Starting phenix.real_space_refine on Fri Sep 19 09:32:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6b_47554/09_2025/9e6b_47554_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6b_47554/09_2025/9e6b_47554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e6b_47554/09_2025/9e6b_47554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6b_47554/09_2025/9e6b_47554.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6b_47554/09_2025/9e6b_47554_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6b_47554/09_2025/9e6b_47554_trim.cif" } resolution = 3.13 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= 0.001 sd= 0.015 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 8090 2.51 5 N 1880 2.21 5 O 2315 1.98 5 H 11950 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 24315 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4766 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "B" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4766 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "C" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4766 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "D" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4766 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "E" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4766 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 97 Unusual residues: {'NAG': 6, 'NRH': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 97 Unusual residues: {'NAG': 6, 'NRH': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 97 Unusual residues: {'NAG': 6, 'NRH': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 97 Unusual residues: {'NAG': 6, 'NRH': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 97 Unusual residues: {'NAG': 6, 'NRH': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.79, per 1000 atoms: 0.20 Number of scatterers: 24315 At special positions: 0 Unit cell: (94.435, 96.305, 121.55, 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 2315 8.00 N 1880 7.00 C 8090 6.00 H 11950 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 A 406 " - " ASN A 157 " " 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 B 406 " - " ASN B 157 " " 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 C 406 " - " ASN C 157 " " 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 D 406 " - " ASN D 157 " " NAG E 402 " - " ASN E 77 " " NAG E 403 " - " ASN E 27 " " NAG E 404 " - " ASN E 180 " " NAG E 405 " - " ASN E 186 " " NAG E 406 " - " ASN E 17 " " NAG E 407 " - " ASN E 157 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 657.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 30 helices and 20 sheets defined 33.2% alpha, 41.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 71 through 76 removed outlier: 4.076A 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 206 through 229 Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 235 through 258 removed outlier: 3.510A 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: 4.081A 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 206 through 229 Proline residue: B 215 - end of helix Processing helix chain 'B' and resid 235 through 258 removed outlier: 3.511A 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: 4.080A 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 206 through 229 Proline residue: C 215 - end of helix Processing helix chain 'C' and resid 235 through 258 removed outlier: 3.511A 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: 4.075A 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 206 through 229 Proline residue: D 215 - end of helix Processing helix chain 'D' and resid 235 through 258 removed outlier: 3.518A 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: 4.074A 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 206 through 229 Proline residue: E 215 - end of helix Processing helix chain 'E' and resid 235 through 258 removed outlier: 3.510A 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 80 through 84 removed outlier: 3.826A pdb=" N TRP A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.590A 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: 3.826A pdb=" N TRP A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP A 63 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE A 52 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASP A 45 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET A 54 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU A 43 " --> pdb=" O MET A 54 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 56 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR A 39 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A 64 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASP A 33 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A 32 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS A 162 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 34 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU A 164 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA A 36 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TYR A 166 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 38 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP A 168 