Starting phenix.real_space_refine on Thu Sep 18 05:35:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fre_50712/09_2025/9fre_50712.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fre_50712/09_2025/9fre_50712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fre_50712/09_2025/9fre_50712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fre_50712/09_2025/9fre_50712.map" model { file = "/net/cci-nas-00/data/ceres_data/9fre_50712/09_2025/9fre_50712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fre_50712/09_2025/9fre_50712.cif" } resolution = 2.19 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= 0.002 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 75 5.16 5 Cl 1 4.86 5 C 9350 2.51 5 N 2220 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14491 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2729 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2729 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2729 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2729 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2729 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 112 Unusual residues: {'D10': 2, 'D12': 1, 'EI7': 2, 'HEX': 4, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {'D10': 2, 'D12': 1, 'EI7': 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: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 93 Unusual residues: {' CL': 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {'D10': 2, 'D12': 1, 'EI7': 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {'D10': 2, 'D12': 1, 'EI7': 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: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Time building chain proxies: 4.38, per 1000 atoms: 0.30 Number of scatterers: 14491 At special positions: 0 Unit cell: (95.495, 94.8225, 134.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 75 16.00 O 2845 8.00 N 2220 7.00 C 9350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 745.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 42.2% alpha, 39.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.541A 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: 4.101A 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: 3.817A pdb=" N PHE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.667A 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 334 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 342 through 378 removed outlier: 3.560A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 removed outlier: 4.090A 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: 3.540A 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: 4.101A 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: 3.817A pdb=" N PHE B 284 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.668A 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 334 Proline residue: B 315 - end of helix Processing helix chain 'B' and resid 342 through 378 removed outlier: 3.560A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 478 removed outlier: 4.090A 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: 3.541A 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: 4.101A 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: 3.818A pdb=" N PHE C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.668A 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 334 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 342 through 378 removed outlier: 3.559A pdb=" N TYR C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 478 removed outlier: 4.090A 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: 3.541A 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: 4.101A 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: 3.817A pdb=" N PHE D 284 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.667A 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 334 Proline residue: D 315 - end of helix Processing helix chain 'D' and resid 342 through 378 removed outlier: 3.560A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 478 removed outlier: 4.090A 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: 3.541A 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: 4.101A 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: 3.817A pdb=" N PHE E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.667A 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 334 Proline residue: E 315 - end of helix Processing helix chain 'E' and resid 342 through 378 removed outlier: 3.560A pdb=" N TYR E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 478 removed outlier: 4.090A 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: 3.615A pdb=" N TRP A 128 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 121 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU A 108 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR A 123 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLU A 106 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG A 125 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLN A 104 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYR A 127 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP A 102 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS A 129 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLY A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 removed outlier: 6.868A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE A 168 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ARG A 191 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP A 128 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 121 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU A 108 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR A 123 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLU A 106 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG A 125 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLN A 104 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYR A 127 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP A 102 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS A 129 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLY A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.586A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 210 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 276 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU A 252 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG A 278 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.750A 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: 3.615A pdb=" N TRP B 128 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR B 121 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU B 108 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR B 123 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLU B 106 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG B 125 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLN B 104 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYR B 127 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP B 102 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS B 129 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLY B 100 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.868A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE