Starting phenix.real_space_refine on Thu Sep 18 05:58:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g55_51078/09_2025/9g55_51078.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g55_51078/09_2025/9g55_51078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g55_51078/09_2025/9g55_51078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g55_51078/09_2025/9g55_51078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g55_51078/09_2025/9g55_51078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g55_51078/09_2025/9g55_51078.map" } resolution = 3.04 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 9365 2.51 5 N 2195 2.21 5 O 2455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s 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: 14090 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2700 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2700 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2700 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2700 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 59 Chain: "E" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2700 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 116 Unusual residues: {'A8Z': 1, 'D10': 2, 'D12': 1, 'HEX': 4, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 116 Unusual residues: {'A8Z': 1, 'D10': 2, 'D12': 1, 'HEX': 4, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 116 Unusual residues: {'A8Z': 1, 'D10': 2, 'D12': 1, 'HEX': 4, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 116 Unusual residues: {'A8Z': 1, 'D10': 2, 'D12': 1, 'HEX': 4, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 116 Unusual residues: {'A8Z': 1, 'D10': 2, 'D12': 1, 'HEX': 4, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.62, per 1000 atoms: 0.26 Number of scatterers: 14090 At special positions: 0 Unit cell: (92.805, 93.4775, 137.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 2455 8.00 N 2195 7.00 C 9365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 212 " distance=2.04 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 212 " distance=2.04 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 212 " distance=2.04 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 Atom "HETATM13512 O5 NAG A 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM13638 O5 NAG B 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM13754 O5 NAG C 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM13870 O5 NAG D 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM13986 O5 NAG E 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM13768 O5 NAG C 503 .*. O " rejected from bonding due to valence issues. Atom "HETATM13526 O5 NAG A 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM13652 O5 NAG B 503 .*. O " rejected from bonding due to valence issues. Atom "HETATM13884 O5 NAG D 503 .*. O " rejected from bonding due to valence issues. Atom "HETATM14000 O5 NAG E 503 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 140 " " NAG A 502 " - " ASN A 234 " " NAG B 502 " - " ASN B 140 " " NAG B 503 " - " ASN B 234 " " NAG C 502 " - " ASN C 140 " " NAG C 503 " - " ASN C 234 " " NAG D 502 " - " ASN D 140 " " NAG D 503 " - " ASN D 234 " " NAG E 502 " - " ASN E 140 " " NAG E 503 " - " ASN E 234 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 466.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 42.3% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.839A pdb=" N HIS A 84 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 146 through 153 removed outlier: 3.618A pdb=" N LEU A 149 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 280 through 300 removed outlier: 3.876A pdb=" N PHE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.765A pdb=" N TRP A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 309 through 333 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 342 through 380 removed outlier: 3.667A pdb=" N VAL A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 removed outlier: 3.925A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.839A pdb=" N HIS B 84 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 146 through 153 removed outlier: 3.619A pdb=" N LEU B 149 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 280 through 300 removed outlier: 3.875A pdb=" N PHE B 284 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.766A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 309 through 333 Proline residue: B 315 - end of helix Processing helix chain 'B' and resid 342 through 380 removed outlier: 3.667A pdb=" N VAL B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 478 removed outlier: 3.924A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.839A pdb=" N HIS C 84 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 146 through 153 removed outlier: 