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU A 40 " --> pdb=" O ASP A 168 " (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: 5.792A pdb=" N SER A 193 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 200 " --> pdb=" O ASN A 180 " (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: 5.792A pdb=" N SER A 193 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 84 removed outlier: 3.832A pdb=" N TRP B 118 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.832A pdb=" N TRP B 118 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP B 63 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE B 52 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASP B 45 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET B 54 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU B 43 " --> pdb=" O MET B 54 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 56 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR B 39 " --> pdb=" O TYR B 58 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE B 64 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP B 33 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL B 32 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N GLU B 163 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 34 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ILE B 165 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA B 36 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLU B 167 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 38 " --> pdb=" O GLU B 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.517A pdb=" N CYS B 150 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N SER B 193 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.517A pdb=" N CYS B 150 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N SER B 193 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 84 removed outlier: 3.822A pdb=" N TRP C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP C 63 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 84 removed outlier: 3.822A pdb=" N TRP C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP C 63 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE C 52 " --> pdb=" O ASP C 45 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP C 45 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET C 54 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU C 43 " --> pdb=" O MET C 54 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG C 56 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR C 39 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE C 64 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP C 33 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL C 32 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LYS C 162 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL C 34 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 164 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA C 36 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TYR C 166 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 38 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASP C 168 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU C 40 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.515A pdb=" N CYS C 150 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER C 193 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 3.605A 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: 3.515A pdb=" N CYS C 150 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER C 193 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 80 through 84 removed outlier: 3.826A pdb=" N TRP D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP D 63 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 80 through 84 removed outlier: 3.826A pdb=" N TRP D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP D 63 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N PHE D 52 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP D 45 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET D 54 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU D 43 " --> pdb=" O MET D 54 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG D 56 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR D 39 " --> pdb=" O TYR D 58 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE D 64 " --> pdb=" O ASP D 33 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP D 33 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL D 32 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS D 162 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL D 34 " --> pdb=" O LYS D 162 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU D 164 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA D 36 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR D 166 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU D 38 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP D 168 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU D 40 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.531A pdb=" N CYS D 150 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER D 193 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 3.613A 