B 168 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARG B 191 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 128 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR B 121 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU B 108 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR B 123 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLU B 106 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG B 125 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLN B 104 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYR B 127 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP B 102 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS B 129 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLY B 100 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.586A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 210 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR B 276 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU B 252 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ARG B 278 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 5.751A 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: 3.615A pdb=" N TRP C 128 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR C 121 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU C 108 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR C 123 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLU C 106 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG C 125 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLN C 104 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYR C 127 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP C 102 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS C 129 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLY C 100 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.869A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE C 168 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ARG C 191 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP C 128 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR C 121 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU C 108 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR C 123 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLU C 106 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG C 125 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLN C 104 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYR C 127 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP C 102 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS C 129 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLY C 100 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.586A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 210 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR C 276 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU C 252 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ARG C 278 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 5.750A 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: 3.615A pdb=" N TRP D 128 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 121 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU D 108 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR D 123 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLU D 106 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG D 125 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLN D 104 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR D 127 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP D 102 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS D 129 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLY D 100 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 163 through 168 removed outlier: 6.868A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE D 168 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ARG D 191 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP D 128 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 121 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU D 108 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR D 123 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLU D 106 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG D 125 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLN D 104 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR D 127 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP D 102 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS D 129 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLY D 100 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.587A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN D 210 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR D 276 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU D 252 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG D 278 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 5.750A 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: 3.615A pdb=" N TRP E 128 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR E 121 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU E 108 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR E 123 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLU E 106 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ARG E 125 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLN E 104 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYR E 127 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP E 102 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS E 129 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLY E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.869A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE E 168 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ARG E 191 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP E 128 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR E 121 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU E 108 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR E 123 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLU E 106 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ARG E 125 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLN E 104 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYR E 127 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP E 102 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS E 129 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLY E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.587A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 210 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR E 276 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLU E 252 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ARG E 278 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE E 250 " --> pdb=" O ARG E 278 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2085 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: 2.36 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4156 1.34 - 1.46: 3116 1.46 - 1.58: 7083 1.58 - 1.70: 0 1.70 - 1.81: 140 Bond restraints: 14495 Sorted by residual: bond pdb=" C GLY D 233 " pdb=" N ASN D 234 " ideal model delta sigma weight residual 1.332 1.492 -0.160 1.52e-02 4.33e+03 1.11e+02 