3.618A pdb=" N LEU C 149 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 280 through 300 removed outlier: 3.876A pdb=" N PHE C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.765A pdb=" N TRP C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 309 through 333 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 342 through 380 removed outlier: 3.667A pdb=" N VAL C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 478 removed outlier: 3.925A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.840A pdb=" N HIS D 84 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 146 through 153 removed outlier: 3.619A pdb=" N LEU D 149 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 280 through 300 removed outlier: 3.876A pdb=" N PHE D 284 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.766A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 309 through 333 Proline residue: D 315 - end of helix Processing helix chain 'D' and resid 342 through 380 removed outlier: 3.667A pdb=" N VAL D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 478 removed outlier: 3.925A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.839A pdb=" N HIS E 84 " --> pdb=" O ILE E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 146 through 153 removed outlier: 3.619A pdb=" N LEU E 149 " --> pdb=" O ASP E 146 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 280 through 300 removed outlier: 3.877A pdb=" N PHE E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.766A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 309 through 333 Proline residue: E 315 - end of helix Processing helix chain 'E' and resid 342 through 380 removed outlier: 3.667A pdb=" N VAL E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 478 removed outlier: 3.925A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 145 removed outlier: 7.385A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 removed outlier: 6.965A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE A 168 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG A 191 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.621A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR A 276 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU A 252 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG A 278 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE A 250 " --> pdb=" O ARG A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145 removed outlier: 7.384A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.964A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE B 168 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG B 191 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.621A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 276 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU B 252 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG B 278 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE B 250 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 145 removed outlier: 7.384A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.964A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE C 168 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ARG C 191 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.621A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR C 276 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU C 252 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG C 278 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE C 250 " --> pdb=" O ARG C 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 143 through 145 removed outlier: 7.385A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 163 through 168 removed outlier: 6.964A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE D 168 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG D 191 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.620A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR D 276 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU D 252 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG D 278 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE D 250 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 145 removed outlier: 7.383A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.964A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE E 168 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ARG E 191 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.620A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR E 276 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU E 252 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG E 278 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE E 250 " --> pdb=" O ARG E 278 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2265 