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: 3.531A pdb=" N CYS D 150 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER D 193 " --> pdb=" O VAL D 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 80 through 84 removed outlier: 3.827A pdb=" N TRP E 118 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.610A 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: 3.827A pdb=" N TRP E 118 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP E 63 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE E 52 " --> pdb=" O ASP E 45 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP E 45 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET E 54 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU E 43 " --> pdb=" O MET E 54 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG E 56 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E 39 " --> pdb=" O TYR E 58 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE E 64 " --> pdb=" O ASP E 33 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP E 33 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E 32 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS E 162 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL E 34 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU E 164 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA E 36 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TYR E 166 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU E 38 " --> pdb=" O TYR E 166 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASP E 168 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU E 40 " --> pdb=" O ASP E 168 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 94 removed outlier: 3.524A pdb=" N CYS E 150 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N SER E 193 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 3.551A 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: 3.524A pdb=" N CYS E 150 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N SER E 193 " --> pdb=" O VAL E 151 " (cutoff:3.500A) 647 hydrogen bonds defined for protein. 1866 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: 5.57 Time building geometry restraints manager: 3.16 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: 11950 1.03 - 1.23: 153 1.23 - 1.43: 5057 1.43 - 1.62: 7315 1.62 - 1.82: 140 Bond restraints: 24615 Sorted by residual: bond pdb=" CA ILE C 214 " pdb=" CB ILE C 214 " ideal model delta sigma weight residual 1.537 1.545 -0.008 5.00e-03 4.00e+04 2.74e+00 bond pdb=" N THR A 1 " pdb=" CA THR A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.70e+00 bond pdb=" N THR B 1 " pdb=" CA THR B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" N THR D 1 " pdb=" CA THR D 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 bond pdb=" N THR C 1 " pdb=" CA THR C 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.58e+00 ... (remaining 24610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 43355 2.27 - 4.54: 943 4.54 - 6.81: 107 6.81 - 9.08: 3 9.08 - 11.36: 12 Bond angle restraints: 44420 Sorted by residual: angle pdb=" C ILE C 214 " pdb=" CA ILE C 214 " pdb=" CB ILE C 214 " ideal model delta sigma weight residual 113.70 110.03 3.67 9.50e-01 1.11e+00 1.49e+01 angle pdb=" CB MET C 273 " pdb=" CG MET C 273 " pdb=" SD MET C 273 " ideal model delta sigma weight residual 112.70 124.06 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CB MET E 273 " pdb=" CG MET E 273 " pdb=" SD MET E 273 " ideal model delta sigma weight residual 112.70 124.04 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CB MET D 273 " pdb=" CG MET D 273 " pdb=" SD MET D 273 " ideal model delta sigma weight residual 112.70 124.01 -11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CB MET A 273 " pdb=" CG MET A 273 " pdb=" SD MET A 273 " ideal model delta sigma weight residual 112.70 124.00 -11.30 3.00e+00 1.11e-01 1.42e+01 ... (remaining 44415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.89: 10246 12.89 - 25.78: 1184 25.78 - 38.68: 392 38.68 - 51.57: 122 51.57 - 64.46: 101 Dihedral angle restraints: 12045 sinusoidal: 6790 harmonic: 5255 Sorted by residual: dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sinusoidal sigma weight residual -86.00 -116.79 30.79 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" CB CYS D 96 " pdb=" SG CYS D 96 " pdb=" SG CYS D 150 " pdb=" CB CYS D 150 " ideal model delta sinusoidal sigma weight residual -86.00 -116.71 30.71 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 150 " pdb=" CB CYS B 150 " ideal model delta sinusoidal sigma weight residual -86.00 -116.60 30.60 1 1.00e+01 1.00e-02 1.34e+01 ... (remaining 12042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1165 0.034 - 0.069: 640 0.069 - 0.103: 232 0.103 - 0.137: 74 0.137 - 0.172: 9 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CA ILE A 147 " pdb=" N ILE A 147 " pdb=" C ILE A 147 " pdb=" CB ILE A 147 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE B 147 " pdb=" N ILE B 147 " pdb=" C ILE B 147 " pdb=" CB ILE B 147 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CA ILE E 147 " pdb=" N ILE E 147 " pdb=" C ILE E 147 " pdb=" CB ILE E 147 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 2117 not shown) Planarity restraints: 