUM E 406 " 0.071 2.00e-02 2.50e+03 pdb=" C8 LUM E 406 " -0.007 2.00e-02 2.50e+03 pdb=" C8M LUM E 406 " -0.048 2.00e-02 2.50e+03 pdb=" C9 LUM E 406 " -0.002 2.00e-02 2.50e+03 pdb=" C9A LUM E 406 " -0.004 2.00e-02 2.50e+03 pdb=" N1 LUM E 406 " 0.016 2.00e-02 2.50e+03 pdb=" N10 LUM E 406 " 0.013 2.00e-02 2.50e+03 pdb=" N3 LUM E 406 " -0.004 2.00e-02 2.50e+03 pdb=" N5 LUM E 406 " -0.003 2.00e-02 2.50e+03 pdb=" O2 LUM E 406 " 0.005 2.00e-02 2.50e+03 pdb=" O4 LUM E 406 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 LUM A 406 " 0.012 2.00e-02 2.50e+03 2.02e-02 1.83e+01 pdb=" C2 LUM A 406 " 0.004 2.00e-02 2.50e+03 pdb=" C4 LUM A 406 " -0.003 2.00e-02 2.50e+03 pdb=" C4A LUM A 406 " 0.006 2.00e-02 2.50e+03 pdb=" C5A LUM A 406 " -0.006 2.00e-02 2.50e+03 pdb=" C6 LUM A 406 " -0.008 2.00e-02 2.50e+03 pdb=" C7 LUM A 406 " -0.007 2.00e-02 2.50e+03 pdb=" C7M LUM A 406 " 0.059 2.00e-02 2.50e+03 pdb=" C8 LUM A 406 " -0.002 2.00e-02 2.50e+03 pdb=" C8M LUM A 406 " -0.047 2.00e-02 2.50e+03 pdb=" C9 LUM A 406 " -0.000 2.00e-02 2.50e+03 pdb=" C9A LUM A 406 " -0.002 2.00e-02 2.50e+03 pdb=" N1 LUM A 406 " 0.012 2.00e-02 2.50e+03 pdb=" N10 LUM A 406 " 0.011 2.00e-02 2.50e+03 pdb=" N3 LUM A 406 " -0.002 2.00e-02 2.50e+03 pdb=" N5 LUM A 406 " -0.002 2.00e-02 2.50e+03 pdb=" O2 LUM A 406 " 0.006 2.00e-02 2.50e+03 pdb=" O4 LUM A 406 " -0.031 2.00e-02 2.50e+03 ... (remaining 3442 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 2160 2.24 - 2.83: 53321 2.83 - 3.42: 60819 3.42 - 4.01: 86227 4.01 - 4.60: 128820 Nonbonded interactions: 331347 Sorted by model distance: nonbonded pdb=" O ASN A 174 " pdb="HD22 ASN E 261 " model vdw 1.646 2.450 nonbonded pdb="HD22 ASN A 261 " pdb=" O ASN B 174 " model vdw 1.655 2.450 nonbonded pdb="HD22 ASN C 261 " pdb=" O ASN D 174 " model vdw 1.658 2.450 nonbonded pdb="HD22 ASN B 261 " pdb=" O ASN C 174 " model vdw 1.662 2.450 nonbonded pdb="HD22 ASN D 261 " pdb=" O ASN E 174 " model vdw 1.667 2.450 ... (remaining 331342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 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: 2.990 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: 0.160 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.290 Find NCS groups from input model: 0.340 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12655 Z= 0.262 Angle : 0.920 9.522 17310 Z= 0.462 Chirality : 0.049 0.270 2095 Planarity : 0.008 0.105 2030 Dihedral : 13.430 72.077 4965 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.22), residues: 1450 helix: 1.53 (0.24), residues: 420 sheet: -1.03 (0.24), residues: 420 loop : -0.52 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A 125 TYR 0.020 0.002 TYR B 58 PHE 0.018 0.002 PHE C 225 TRP 0.009 0.001 TRP A 63 HIS 0.005 0.002 HIS E 154 Details of bonding type rmsd covalent geometry : bond 0.00606 (12620) covalent geometry : angle 0.91863 (17215) SS BOND : bond 0.00795 ( 10) SS BOND : angle 1.04753 ( 20) hydrogen bonds : bond 0.17496 ( 614) hydrogen bonds : angle 6.47213 ( 2034) link_NAG-ASN : bond 0.00215 ( 25) link_NAG-ASN : angle 1.23194 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.700 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: A 97 ASN cc_start: 0.8465 (t0) cc_final: 0.8228 (t0) REVERT: B 225 PHE cc_start: 0.9009 (t80) cc_final: 0.8650 (t80) REVERT: C 225 PHE cc_start: 0.9032 (t80) cc_final: 0.8683 (t80) REVERT: D 225 PHE cc_start: 0.9058 (t80) cc_final: 0.8643 (t80) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2083 time to fit residues: 46.1293 Evaluate side-chains 123 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.087883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060792 restraints weight = 99785.541| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.39 r_work: 0.2800 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12655 Z= 0.168 Angle : 