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: 2.28 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3814 1.34 - 1.46: 3979 1.46 - 1.59: 6497 1.59 - 1.71: 0 1.71 - 1.84: 140 Bond restraints: 14430 Sorted by residual: bond pdb=" CB THR C 121 " pdb=" CG2 THR C 121 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.72e+00 bond pdb=" CB THR A 121 " pdb=" CG2 THR A 121 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.68e+00 bond pdb=" CB THR D 121 " pdb=" CG2 THR D 121 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.65e+00 bond pdb=" CB THR B 121 " pdb=" CG2 THR B 121 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.64e+00 bond pdb=" CB THR E 121 " pdb=" CG2 THR E 121 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.59e+00 ... (remaining 14425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 18252 1.96 - 3.92: 994 3.92 - 5.88: 219 5.88 - 7.84: 65 7.84 - 9.80: 15 Bond angle restraints: 19545 Sorted by residual: angle pdb=" N GLY C 266 " pdb=" CA GLY C 266 " pdb=" C GLY C 266 " ideal model delta sigma weight residual 110.38 117.77 -7.39 1.28e+00 6.10e-01 3.34e+01 angle pdb=" N GLY B 266 " pdb=" CA GLY B 266 " pdb=" C GLY B 266 " ideal model delta sigma weight residual 110.38 117.76 -7.38 1.28e+00 6.10e-01 3.33e+01 angle pdb=" N GLY E 266 " pdb=" CA GLY E 266 " pdb=" C GLY E 266 " ideal model delta sigma weight residual 110.38 117.74 -7.36 1.28e+00 6.10e-01 3.31e+01 angle pdb=" N GLY D 266 " pdb=" CA GLY D 266 " pdb=" C GLY D 266 " ideal model delta sigma weight residual 110.38 117.74 -7.36 1.28e+00 6.10e-01 3.30e+01 angle pdb=" N GLY A 266 " pdb=" CA GLY A 266 " pdb=" C GLY A 266 " ideal model delta sigma weight residual 110.38 117.73 -7.35 1.28e+00 6.10e-01 3.30e+01 ... (remaining 19540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 8338 16.90 - 33.79: 392 33.79 - 50.69: 70 50.69 - 67.59: 10 67.59 - 84.49: 10 Dihedral angle restraints: 8820 sinusoidal: 3805 harmonic: 5015 Sorted by residual: dihedral pdb=" CA TYR D 340 " pdb=" C TYR D 340 " pdb=" N ILE D 341 " pdb=" CA ILE D 341 " ideal model delta harmonic sigma weight residual 180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA TYR A 340 " pdb=" C TYR A 340 " pdb=" N ILE A 341 " pdb=" CA ILE A 341 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA TYR B 340 " pdb=" C TYR B 340 " pdb=" N ILE B 341 " pdb=" CA ILE B 341 " ideal model delta harmonic sigma weight residual 180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 8817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.262: 2245 0.262 - 0.525: 10 0.525 - 0.787: 0 0.787 - 1.050: 0 1.050 - 1.312: 5 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C1 NAG D 503 " pdb=" ND2 ASN D 234 " pdb=" C2 NAG D 503 " pdb=" O5 NAG D 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.09 -1.31 2.00e-01 2.50e+01 4.31e+01 chirality pdb=" C1 NAG B 503 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B 503 " pdb=" O5 NAG B 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.09 -1.31 2.00e-01 2.50e+01 4.30e+01 chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.09 -1.31 2.00e-01 2.50e+01 4.30e+01 ... (remaining 2257 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.132 2.00e-02 2.50e+03 2.78e-01 9.67e+02 pdb=" CG ASN B 234 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.137 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.501 2.00e-02 2.50e+03 pdb=" C1 NAG B 503 " 0.306 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " 0.133 2.00e-02 2.50e+03 2.78e-01 9.66e+02 pdb=" CG ASN E 234 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " 0.137 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " -0.501 2.00e-02 2.50e+03 pdb=" C1 NAG E 503 " 0.306 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " 0.132 2.00e-02 2.50e+03 2.78e-01 9.65e+02 pdb=" CG ASN C 234 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " 0.137 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.500 2.00e-02 2.50e+03 pdb=" C1 NAG C 503 " 0.306 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 5054 2.88 - 3.38: 11728 3.38 - 3.89: 21415 3.89 - 4.39: 24719 4.39 - 4.90: 44177 Nonbonded interactions: 107093 Sorted by model distance: nonbonded pdb=" CG ASN D 140 " pdb=" O5 NAG D 502 " model vdw 2.371 2.616 nonbonded pdb=" CG ASN B 140 " pdb=" O5 NAG B 502 " model vdw 2.371 2.616 nonbonded pdb=" CG ASN C 140 " pdb=" O5 NAG C 502 " model vdw 2.371 2.616 nonbonded pdb=" CG ASN E 140 " pdb=" O5 NAG E 502 " model vdw 2.371 2.616 nonbonded pdb=" CG ASN A 140 " pdb=" O5 NAG A 501 " model vdw 2.372 2.616 ... (remaining 107088 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' and (resid 74 through 479 or resid 502 or resid 505 through 506)) selection = (chain 'B' and (resid 74 through 479 or resid 502 or resid 505 through 506)) selection = (chain 'C' and (resid 74 