3455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 27 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ASN D 27 " 0.059 2.00e-02 2.50e+03 pdb=" O ASN D 27 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU D 28 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 121 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.69e+00 pdb=" C MET E 121 " -0.037 2.00e-02 2.50e+03 pdb=" O MET E 121 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP E 122 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 239 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C LEU B 239 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU B 239 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA B 240 " -0.011 2.00e-02 2.50e+03 ... (remaining 3452 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 2425 2.25 - 2.83: 53408 2.83 - 3.42: 60808 3.42 - 4.01: 86689 4.01 - 4.60: 128871 Nonbonded interactions: 332201 Sorted by model distance: nonbonded pdb=" O ASN A 174 " pdb="HD22 ASN E 261 " model vdw 1.657 2.450 nonbonded pdb="HD22 ASN A 261 " pdb=" O ASN B 174 " model vdw 1.658 2.450 nonbonded pdb="HD22 ASN C 261 " pdb=" O ASN D 174 " model vdw 1.659 2.450 nonbonded pdb="HD22 ASN B 261 " pdb=" O ASN C 174 " model vdw 1.659 2.450 nonbonded pdb="HD22 ASN D 261 " pdb=" O ASN E 174 " model vdw 1.663 2.450 ... (remaining 332196 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 292 or resid 402 through 406)) selection = (chain 'B' and (resid 1 through 292 or resid 402 through 406)) selection = (chain 'C' and (resid 1 through 292 or resid 402 through 406)) selection = (chain 'D' and (resid 1 through 292 or resid 402 through 406)) selection = (chain 'E' and (resid 1 through 292 or resid 402 through 406)) } 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.860 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 0.046 12705 Z= 0.256 Angle : 0.936 11.355 17375 Z= 0.459 Chirality : 0.048 0.172 2120 Planarity : 0.005 0.043 2035 Dihedral : 13.372 64.461 5070 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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: -0.70 (0.22), residues: 1450 helix: 1.42 (0.24), residues: 420 sheet: -1.19 (0.24), residues: 405 loop : -1.21 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 203 TYR 0.020 0.002 TYR C 58 PHE 0.012 0.002 PHE C 124 TRP 0.011 0.002 TRP E 63 HIS 0.005 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00590 (12665) covalent geometry : angle 0.93150 (17265) SS BOND : bond 0.01014 ( 10) SS BOND : angle 1.73866 ( 20) hydrogen bonds : bond 0.14849 ( 557) hydrogen bonds : angle 6.13530 ( 1866) link_NAG-ASN : bond 0.00221 ( 30) link_NAG-ASN : angle 1.47919 ( 90) *********************** 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 95 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.727 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 outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2212 time to fit residues: 32.2026 Evaluate side-chains 92 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.105603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.071768 restraints weight = 77069.402| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.39 r_work: 0.2928 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12705 Z= 0.153 Angle : 0.558 4.467 17375 Z= 0.292 Chirality : 0.041 0.140 2120 Planarity : 0.004 0.040 2035 Dihedral : 7.697 59.965 2225 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: -0.13 (0.22), residues: 1450 helix: 2.16 (0.24), residues: 430 sheet: -1.08 (0.24), residues: 415 loop : -0.95 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 160 TYR 0.015 0.001 TYR C 271 PHE 0.010 0.001 PHE B 192 TRP 0.005 0.001 TRP B 122 HIS 0.005 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00335 (12665) covalent geometry : angle 0.54847 (17265) SS BOND : bond 0.00786 ( 10) SS BOND : angle 1.48198 ( 20) hydrogen bonds : bond 0.04156 ( 557) hydrogen bonds : angle 4.85424 ( 1866) link_NAG-ASN : bond 0.00202 ( 30) link_NAG-ASN : angle 1.39370 ( 90) *********************** 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 86 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.645 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: C 173 GLN cc_start: 0.8248 (mp10) cc_final: 0.7990 (mp10) REVERT: D 199 MET cc_start: 0.8902 (ttm) cc_final: 0.8578 (ttp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2268 time to fit residues: 29.9195 Evaluate side-chains 85 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 24 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.103318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.068768 restraints weight = 77756.153| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.39 r_work: 0.2877 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12705 Z= 0.262 Angle : 0.577 6.671 17375 Z= 0.299 Chirality : 0.041 0.141 2120 Planarity : 0.004 0.042 2035 Dihedral : 6.901 57.821 2225 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % 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: 0.07 (0.23), residues: 1450 helix: 2.63 (0.24), residues: 420 sheet: -1.18 (0.23), residues: 425 loop : -0.82 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 23 TYR 0.017 0.001 TYR A 271 PHE 0.011 0.001 