0.622 6.200 17310 Z= 0.330 Chirality : 0.042 0.156 2095 Planarity : 0.005 0.039 2030 Dihedral : 8.200 53.969 2120 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.37 % Allowed : 5.59 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.22), residues: 1450 helix: 2.26 (0.24), residues: 420 sheet: -0.80 (0.24), residues: 410 loop : -0.49 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 160 TYR 0.014 0.001 TYR B 58 PHE 0.016 0.001 PHE E 192 TRP 0.007 0.001 TRP D 63 HIS 0.002 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00367 (12620) covalent geometry : angle 0.61765 (17215) SS BOND : bond 0.00754 ( 10) SS BOND : angle 1.24401 ( 20) hydrogen bonds : bond 0.05129 ( 614) hydrogen bonds : angle 5.05303 ( 2034) link_NAG-ASN : bond 0.00164 ( 25) link_NAG-ASN : angle 1.11578 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.705 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 212 MET cc_start: 0.9418 (tmm) cc_final: 0.9156 (tmm) REVERT: B 224 ILE cc_start: 0.9145 (tp) cc_final: 0.8935 (pt) REVERT: B 225 PHE cc_start: 0.8996 (t80) cc_final: 0.8584 (t80) REVERT: B 264 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: C 225 PHE cc_start: 0.9009 (t80) cc_final: 0.8630 (t80) REVERT: D 225 PHE cc_start: 0.9075 (t80) cc_final: 0.8668 (t80) REVERT: E 54 MET cc_start: 0.8812 (mtp) cc_final: 0.8587 (mpp) outliers start: 5 outliers final: 1 residues processed: 123 average time/residue: 0.2067 time to fit residues: 40.3348 Evaluate side-chains 117 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 264 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 261 ASN B 41 GLN D 51 ASN D 261 ASN E 51 ASN E 261 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.087871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.060623 restraints weight = 100243.293| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.41 r_work: 0.2793 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12655 Z= 0.163 Angle : 0.584 7.133 17310 Z= 0.306 Chirality : 0.041 0.144 2095 Planarity : 0.004 0.040 2030 Dihedral : 6.998 50.164 2120 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.66 % Allowed : 7.13 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.22), residues: 1450 helix: 2.35 (0.24), residues: 420 sheet: -0.79 (0.24), residues: 410 loop : -0.39 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 125 TYR 0.018 0.001 TYR A 271 PHE 0.011 0.001 PHE A 192 TRP 0.008 0.001 TRP D 63 HIS 0.004 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00362 (12620) covalent geometry : angle 0.57957 (17215) SS BOND : bond 0.00612 ( 10) SS BOND : angle 1.11903 ( 20) hydrogen bonds : bond 0.04533 ( 614) hydrogen bonds : angle 4.77648 ( 2034) link_NAG-ASN : bond 0.00157 ( 25) link_NAG-ASN : angle 1.10899 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.713 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: B 225 PHE cc_start: 0.8999 (t80) cc_final: 0.8584 (t80) REVERT: C 225 PHE cc_start: 0.9052 (t80) cc_final: 0.8688 (t80) REVERT: D 45 ASP cc_start: 0.8745 (t0) cc_final: 0.8522 (t0) REVERT: D 225 PHE cc_start: 0.9078 (t80) cc_final: 0.8645 (t80) outliers start: 9 outliers final: 6 residues processed: 121 average time/residue: 0.1990 time to fit residues: 38.4342 Evaluate side-chains 116 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 264 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 60 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 51 ASN A 261 ASN B 51 ASN B 261 ASN C 51 ASN C 261 ASN E 41 GLN E 51 ASN E 261 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.088174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061352 restraints weight = 99225.445| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.32 r_work: 0.2812 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12655 Z= 0.121 Angle : 0.559 7.527 17310 Z= 0.291 Chirality : 0.040 0.145 2095 Planarity : 0.004 0.042 2030 Dihedral : 5.953 47.194 2120 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.51 % Allowed : 8.38 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.22), residues: 1450 helix: 2.44 (0.24), residues: 420 sheet: -0.71 (0.24), residues: 410 loop : -0.35 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 125 TYR 0.019 0.001 TYR B 271 PHE 0.009 0.001 PHE B 192 TRP 0.007 0.001 TRP C 63 HIS 0.004 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00267 (12620) covalent geometry : angle 0.55496 (17215) SS BOND : bond 0.00415 ( 10) SS BOND : angle 0.98264 ( 20) hydrogen bonds : bond 0.04079 ( 614) hydrogen bonds : angle 4.60224 ( 2034) link_NAG-ASN : bond 0.00093 ( 25) link_NAG-ASN : angle 1.02382 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.801 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: A 54 MET cc_start: 0.8827 (mtp) cc_final: 0.8410 (mmt) REVERT: B 225 PHE cc_start: 0.8994 (t80) cc_final: 0.8566 (t80) REVERT: C 54 MET cc_start: 0.8784 (mtp) cc_final: 0.8532 (mpp) REVERT: C 225 PHE cc_start: 0.9066 (t80) cc_final: 0.8695 (t80) REVERT: D 45 ASP cc_start: 0.8692 (t0) cc_final: 0.8319 (t0) REVERT: D 225 PHE cc_start: 0.9095 (t80) cc_final: 0.8653 (t80) outliers start: 7 outliers final: 5 residues processed: 116 average time/residue: 0.2007 time to fit residues: 37.5116 Evaluate side-chains 116 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 86 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 261 ASN C 51 ASN C 261 ASN E 51 ASN E 261 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.088013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060830 restraints weight = 99772.151| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.41 r_work: 0.2797 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12655 Z= 0.147 Angle : 0.553 7.847 17310 Z= 0.286 Chirality : 0.040 0.140 2095 Planarity : 0.004 0.042 2030 Dihedral : 5.549 47.611 2120 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.59 % Allowed : 8.82 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.23), residues: 1450 helix: 2.56 (0.24), residues: 420 sheet: -0.60 (0.24), residues: 410 loop : -0.27 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 125 TYR 0.019 0.001 TYR B 271 PHE 0.009 0.001 PHE B 192 TRP 0.007 0.001 TRP C 63 HIS 0.003 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00326 (12620) covalent geometry : angle 0.54904 (17215) SS BOND : bond 0.00497 ( 10) SS BOND : angle 0.94932 ( 20) hydrogen bonds : bond 0.04005 ( 614) hydrogen bonds : angle 4.54907 ( 2034) link_NAG-ASN : bond 0.00129 ( 25) link_NAG-ASN : angle 1.07464 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.736 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 54 MET cc_start: 0.8832 (mtp) cc_final: 0.8387 (mmt) REVERT: B 54 MET cc_start: 0.8837 (mtp) cc_final: 0.8492 (mmt) REVERT: B 225 PHE cc_start: 0.8997 (t80) cc_final: 0.8559 (t80) REVERT: B 264 TYR cc_start: 0.6771 (m-80) cc_final: 0.6404 (m-80) REVERT: C 54 MET cc_start: 0.8846 (mtp) cc_final: 0.8437 (mmt) REVERT: C 225 PHE cc_start: 0.9081 (t80) cc_final: 0.8708 (t80) REVERT: D 45 ASP cc_start: 0.8642 (t0) cc_final: 0.8253 (t0) REVERT: D 54 MET cc_start: 0.8379 (mpp) cc_final: 0.8085 (mmt) REVERT: D 225 PHE cc_start: 0.9104 (t80) cc_final: 0.8663 (t80) REVERT: E 54 MET cc_start: 0.8806 (mtp) cc_final: 0.8397 (mmt) REVERT: E 212 MET cc_start: 0.9281 (tmm) cc_final: 0.8964 (ppp) outliers start: 8 outliers final: 7 residues processed: 114 average time/residue: 0.2018 time to fit residues: 36.9684 Evaluate side-chains 118 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 137 optimal weight: 0.0370 chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 ASN C 132 GLN C 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.088054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060930 