through 479 or resid 502 or resid 505 through 506)) selection = (chain 'D' and (resid 74 through 479 or resid 502 or resid 505 through 506)) selection = (chain 'E' and (resid 74 through 479 or resid 502 or resid 505 through 506)) } 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.570 Find NCS groups from input model: 0.330 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 : 0.009 0.326 14445 Z= 0.440 Angle : 1.728 47.896 19585 Z= 0.710 Chirality : 0.087 1.312 2260 Planarity : 0.011 0.099 2330 Dihedral : 10.656 84.485 5545 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.34 % Allowed : 3.78 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 0.40 (0.18), residues: 1660 helix: 0.46 (0.21), residues: 565 sheet: 0.98 (0.22), residues: 430 loop : -0.26 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.004 ARG C 308 TYR 0.043 0.008 TYR E 188 PHE 0.036 0.006 PHE E 275 TRP 0.038 0.005 TRP D 154 HIS 0.027 0.008 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00625 (14430) covalent geometry : angle 1.12218 (19545) SS BOND : bond 0.01307 ( 5) SS BOND : angle 3.80783 ( 10) hydrogen bonds : bond 0.20640 ( 725) hydrogen bonds : angle 6.25356 ( 2265) link_NAG-ASN : bond 0.25224 ( 10) link_NAG-ASN : angle 33.53525 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 295 time to evaluate : 0.529 Fit side-chains REVERT: A 152 LYS cc_start: 0.8207 (mttp) cc_final: 0.7962 (mttt) REVERT: A 179 ARG cc_start: 0.8368 (ttp-170) cc_final: 0.8125 (mtp85) REVERT: A 223 GLU cc_start: 0.7502 (pt0) cc_final: 0.7006 (tm-30) REVERT: A 238 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7326 (mtmm) REVERT: A 337 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7881 (tpp-160) REVERT: B 157 ASP cc_start: 0.8897 (p0) cc_final: 0.8693 (p0) REVERT: B 223 GLU cc_start: 0.7601 (pt0) cc_final: 0.6976 (tm-30) REVERT: B 227 MET cc_start: 0.8648 (ttp) cc_final: 0.8384 (ttm) REVERT: B 238 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7678 (mmtp) REVERT: B 337 ARG cc_start: 0.8209 (mtp180) cc_final: 0.7934 (tpp-160) REVERT: C 152 LYS cc_start: 0.8104 (mttp) cc_final: 0.7885 (mttt) REVERT: C 238 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7303 (mtmt) REVERT: C 337 ARG cc_start: 0.8259 (mtp180) cc_final: 0.8038 (tpp80) REVERT: D 152 LYS cc_start: 0.8358 (mttp) cc_final: 0.8158 (mttt) REVERT: D 179 ARG cc_start: 0.8350 (ttp-170) cc_final: 0.8048 (ttm110) REVERT: D 223 GLU cc_start: 0.7727 (pt0) cc_final: 0.7310 (tm-30) REVERT: D 238 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7099 (mtmt) REVERT: D 337 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7900 (tpp-160) REVERT: E 152 LYS cc_start: 0.8267 (mttp) cc_final: 0.8003 (mttt) REVERT: E 223 GLU cc_start: 0.7574 (pt0) cc_final: 0.7115 (tm-30) REVERT: E 238 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7607 (mmtm) REVERT: E 337 ARG cc_start: 0.8243 (mtp180) cc_final: 0.7884 (tpp-160) outliers start: 5 outliers final: 0 residues processed: 300 average time/residue: 0.1659 time to fit residues: 66.3045 Evaluate side-chains 203 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS B 332 ASN C 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.097928 restraints weight = 17254.607| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.00 r_work: 0.2836 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14445 Z= 0.223 Angle : 0.725 9.390 19585 Z= 0.373 Chirality : 0.047 0.171 2260 Planarity : 0.005 0.041 2330 Dihedral : 5.923 35.633 2570 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.20 % Allowed : 8.18 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.25 (0.20), residues: 1660 helix: 1.89 (0.23), residues: 540 sheet: 0.68 (0.22), residues: 500 loop : 0.12 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 191 TYR 0.018 0.002 TYR E 127 PHE 0.025 0.002 PHE D 356 TRP 0.019 0.002 TRP A 349 HIS 0.007 0.002 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00510 (14430) covalent geometry : angle 0.70786 (19545) SS BOND : bond 0.00358 ( 5) SS BOND : angle 1.06769 ( 10) hydrogen bonds : bond 0.09264 ( 725) hydrogen bonds : angle 4.61744 ( 2265) link_NAG-ASN : bond 0.01364 ( 10) link_NAG-ASN : angle 4.09477 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6883 (mt-10) REVERT: B 227 MET cc_start: 0.8444 (ttp) cc_final: 0.8185 (ttm) REVERT: B 337 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7723 (tpp-160) REVERT: C 152 LYS cc_start: 0.8081 (mttp) cc_final: 0.7842 (mttt) REVERT: C 232 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7899 (mtmm) REVERT: C 337 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7792 (tpp-160) REVERT: D 129 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8344 (tttm) REVERT: D 152 LYS cc_start: 0.8232 (mttp) cc_final: 0.8032 (mttt) REVERT: D 337 ARG cc_start: 0.8002 (mtp180) cc_final: 0.7768 (tpp-160) REVERT: E 129 LYS cc_start: 0.8641 (ttmm) cc_final: 0.8426 (tttm) REVERT: E 152 LYS cc_start: 0.8281 (mttp) cc_final: 0.8079 (mttt) REVERT: E 337 ARG cc_start: 0.8035 (mtp180) cc_final: 0.7780 (tpp-160) outliers start: 32 outliers final: 24 residues processed: 231 average time/residue: 0.1573 time to fit residues: 49.4691 Evaluate side-chains 205 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 2 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 108 optimal weight: 0.0470 chunk 158 optimal weight: 4.