PHE B 192 TRP 0.011 0.002 TRP B 122 HIS 0.005 0.002 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00578 (12665) covalent geometry : angle 0.56514 (17265) SS BOND : bond 0.00875 ( 10) SS BOND : angle 1.89063 ( 20) hydrogen bonds : bond 0.03932 ( 557) hydrogen bonds : angle 4.51673 ( 1866) link_NAG-ASN : bond 0.00351 ( 30) link_NAG-ASN : angle 1.49668 ( 90) *********************** 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 90 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.671 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: D 199 MET cc_start: 0.8914 (ttm) cc_final: 0.8625 (ttp) REVERT: E 173 GLN cc_start: 0.8479 (mp10) cc_final: 0.8084 (mp10) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2234 time to fit residues: 30.9081 Evaluate side-chains 88 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 35 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 116 optimal weight: 0.0870 chunk 137 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 132 GLN A 261 ASN B 51 ASN B 132 GLN B 261 ASN C 51 ASN C 132 GLN C 261 ASN D 51 ASN D 132 GLN D 261 ASN E 51 ASN E 132 GLN E 261 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.069847 restraints weight = 77390.761| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.40 r_work: 0.2895 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12705 Z= 0.159 Angle : 0.513 5.600 17375 Z= 0.265 Chirality : 0.040 0.136 2120 Planarity : 0.004 0.041 2035 Dihedral : 6.455 56.335 2225 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.22 % Allowed : 9.34 % Favored : 90.44 % 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: 0.30 (0.23), residues: 1450 helix: 2.95 (0.24), residues: 420 sheet: -1.06 (0.24), residues: 415 loop : -0.80 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 23 TYR 0.015 0.001 TYR B 271 PHE 0.005 0.001 PHE B 124 TRP 0.006 0.001 TRP B 122 HIS 0.004 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00352 (12665) covalent geometry : angle 0.50486 (17265) SS BOND : bond 0.00635 ( 10) SS BOND : angle 1.33499 ( 20) hydrogen bonds : bond 0.03429 ( 557) hydrogen bonds : angle 4.29480 ( 1866) link_NAG-ASN : bond 0.00122 ( 30) link_NAG-ASN : angle 1.19171 ( 90) *********************** 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 94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.665 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: D 199 MET cc_start: 0.8874 (ttm) cc_final: 0.8624 (ttp) REVERT: E 136 TYR cc_start: 0.6317 (t80) cc_final: 0.6111 (t80) REVERT: E 173 GLN cc_start: 0.8467 (mp10) cc_final: 0.8072 (mp10) outliers start: 3 outliers final: 1 residues processed: 92 average time/residue: 0.2317 time to fit residues: 32.8421 Evaluate side-chains 91 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 88 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 83 optimal weight: 20.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 261 ASN B 132 GLN B 261 ASN C 132 GLN C 261 ASN D 132 GLN D 261 ASN E 132 GLN E 261 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.105219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.071167 restraints weight = 76719.937| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.44 r_work: 0.2930 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12705 Z= 0.094 Angle : 0.483 6.114 17375 Z= 0.247 Chirality : 0.040 0.156 2120 Planarity : 0.004 0.044 2035 Dihedral : 5.913 53.296 2225 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.29 % Allowed : 9.49 % Favored : 90.22 % 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: 0.53 (0.23), residues: 1450 helix: 3.15 (0.24), residues: 420 sheet: -0.94 (0.24), residues: 415 loop : -0.66 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 203 TYR 0.012 0.001 TYR D 271 PHE 0.004 0.001 PHE E 52 TRP 0.004 0.001 TRP B 122 HIS 0.003 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00215 (12665) covalent geometry : angle 0.47647 (17265) SS BOND : bond 0.00388 ( 10) SS BOND : angle 1.03810 ( 20) hydrogen bonds : bond 0.03148 ( 557) hydrogen bonds : angle 4.09752 ( 1866) link_NAG-ASN : bond 0.00118 ( 30) link_NAG-ASN : angle 1.09861 ( 90) *********************** 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 94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.604 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: D 199 MET cc_start: 0.8788 (ttm) cc_final: 0.8523 (ttp) REVERT: E 173 GLN cc_start: 0.8399 (mp10) cc_final: 0.7993 (mp10) outliers start: 4 outliers final: 3 residues processed: 92 average time/residue: 0.2279 time to fit residues: 32.3258 Evaluate side-chains 93 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain E residue 213 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 143 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 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** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.104703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.070196 restraints weight = 77223.616| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.39 r_work: 0.2900 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12705 Z= 0.154 Angle : 0.497 6.428 17375 Z= 0.254 Chirality : 0.040 0.164 2120 Planarity : 0.004 0.044 2035 Dihedral : 5.540 47.426 