restraints weight = 99314.977| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.40 r_work: 0.2798 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12655 Z= 0.131 Angle : 0.543 8.548 17310 Z= 0.280 Chirality : 0.040 0.138 2095 Planarity : 0.004 0.042 2030 Dihedral : 5.287 46.593 2120 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.37 % Allowed : 9.34 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.23), residues: 1450 helix: 2.67 (0.24), residues: 420 sheet: -0.52 (0.25), residues: 410 loop : -0.20 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 125 TYR 0.020 0.001 TYR A 271 PHE 0.008 0.001 PHE B 192 TRP 0.007 0.001 TRP C 63 HIS 0.003 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00291 (12620) covalent geometry : angle 0.53950 (17215) SS BOND : bond 0.00480 ( 10) SS BOND : angle 0.91384 ( 20) hydrogen bonds : bond 0.03865 ( 614) hydrogen bonds : angle 4.46355 ( 2034) link_NAG-ASN : bond 0.00074 ( 25) link_NAG-ASN : angle 1.02100 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.625 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 54 MET cc_start: 0.8845 (mtp) cc_final: 0.8413 (mmt) REVERT: B 54 MET cc_start: 0.8824 (mtp) cc_final: 0.8473 (mmt) REVERT: B 225 PHE cc_start: 0.9033 (t80) cc_final: 0.8596 (t80) REVERT: B 264 TYR cc_start: 0.6695 (m-80) cc_final: 0.6340 (m-80) REVERT: C 54 MET cc_start: 0.8847 (mtp) cc_final: 0.8470 (mpp) REVERT: C 225 PHE cc_start: 0.9093 (t80) cc_final: 0.8715 (t80) REVERT: D 45 ASP cc_start: 0.8743 (t0) cc_final: 0.8321 (t0) REVERT: D 54 MET cc_start: 0.8373 (mpp) cc_final: 0.8087 (mmt) REVERT: D 225 PHE cc_start: 0.9076 (t80) cc_final: 0.8633 (t80) REVERT: E 54 MET cc_start: 0.8822 (mtp) cc_final: 0.8393 (mmt) outliers start: 5 outliers final: 5 residues processed: 116 average time/residue: 0.1805 time to fit residues: 33.6037 Evaluate side-chains 118 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 141 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.088062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060821 restraints weight = 99197.753| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.39 r_work: 0.2794 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12655 Z= 0.142 Angle : 0.547 8.676 17310 Z= 0.280 Chirality : 0.040 0.134 2095 Planarity : 0.004 0.042 2030 Dihedral : 5.198 46.859 2120 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.66 % Allowed : 9.63 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.23), residues: 1450 helix: 2.59 (0.24), residues: 430 sheet: -0.47 (0.25), residues: 410 loop : -0.23 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 56 TYR 0.016 0.001 TYR A 271 PHE 0.008 0.001 PHE B 192 TRP 0.007 0.001 TRP C 63 HIS 0.003 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00316 (12620) covalent geometry : angle 0.54371 (17215) SS BOND : bond 0.00491 ( 10) SS BOND : angle 0.81773 ( 20) hydrogen bonds : bond 0.03836 ( 614) hydrogen bonds : angle 4.42582 ( 2034) link_NAG-ASN : bond 0.00092 ( 25) link_NAG-ASN : angle 1.07157 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.776 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 54 MET cc_start: 0.8853 (mtp) cc_final: 0.8410 (mmt) REVERT: B 54 MET cc_start: 0.8799 (mtp) cc_final: 0.8471 (mmt) REVERT: B 225 PHE cc_start: 0.9046 (t80) cc_final: 0.8612 (t80) REVERT: B 264 TYR cc_start: 0.6671 (m-80) cc_final: 0.6324 (m-80) REVERT: C 54 MET cc_start: 0.8880 (mtp) cc_final: 0.8520 (mpp) REVERT: C 212 MET cc_start: 0.9237 (tmm) cc_final: 0.8821 (ppp) REVERT: D 45 ASP cc_start: 0.8718 (t0) cc_final: 0.8290 (t0) REVERT: D 54 MET cc_start: 0.8363 (mpp) cc_final: 0.8085 (mmt) REVERT: D 225 PHE cc_start: 0.9110 (t80) cc_final: 0.8662 (t80) REVERT: D 264 TYR cc_start: 0.6963 (m-80) cc_final: 0.6708 (m-80) REVERT: E 54 MET cc_start: 0.8820 (mtp) cc_final: 