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 332 ASN B 181 GLN B 199 ASN B 332 ASN C 332 ASN E 280 HIS E 332 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.098852 restraints weight = 17222.112| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.26 r_work: 0.2970 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14445 Z= 0.124 Angle : 0.520 5.659 19585 Z= 0.275 Chirality : 0.041 0.150 2260 Planarity : 0.004 0.037 2330 Dihedral : 4.771 37.319 2570 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.20 % Allowed : 9.14 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.74 (0.21), residues: 1660 helix: 2.43 (0.23), residues: 540 sheet: 0.76 (0.23), residues: 505 loop : 0.47 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 179 TYR 0.015 0.001 TYR B 340 PHE 0.013 0.001 PHE B 356 TRP 0.012 0.001 TRP E 349 HIS 0.003 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00240 (14430) covalent geometry : angle 0.51055 (19545) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.58365 ( 10) hydrogen bonds : bond 0.06474 ( 725) hydrogen bonds : angle 4.12543 ( 2265) link_NAG-ASN : bond 0.00959 ( 10) link_NAG-ASN : angle 2.61847 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.6428 (mp10) REVERT: B 76 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6795 (mt-10) REVERT: B 227 MET cc_start: 0.8423 (ttp) cc_final: 0.8168 (ttm) REVERT: C 157 ASP cc_start: 0.8869 (p0) cc_final: 0.8625 (p0) REVERT: C 232 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7878 (mtmm) REVERT: C 337 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7769 (tpp-160) REVERT: D 129 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8335 (tttm) REVERT: D 152 LYS cc_start: 0.8227 (mttp) cc_final: 0.8016 (mttt) REVERT: D 287 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.6542 (mp10) REVERT: D 337 ARG cc_start: 0.8048 (mtp180) cc_final: 0.7743 (tpp-160) REVERT: E 129 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8299 (tttm) REVERT: E 152 LYS cc_start: 0.8291 (mttp) cc_final: 0.8086 (mttt) REVERT: E 287 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.6588 (mp10) REVERT: E 337 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7729 (tpp-160) outliers start: 32 outliers final: 21 residues processed: 204 average time/residue: 0.1564 time to fit residues: 44.1624 Evaluate side-chains 195 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 116 optimal weight: 0.3980 chunk 136 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 GLN D 280 HIS D 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.094171 restraints weight = 17417.290| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.10 r_work: 0.2877 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14445 Z= 0.231 Angle : 0.670 7.697 19585 Z= 0.353 Chirality : 0.046 0.171 2260 Planarity : 0.005 0.045 2330 Dihedral : 5.714 36.695 2570 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.47 % Allowed : 10.65 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.21 (0.20), residues: 1660 helix: 2.14 (0.23), residues: 540 sheet: 0.56 (0.22), residues: 495 loop : -0.10 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 179 TYR 0.016 0.002 TYR E 123 PHE 0.022 0.002 PHE D 356 TRP 0.011 0.002 TRP E 349 HIS 0.008 0.002 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00557 (14430) covalent geometry : angle 0.66348 (19545) SS BOND : bond 0.01062 ( 5) SS BOND : angle 2.83332 ( 10) hydrogen bonds : bond 0.09229 ( 725) hydrogen bonds : angle 4.34157 ( 2265) link_NAG-ASN : bond 0.00591 ( 10) link_NAG-ASN : angle 1.98817 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6935 (mp0) REVERT: B 227 MET cc_start: 0.8616 (ttp) cc_final: 0.8391 (ttm) REVERT: C 337 ARG cc_start: 0.8048 (mtp180) cc_final: 0.7795 (tpp-160) REVERT: D 157 ASP cc_start: 0.8818 (p0) cc_final: 0.8604 (p0) REVERT: D 337 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7784 (tpp-160) REVERT: E 152 LYS cc_start: 0.8454 (mttp) cc_final: 0.8224 (mttt) REVERT: E 337 ARG cc_start: 0.8053 (mtp180) cc_final: 0.7805 (tpp-160) outliers start: 36 outliers final: 34 residues processed: 227 average time/residue: 0.1520 time to fit residues: 48.0424 Evaluate side-chains 217 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN C 280 HIS D 