2225 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.22 % Allowed : 9.93 % Favored : 89.85 % 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 (0.23), residues: 1450 helix: 3.04 (0.24), residues: 430 sheet: -0.98 (0.25), residues: 415 loop : -0.69 (0.28), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 23 TYR 0.012 0.001 TYR B 271 PHE 0.005 0.001 PHE E 52 TRP 0.005 0.001 TRP B 118 HIS 0.003 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00341 (12665) covalent geometry : angle 0.48920 (17265) SS BOND : bond 0.00577 ( 10) SS BOND : angle 1.22574 ( 20) hydrogen bonds : bond 0.03183 ( 557) hydrogen bonds : angle 4.04882 ( 1866) link_NAG-ASN : bond 0.00145 ( 30) link_NAG-ASN : angle 1.23605 ( 90) *********************** 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 98 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.604 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: C 173 GLN cc_start: 0.8356 (mp10) cc_final: 0.7971 (mp10) REVERT: D 199 MET cc_start: 0.8820 (ttm) cc_final: 0.8532 (ttp) REVERT: E 173 GLN cc_start: 0.8495 (mp10) cc_final: 0.8091 (mp10) outliers start: 3 outliers final: 3 residues processed: 97 average time/residue: 0.2142 time to fit residues: 31.9943 Evaluate side-chains 94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain E residue 213 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 126 optimal weight: 0.0670 chunk 121 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 31 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 261 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 261 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN E 261 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.070427 restraints weight = 76952.811| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.43 r_work: 0.2914 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12705 Z= 0.138 Angle : 0.493 6.609 17375 Z= 0.250 Chirality : 0.040 0.142 2120 Planarity : 0.004 0.045 2035 Dihedral : 5.117 38.715 2225 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.51 % Allowed : 10.29 % 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: 0.53 (0.24), residues: 1450 helix: 3.07 (0.24), residues: 430 sheet: -0.95 (0.25), residues: 415 loop : -0.65 (0.28), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 11 TYR 0.012 0.001 TYR B 271 PHE 0.006 0.001 PHE E 52 TRP 0.005 0.001 TRP A 118 HIS 0.003 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00307 (12665) covalent geometry : angle 0.48618 (17265) SS BOND : bond 0.00510 ( 10) SS BOND : angle 1.06621 ( 20) hydrogen bonds : bond 0.03103 ( 557) hydrogen bonds : angle 3.98142 ( 1866) link_NAG-ASN : bond 0.00093 ( 30) link_NAG-ASN : angle 1.16324 ( 90) *********************** 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 98 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.555 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: C 173 GLN cc_start: 0.8408 (mp10) cc_final: 0.8013 (mp10) REVERT: D 199 MET cc_start: 0.8798 (ttm) cc_final: 0.8527 (ttp) REVERT: E 173 GLN cc_start: 0.8502 (mp10) cc_final: 0.8067 (mp10) outliers start: 7 outliers final: 6 residues processed: 96 average time/residue: 0.2173 time to fit residues: 32.0542 Evaluate side-chains 96 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 213 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 2 optimal weight: 0.0970 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 261 ASN C 132 GLN C 261 ASN D 132 GLN D 261 ASN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.070179 restraints weight = 77102.811| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.43 r_work: 0.2893 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12705 Z= 0.150 Angle : 0.495 6.864 17375 Z= 0.251 Chirality : 0.040 0.147 2120 Planarity : 0.004 0.045 2035 Dihedral : 4.792 37.974 2225 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.37 % Allowed : 10.81 % Favored : 88.82 % 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: 0.58 (0.24), residues: 1450 helix: 3.11 (0.24), residues: 430 sheet: -0.94 (0.25), residues: 425 loop : -0.59 (0.28), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 23 TYR 0.012 0.001 TYR D 271 PHE 0.006 0.001 PHE E 52 TRP 0.005 0.001 TRP C 118 HIS 0.003 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00333 (12665) covalent geometry : angle 0.48755 (17265) SS BOND : bond 0.00556 ( 10) SS BOND : angle 1.08882 ( 20) hydrogen bonds : bond 0.03077 ( 557) hydrogen bonds : angle 3.93480 ( 1866) link_NAG-ASN : bond 0.00126 ( 30) link_NAG-ASN : angle 1.22030 ( 90) *********************** 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 96 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.682 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: C 173 GLN cc_start: 0.8432 (mp10) cc_final: 0.8026 (mp10) REVERT: D 199 MET cc_start: 0.8811 (ttm) cc_final: 0.8546 (ttp) REVERT: E 173 GLN cc_start: 0.8552 (mp10) cc_final: 0.8131 (mp10) outliers start: 5 outliers final: 4 residues processed: 94 average time/residue: 0.2245 time to fit residues: 32.3436 Evaluate side-chains 95 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 213 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 81 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 