0.8414 (mmt) REVERT: E 212 MET cc_start: 0.9309 (tmm) cc_final: 0.8940 (ppp) outliers start: 9 outliers final: 5 residues processed: 119 average time/residue: 0.2017 time to fit residues: 38.6226 Evaluate side-chains 119 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.087449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.060107 restraints weight = 99067.321| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.41 r_work: 0.2787 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12655 Z= 0.154 Angle : 0.551 7.978 17310 Z= 0.284 Chirality : 0.040 0.135 2095 Planarity : 0.004 0.042 2030 Dihedral : 5.171 47.487 2120 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.51 % Allowed : 9.78 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.23), residues: 1450 helix: 2.80 (0.24), residues: 420 sheet: -0.42 (0.26), residues: 410 loop : -0.14 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 56 TYR 0.016 0.001 TYR A 271 PHE 0.007 0.001 PHE E 192 TRP 0.006 0.001 TRP C 63 HIS 0.003 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00343 (12620) covalent geometry : angle 0.54703 (17215) SS BOND : bond 0.00539 ( 10) SS BOND : angle 0.85429 ( 20) hydrogen bonds : bond 0.03849 ( 614) hydrogen bonds : angle 4.42192 ( 2034) link_NAG-ASN : bond 0.00111 ( 25) link_NAG-ASN : angle 1.07929 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.676 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 54 MET cc_start: 0.8848 (mtp) cc_final: 0.8405 (mmt) REVERT: B 54 MET cc_start: 0.8822 (mtp) cc_final: 0.8388 (mmt) REVERT: B 212 MET cc_start: 0.9548 (tmm) cc_final: 0.9324 (tmm) REVERT: B 225 PHE cc_start: 0.9068 (t80) cc_final: 0.8628 (t80) REVERT: B 264 TYR cc_start: 0.6668 (m-80) cc_final: 0.6330 (m-80) REVERT: C 54 MET cc_start: 0.8879 (mtp) cc_final: 0.8496 (mpp) REVERT: D 45 ASP cc_start: 0.8792 (t0) cc_final: 0.8356 (t0) REVERT: D 54 MET cc_start: 0.8333 (mpp) cc_final: 0.8058 (mmt) REVERT: D 225 PHE cc_start: 0.9122 (t80) cc_final: 0.8669 (t80) REVERT: E 54 MET cc_start: 0.8823 (mtp) cc_final: 0.8413 (mmt) REVERT: E 212 MET cc_start: 0.9326 (tmm) cc_final: 0.8993 (ppp) outliers start: 7 outliers final: 5 residues processed: 118 average time/residue: 0.1950 time to fit residues: 36.8094 Evaluate side-chains 116 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.087818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.060625 restraints weight = 98883.266| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.38 r_work: 0.2789 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12655 Z= 0.148 Angle : 0.562 7.499 17310 Z= 0.286 Chirality : 0.040 0.136 2095 Planarity : 0.004 0.042 2030 Dihedral : 5.131 47.441 2120 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.51 % Allowed : 10.00 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.23), residues: 1450 helix: 2.82 (0.24), residues: 420 sheet: -0.40 (0.26), residues: 410 loop : -0.16 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 56 TYR 0.015 0.001 TYR C 271 PHE 0.010 0.001 PHE A 244 TRP 0.006 0.001 TRP C 63 HIS 0.003 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00331 (12620) covalent geometry : angle 0.55838 (17215) SS BOND : bond 0.00484 ( 10) SS BOND : angle 0.67925 ( 20) hydrogen bonds : bond 0.03838 ( 614) hydrogen bonds : angle 4.38045 ( 2034) link_NAG-ASN : bond 0.00090 ( 25) link_NAG-ASN : angle 1.06564 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.678 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 54 MET cc_start: 0.8843 (mtp) cc_final: 0.8409 (mmt) REVERT: B 54 MET cc_start: 0.8809 (mtp) cc_final: 0.8413 (mmt) REVERT: B 212 MET cc_start: 0.9558 (tmm) cc_final: 0.9326 (tmm) REVERT: B 225 PHE cc_start: 0.9072 (t80) cc_final: 0.8631 (t80) REVERT: B 264 TYR cc_start: 0.6653 (m-80) cc_final: 0.6321 (m-80) REVERT: C 54 MET cc_start: 0.8884 (mtp) cc_final: 