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095830 restraints weight = 17101.283| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.21 r_work: 0.2936 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14445 Z= 0.130 Angle : 0.516 4.855 19585 Z= 0.277 Chirality : 0.042 0.150 2260 Planarity : 0.004 0.041 2330 Dihedral : 4.926 37.082 2570 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.47 % Allowed : 11.00 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.51 (0.21), residues: 1660 helix: 2.38 (0.24), residues: 540 sheet: 0.74 (0.22), residues: 470 loop : 0.09 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 270 TYR 0.016 0.002 TYR C 340 PHE 0.014 0.001 PHE C 356 TRP 0.011 0.001 TRP B 349 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00266 (14430) covalent geometry : angle 0.51131 (19545) SS BOND : bond 0.00648 ( 5) SS BOND : angle 1.68430 ( 10) hydrogen bonds : bond 0.06644 ( 725) hydrogen bonds : angle 3.99101 ( 2265) link_NAG-ASN : bond 0.00573 ( 10) link_NAG-ASN : angle 1.49820 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.6665 (mp10) REVERT: B 76 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6836 (mp0) REVERT: B 152 LYS cc_start: 0.8375 (mttm) cc_final: 0.8059 (mttt) REVERT: B 227 MET cc_start: 0.8508 (ttp) cc_final: 0.8261 (ttm) REVERT: C 337 ARG cc_start: 0.8050 (mtp180) cc_final: 0.7740 (tpp-160) REVERT: D 157 ASP cc_start: 0.8824 (p0) cc_final: 0.8623 (p0) REVERT: D 287 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.6584 (mp10) REVERT: D 337 ARG cc_start: 0.8004 (mtp180) cc_final: 0.7751 (tpp-160) REVERT: E 152 LYS cc_start: 0.8365 (mttp) cc_final: 0.8136 (mttt) REVERT: E 287 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.6702 (mp10) REVERT: E 337 ARG cc_start: 0.8033 (mtp180) cc_final: 0.7706 (tpp-160) outliers start: 36 outliers final: 22 residues processed: 192 average time/residue: 0.1439 time to fit residues: 39.3865 Evaluate side-chains 189 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 112 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.090349 restraints weight = 16975.886| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.31 r_work: 0.2749 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14445 Z= 0.188 Angle : 0.604 6.348 19585 Z= 0.320 Chirality : 0.044 0.163 2260 Planarity : 0.004 0.043 2330 Dihedral : 5.376 36.810 2570 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.41 % Allowed : 11.41 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.33 (0.20), residues: 1660 helix: 2.29 (0.23), residues: 540 sheet: 0.62 (0.22), residues: 465 loop : -0.06 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 179 TYR 0.014 0.002 TYR E 123 PHE 0.020 0.002 PHE D 356 TRP 0.010 0.001 TRP E 349 HIS 0.007 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00443 (14430) covalent geometry : angle 0.59763 (19545) SS BOND : bond 0.01046 ( 5) SS BOND : angle 3.21932 ( 10) hydrogen bonds : bond 0.08077 ( 725) hydrogen bonds : angle 4.06421 ( 2265) link_NAG-ASN : bond 0.00533 ( 10) link_NAG-ASN : angle 1.29699 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.6734 (mp10) REVERT: B 76 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6779 (mp0) REVERT: B 152 LYS cc_start: 0.8341 (mttm) cc_final: 0.8005 (mttt) REVERT: B 227 MET cc_start: 0.8535 (ttp) cc_final: 0.8259 (ttm) REVERT: C 337 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7681 (tpp-160) REVERT: D 157 ASP cc_start: 0.8889 (p0) cc_final: 0.8679 (p0) REVERT: D 287 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.6625 (mp10) REVERT: D 337 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7698 (tpp-160) REVERT: E 152 LYS cc_start: 0.8309 (mttp) cc_final: 0.8074 (mttt) REVERT: E 223 GLU cc_start: 0.7945 (tt0) cc_final: 0.7689 (tp30) REVERT: E 287 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.6711 (mp10) REVERT: E 337 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7674 (tpp-160) outliers start: 35 outliers final: 27 residues processed: 199 average time/residue: 0.1463 time to fit residues: 40.9077 Evaluate side-chains 203 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 130 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 332 ASN C 332 ASN D 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.092992 restraints weight = 16901.208| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.36 r_work: 0.2882 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14445 Z= 0.132 Angle : 0.522 5.074 19585 Z= 0.280 Chirality : 0.042 0.153 2260 Planarity : 0.004 0.042 2330 Dihedral : 5.008 36.750 2570 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.61 % Allowed : 11.20 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.50 (0.20), residues: 1660 helix: 2.39 (0.23), residues: 540 sheet: 0.73 (0.22), residues: 470 loop : 0.08 