261 ASN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 261 ASN E 132 GLN E 261 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.105242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.071151 restraints weight = 76617.747| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.44 r_work: 0.2926 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12705 Z= 0.099 Angle : 0.481 8.919 17375 Z= 0.243 Chirality : 0.040 0.140 2120 Planarity : 0.004 0.046 2035 Dihedral : 4.565 36.747 2225 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.44 % Allowed : 10.66 % Favored : 88.90 % 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: 0.68 (0.24), residues: 1450 helix: 3.21 (0.24), residues: 430 sheet: -0.85 (0.25), residues: 415 loop : -0.59 (0.28), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 203 TYR 0.011 0.001 TYR B 271 PHE 0.005 0.001 PHE C 52 TRP 0.004 0.001 TRP C 118 HIS 0.003 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00225 (12665) covalent geometry : angle 0.47613 (17265) SS BOND : bond 0.00373 ( 10) SS BOND : angle 0.84541 ( 20) hydrogen bonds : bond 0.02931 ( 557) hydrogen bonds : angle 3.84480 ( 1866) link_NAG-ASN : bond 0.00107 ( 30) link_NAG-ASN : angle 1.05314 ( 90) *********************** 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 96 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.704 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 212 MET cc_start: 0.9380 (tmm) cc_final: 0.8755 (ppp) REVERT: C 173 GLN cc_start: 0.8376 (mp10) cc_final: 0.7956 (mp10) REVERT: D 199 MET cc_start: 0.8776 (ttm) cc_final: 0.8516 (ttp) REVERT: E 173 GLN cc_start: 0.8474 (mp10) cc_final: 0.8029 (mp10) outliers start: 6 outliers final: 4 residues processed: 95 average time/residue: 0.2341 time to fit residues: 34.0298 Evaluate side-chains 94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 213 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 44 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 120 optimal weight: 0.0470 chunk 54 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 261 ASN C 132 GLN C 261 ASN D 132 GLN D 261 ASN E 132 GLN E 261 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.108365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.074882 restraints weight = 76483.782| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.40 r_work: 0.2932 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12705 Z= 0.102 Angle : 0.472 6.679 17375 Z= 0.239 Chirality : 0.040 0.142 2120 Planarity : 0.004 0.046 2035 Dihedral : 4.397 36.012 2225 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.22 % Allowed : 11.18 % Favored : 88.60 % 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: 0.77 (0.24), residues: 1450 helix: 3.28 (0.24), residues: 430 sheet: -0.79 (0.26), residues: 415 loop : -0.54 (0.28), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 203 TYR 0.010 0.001 TYR B 271 PHE 0.005 0.001 PHE B 52 TRP 0.004 0.001 TRP D 118 HIS 0.003 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00231 (12665) covalent geometry : angle 0.46602 (17265) SS BOND : bond 0.00400 ( 10) SS BOND : angle 0.88237 ( 20) hydrogen bonds : bond 0.02875 ( 557) hydrogen bonds : angle 3.78227 ( 1866) link_NAG-ASN : bond 0.00100 ( 30) link_NAG-ASN : angle 1.08447 ( 90) ********************** 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 99 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.660 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: B 45 ASP cc_start: 0.8927 (t0) cc_final: 0.8663 (t0) REVERT: C 173 GLN cc_start: 0.8396 (mp10) cc_final: 0.8007 (mp10) REVERT: E 173 GLN cc_start: 0.8515 (mp10) cc_final: 0.8087 (mp10) outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 0.2285 time to fit residues: 33.8694 Evaluate side-chains 95 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 213 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 261 ASN C 132 GLN C 261 ASN D 132 GLN D 261 ASN E 132 GLN E 261 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.105098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.070376 restraints weight = 77061.978| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.45 r_work: 0.2916 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12705 Z= 0.143 Angle : 0.486 6.602 17375 Z= 0.246 Chirality : 0.040 0.145 2120 Planarity : 0.004 0.045 2035 Dihedral : 4.402 36.205 2225 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.22 % Allowed : 10.88 % Favored : 88.90 % 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: 0.80 (0.24), residues: 1450 helix: 3.30 (0.24), residues: 430 sheet: -0.81 (0.26), residues: 425 loop : -0.47 (0.28), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 23 TYR 0.011 0.001 TYR D 271 PHE 0.005 0.001 PHE E 52 TRP 0.005 0.001 TRP C 118 HIS 0.003 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00320 (12665) covalent geometry : angle 0.47912 (17265) SS BOND : bond 0.00514 ( 10) SS BOND : angle 1.09165 ( 20) hydrogen bonds : bond 0.02967 ( 557) hydrogen bonds : angle 3.81595 ( 1866) link_NAG-ASN : bond 0.00108 ( 30) link_NAG-ASN : angle 1.15796 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5466.21 seconds wall clock time: 93 minutes 29.64 seconds (5609.64 seconds total)