0.8497 (mpp) REVERT: C 212 MET cc_start: 0.9247 (tmm) cc_final: 0.8785 (ppp) REVERT: D 45 ASP cc_start: 0.8786 (t0) cc_final: 0.8344 (t0) REVERT: D 54 MET cc_start: 0.8322 (mpp) cc_final: 0.8051 (mmt) REVERT: D 225 PHE cc_start: 0.9121 (t80) cc_final: 0.8650 (t80) REVERT: E 54 MET cc_start: 0.8823 (mtp) cc_final: 0.8419 (mmt) REVERT: E 212 MET cc_start: 0.9342 (tmm) cc_final: 0.9000 (ppp) outliers start: 7 outliers final: 5 residues processed: 115 average time/residue: 0.1941 time to fit residues: 36.0234 Evaluate side-chains 114 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 141 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060987 restraints weight = 98477.553| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.38 r_work: 0.2800 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12655 Z= 0.114 Angle : 0.544 7.299 17310 Z= 0.278 Chirality : 0.040 0.136 2095 Planarity : 0.004 0.042 2030 Dihedral : 4.991 45.582 2120 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.37 % Allowed : 10.15 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.23), residues: 1450 helix: 2.74 (0.24), residues: 430 sheet: -0.52 (0.25), residues: 435 loop : -0.14 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 125 TYR 0.014 0.001 TYR C 271 PHE 0.007 0.001 PHE B 192 TRP 0.007 0.001 TRP C 63 HIS 0.002 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00258 (12620) covalent geometry : angle 0.54125 (17215) SS BOND : bond 0.00372 ( 10) SS BOND : angle 0.58567 ( 20) hydrogen bonds : bond 0.03722 ( 614) hydrogen bonds : angle 4.30435 ( 2034) link_NAG-ASN : bond 0.00073 ( 25) link_NAG-ASN : angle 1.00993 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.519 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 54 MET cc_start: 0.8825 (mtp) cc_final: 0.8389 (mmt) REVERT: B 54 MET cc_start: 0.8800 (mtp) cc_final: 0.8364 (mmt) REVERT: B 225 PHE cc_start: 0.9104 (t80) cc_final: 0.8642 (t80) REVERT: B 264 TYR cc_start: 0.6625 (m-80) cc_final: 0.6301 (m-80) REVERT: C 54 MET cc_start: 0.8876 (mtp) cc_final: 0.8497 (mpp) REVERT: C 212 MET cc_start: 0.9263 (tmm) cc_final: 0.8771 (ppp) REVERT: D 45 ASP cc_start: 0.8781 (t0) cc_final: 0.8350 (t0) REVERT: D 54 MET cc_start: 0.8329 (mpp) cc_final: 0.8067 (mmt) REVERT: D 225 PHE cc_start: 0.9130 (t80) cc_final: 0.8668 (t80) REVERT: E 54 MET cc_start: 0.8820 (mtp) cc_final: 0.8444 (mmt) REVERT: E 212 MET cc_start: 0.9354 (tmm) cc_final: 0.9069 (ppp) outliers start: 5 outliers final: 4 residues processed: 113 average time/residue: 0.1936 time to fit residues: 35.1560 Evaluate side-chains 115 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 94 optimal weight: 0.0980 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.060951 restraints weight = 98732.048| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.38 r_work: 0.2800 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12655 Z= 0.123 Angle : 0.558 9.236 17310 Z= 0.282 Chirality : 0.040 0.133 2095 Planarity : 0.004 0.042 2030 Dihedral : 4.925 45.450 2120 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.44 % Allowed : 10.37 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.23), residues: 1450 helix: 2.75 (0.24), residues: 430 sheet: -0.58 (0.25), residues: 440 loop : -0.08 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 56 TYR 0.017 0.001 TYR A 271 PHE 0.012 0.001 PHE E 227 TRP 0.007 0.001 TRP C 63 HIS 0.002 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00276 (12620) covalent geometry : angle 0.55499 (17215) SS BOND : bond 0.00392 ( 10) SS BOND : angle 0.60834 ( 20) hydrogen bonds : bond 0.03709 ( 614) hydrogen bonds : angle 4.28435 ( 2034) link_NAG-ASN : bond 0.00060 ( 25) link_NAG-ASN : angle 1.05666 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5702.61 seconds wall clock time: 97 minutes 41.19 seconds (5861.19 seconds total)