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 179 TYR 0.016 0.002 TYR C 340 PHE 0.015 0.001 PHE C 356 TRP 0.012 0.001 TRP B 349 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00276 (14430) covalent geometry : angle 0.51834 (19545) SS BOND : bond 0.00717 ( 5) SS BOND : angle 2.25614 ( 10) hydrogen bonds : bond 0.06737 ( 725) hydrogen bonds : angle 3.88656 ( 2265) link_NAG-ASN : bond 0.00542 ( 10) link_NAG-ASN : angle 1.09592 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8065 (tt0) cc_final: 0.7705 (tp30) REVERT: A 287 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.6635 (mp10) REVERT: B 76 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6837 (mp0) REVERT: B 152 LYS cc_start: 0.8376 (mttm) cc_final: 0.8053 (mttt) REVERT: B 227 MET cc_start: 0.8524 (ttp) cc_final: 0.8280 (ttm) REVERT: C 337 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7738 (tpp-160) REVERT: D 287 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.6548 (mp10) REVERT: D 337 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7750 (tpp-160) REVERT: E 152 LYS cc_start: 0.8326 (mttp) cc_final: 0.8100 (mttt) REVERT: E 223 GLU cc_start: 0.7935 (tt0) cc_final: 0.7652 (tp30) REVERT: E 287 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.6611 (mp10) REVERT: E 337 ARG cc_start: 0.8060 (mtp180) cc_final: 0.7677 (tpp-160) outliers start: 38 outliers final: 34 residues processed: 186 average time/residue: 0.1441 time to fit residues: 37.5859 Evaluate side-chains 192 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 33 optimal weight: 0.0060 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN C 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.091093 restraints weight = 17045.526| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.35 r_work: 0.2860 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14445 Z= 0.152 Angle : 0.549 5.742 19585 Z= 0.293 Chirality : 0.042 0.157 2260 Planarity : 0.004 0.042 2330 Dihedral : 5.159 36.434 2570 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.34 % Allowed : 11.82 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.47 (0.20), residues: 1660 helix: 2.38 (0.23), residues: 540 sheet: 0.72 (0.22), residues: 470 loop : 0.04 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 179 TYR 0.013 0.002 TYR B 340 PHE 0.017 0.002 PHE D 356 TRP 0.010 0.001 TRP B 128 HIS 0.006 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00338 (14430) covalent geometry : angle 0.54644 (19545) SS BOND : bond 0.00792 ( 5) SS BOND : angle 2.13532 ( 10) hydrogen bonds : bond 0.07271 ( 725) hydrogen bonds : angle 3.89702 ( 2265) link_NAG-ASN : bond 0.00512 ( 10) link_NAG-ASN : angle 0.98950 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8123 (tt0) cc_final: 0.7797 (tp30) REVERT: A 287 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.6644 (mp10) REVERT: B 152 LYS cc_start: 0.8386 (mttm) cc_final: 0.8010 (mttt) REVERT: B 227 MET cc_start: 0.8536 (ttp) cc_final: 0.8258 (ttm) REVERT: C 337 ARG cc_start: 0.8108 (mtp180) cc_final: 0.7726 (tpp-160) REVERT: D 287 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.6626 (mp10) REVERT: D 337 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7743 (tpp-160) REVERT: E 152 LYS cc_start: 0.8336 (mttp) cc_final: 0.8105 (mttt) REVERT: E 223 GLU cc_start: 0.7958 (tt0) cc_final: 0.7698 (tp30) REVERT: E 287 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.6700 (mp10) REVERT: E 337 ARG cc_start: 0.8097 (mtp180) cc_final: 0.7758 (tpp-160) outliers start: 34 outliers final: 31 residues processed: 182 average time/residue: 0.1448 time to fit residues: 36.7992 Evaluate side-chains 196 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 49 optimal weight: 0.0170 chunk 134 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 156 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.096837 restraints weight = 16882.475| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.36 r_work: 0.2942 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14445 Z= 0.109 Angle : 0.472 4.875 19585 Z= 0.253 Chirality : 0.041 0.147 2260 Planarity : 0.004 0.040 2330 Dihedral : 4.629 36.257 2570 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.13 % Allowed : 12.16 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.69 (0.21), residues: 1660 helix: 2.51 (0.23), residues: 540 sheet: 0.81 (0.22), residues: 470 loop : 0.26 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 270 TYR 0.017 0.001 TYR C 340 PHE 0.011 0.001 PHE A 356 TRP 0.014 0.001 TRP D 349 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00214 (14430) covalent geometry : angle 0.46981 (19545) SS BOND : bond 0.00528 ( 5) SS BOND : angle 1.68679 ( 10) hydrogen bonds : bond 0.05482 ( 725) hydrogen bonds : angle 3.67195 ( 2265) link_NAG-ASN : bond 0.00530 ( 10) link_NAG-ASN : angle 0.88702 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7992 (tt0) cc_final: 0.7671 (tp30) REVERT: A 287 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.6444 (mp10) REVERT: B 76 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6753 (mp0) REVERT: B 152 LYS cc_start: 0.8325 (mttm) cc_final: 0.7970 (mttt) REVERT: B 227 MET cc_start: 0.8489 (ttp) cc_final: 0.8240 (ttm) REVERT: C 337 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7744 (tpp-160) REVERT: D 199 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7191 (m-40) REVERT: D 287 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.6421 (mp10) REVERT: D 337 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7724 (tpp-160) REVERT: E 152 LYS cc_start: 0.8316 (mttp) cc_final: 0.8100 (mttt) REVERT: E 223 GLU cc_start: 0.7850 (tt0) cc_final: 0.7543 (tp30) REVERT: E 287 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.6479 (mp10) REVERT: E 337 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7679 (tpp-160) outliers start: 31 outliers final: 25 residues processed: 193 average time/residue: 0.1372 time to fit residues: 37.6137 Evaluate side-chains 193 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 153 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.095793 restraints weight = 16921.431| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.36 r_work: 0.2926 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14445 Z= 0.113 Angle : 0.487 4.926 19585 Z= 0.260 Chirality : 0.041 0.152 2260 Planarity : 0.004 0.040 2330 Dihedral : 4.610 35.755 2570 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.20 % Allowed : 12.99 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.83 (0.21), residues: 1660 helix: 2.59 (0.23), residues: 540 sheet: 1.02 (0.23), residues: 425 loop : 0.30 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.015 0.002 TYR C 340 PHE 0.013 0.001 PHE A 356 TRP 0.012 0.001 TRP B 349 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00228 (14430) covalent geometry : angle 0.48495 (19545) SS BOND : bond 0.00554 ( 5) SS BOND : angle 1.71381 ( 10) hydrogen bonds : bond 0.05740 ( 725) hydrogen bonds : angle 3.62813 ( 2265) link_NAG-ASN : bond 0.00476 ( 10) link_NAG-ASN : angle 0.88575 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7961 (tt0) cc_final: 0.7654 (tp30) REVERT: A 287 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.6507 (mp10) REVERT: B 76 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6785 (mp0) REVERT: B 152 LYS cc_start: 0.8310 (mttm) cc_final: 0.7963 (mttt) REVERT: B 227 MET cc_start: 0.8481 (ttp) cc_final: 0.8225 (ttm) REVERT: C 337 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7736 (tpp-160) REVERT: D 199 ASN cc_start: 0.7474 (OUTLIER) cc_final: 0.7253 (m-40) REVERT: D 287 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.6461 (mp10) REVERT: D 337 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7737 (tpp-160) REVERT: E 152 LYS cc_start: 0.8301 (mttp) cc_final: 0.8088 (mttt) REVERT: E 179 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7753 (ttp80) REVERT: E 223 GLU cc_start: 0.7824 (tt0) cc_final: 0.7524 (tp30) REVERT: E 287 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.6539 (mp10) REVERT: E 337 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7685 (tpp-160) outliers start: 32 outliers final: 26 residues processed: 190 average time/residue: 0.1326 time to fit residues: 35.8385 Evaluate side-chains 198 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 451 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 9 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.121547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.089714 restraints weight = 17049.559| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.27 r_work: 0.2727 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 14445 Z= 0.198 Angle : 0.613 6.759 19585 Z= 0.324 Chirality : 0.044 0.167 2260 Planarity : 0.004 0.042 2330 Dihedral : 5.521 35.696 2570 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.41 % Allowed : 13.13 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.41 (0.20), residues: 1660 helix: 2.32 (0.23), residues: 540 sheet: 0.70 (0.22), residues: 465 loop : 0.01 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 270 TYR 0.015 0.002 TYR B 127 PHE 0.019 0.002 PHE D 356 TRP 0.009 0.001 TRP E 128 HIS 0.007 0.002 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00474 (14430) covalent geometry : angle 0.60976 (19545) SS BOND : bond 0.00929 ( 5) SS BOND : angle 2.36532 ( 10) hydrogen bonds : bond 0.08253 ( 725) hydrogen bonds : angle 3.94212 ( 2265) link_NAG-ASN : bond 0.00435 ( 10) link_NAG-ASN : angle 0.92081 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3571.76 seconds wall clock time: 61 minutes 54.51 seconds (3714.51 seconds total)