bond pdb=" C GLY C 233 " pdb=" N ASN C 234 " ideal model delta sigma weight residual 1.332 1.492 -0.160 1.52e-02 4.33e+03 1.11e+02 bond pdb=" C GLY A 233 " pdb=" N ASN A 234 " ideal model delta sigma weight residual 1.332 1.492 -0.160 1.52e-02 4.33e+03 1.11e+02 bond pdb=" C GLY B 233 " pdb=" N ASN B 234 " ideal model delta sigma weight residual 1.332 1.492 -0.160 1.52e-02 4.33e+03 1.11e+02 bond pdb=" C GLY E 233 " pdb=" N ASN E 234 " ideal model delta sigma weight residual 1.332 1.492 -0.160 1.52e-02 4.33e+03 1.10e+02 ... (remaining 14490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 18567 2.12 - 4.23: 823 4.23 - 6.35: 160 6.35 - 8.46: 25 8.46 - 10.57: 5 Bond angle restraints: 19580 Sorted by residual: angle pdb=" N GLY E 266 " pdb=" CA GLY E 266 " pdb=" C GLY E 266 " ideal model delta sigma weight residual 110.43 121.00 -10.57 1.35e+00 5.49e-01 6.14e+01 angle pdb=" N GLY D 266 " pdb=" CA GLY D 266 " pdb=" C GLY D 266 " ideal model delta sigma weight residual 110.43 120.96 -10.53 1.35e+00 5.49e-01 6.09e+01 angle pdb=" N GLY B 266 " pdb=" CA GLY B 266 " pdb=" C GLY B 266 " ideal model delta sigma weight residual 110.43 120.96 -10.53 1.35e+00 5.49e-01 6.09e+01 angle pdb=" N GLY A 266 " pdb=" CA GLY A 266 " pdb=" C GLY A 266 " ideal model delta sigma weight residual 110.43 120.96 -10.53 1.35e+00 5.49e-01 6.08e+01 angle pdb=" N GLY C 266 " pdb=" CA GLY C 266 " pdb=" C GLY C 266 " ideal model delta sigma weight residual 110.43 120.91 -10.48 1.35e+00 5.49e-01 6.02e+01 ... (remaining 19575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.35: 8545 25.35 - 50.70: 125 50.70 - 76.04: 5 76.04 - 101.39: 15 101.39 - 126.74: 5 Dihedral angle restraints: 8695 sinusoidal: 3710 harmonic: 4985 Sorted by residual: dihedral pdb=" C3 EI7 E 601 " pdb=" C4 EI7 E 601 " pdb=" N1 EI7 E 601 " pdb=" C5 EI7 E 601 " ideal model delta sinusoidal sigma weight residual 61.91 -64.83 126.74 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C3 EI7 A 601 " pdb=" C4 EI7 A 601 " pdb=" N1 EI7 A 601 " pdb=" C5 EI7 A 601 " ideal model delta sinusoidal sigma weight residual 61.91 -64.78 126.69 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C3 EI7 A 611 " pdb=" C4 EI7 A 611 " pdb=" N1 EI7 A 611 " pdb=" C5 EI7 A 611 " ideal model delta sinusoidal sigma weight residual 61.91 -64.78 126.69 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 8692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1895 0.076 - 0.153: 304 0.153 - 0.229: 6 0.229 - 0.306: 0 0.306 - 0.382: 5 Chirality restraints: 2210 Sorted by residual: chirality pdb=" CG LEU D 286 " pdb=" CB LEU D 286 " pdb=" CD1 LEU D 286 " pdb=" CD2 LEU D 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CG LEU A 286 " pdb=" CB LEU A 286 " pdb=" CD1 LEU A 286 " pdb=" CD2 LEU A 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CG LEU E 286 " pdb=" CB LEU E 286 " pdb=" CD1 LEU E 286 " pdb=" CD2 LEU E 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 2207 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 123 " -0.007 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR D 123 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR D 123 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 123 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 123 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR D 123 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR D 123 " 0.060 2.00e-02 2.50e+03 pdb=" OH TYR D 123 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 123 " 0.007 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR A 123 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR A 123 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 123 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 123 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 123 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 123 " -0.060 2.00e-02 2.50e+03 pdb=" OH TYR A 123 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 123 " 0.006 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR B 123 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 123 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 123 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 123 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR B 123 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 123 " -0.060 2.00e-02 2.50e+03 pdb=" OH TYR B 123 " 0.024 2.00e-02 2.50e+03 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 59 2.59 - 3.17: 11404 3.17 - 3.74: 20791 3.74 - 4.32: 31867 4.32 - 4.90: 52166 Nonbonded interactions: 116287 Sorted by model distance: nonbonded pdb=" ND2 ASN C 234 " pdb=" C1 NAG C 503 " model vdw 2.010 3.550 nonbonded pdb=" ND2 ASN A 234 " pdb=" C1 NAG A 603 " model vdw 2.010 3.550 nonbonded pdb=" ND2 ASN E 234 " pdb=" C1 NAG E 604 " model vdw 2.010 3.550 nonbonded pdb=" ND2 ASN B 234 " pdb=" C1 NAG B 504 " model vdw 2.010 3.550 nonbonded pdb=" ND2 ASN D 234 " pdb=" C1 NAG D 604 " model vdw 2.011 3.550 ... (remaining 116282 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 479 or resid 603 or resid 605 through 606)) selection = (chain 'B' and (resid 74 through 479 or resid 503 or resid 505 through 506)) selection = (chain 'C' and (resid 74 through 479 or resid 503 or resid 505 through 506)) selection = (chain 'D' and (resid 74 through 479 or resid 603 or resid 605 through 606)) selection = (chain 'E' and (resid 74 through 479 or resid 603 or resid 605 through 606)) } 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: 7.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 15.200 Find NCS groups from input model: 0.350 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:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.160 14495 Z= 0.340 Angle : 1.006 10.575 19580 Z= 0.519 Chirality : 0.055 0.382 2210 Planarity : 0.010 0.051 2360 Dihedral : 10.733 126.739 5455 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: 1.59 (0.20), residues: 1650 helix: 1.72 (0.22), residues: 560 sheet: 0.46 (0.23), residues: 425 loop : 1.11 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.004 ARG C 460 TYR 0.060 0.007 TYR D 123 PHE 0.044 0.007 PHE E 86 TRP 0.044 0.006 TRP C 267 HIS 0.015 0.005 HIS E 280 Details of bonding type rmsd covalent geometry : bond 0.00593 (14495) covalent geometry : angle 1.00626 (19580) hydrogen bonds : bond 0.19656 ( 700) hydrogen bonds : angle 6.27580 ( 2085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.615 Fit side-chains REVERT: A 179 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.8071 (ttp80) REVERT: A 238 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8130 (mppt) REVERT: A 337 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7290 (mmt90) REVERT: A 458 TYR cc_start: 0.8410 (m-80) cc_final: 0.8204 (m-80) REVERT: B 179 ARG cc_start: 0.8359 (mtt-85) cc_final: 0.8011 (ttp80) REVERT: C 179 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.7921 (mtm110) REVERT: C 238 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8078 (mppt) REVERT: C 337 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7311 (mmt90) REVERT: D 179 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7933 (ttp80) REVERT: D 337 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7353 (mmt90) REVERT: E 179 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7950 (ttp80) REVERT: E 337 ARG cc_start: 0.8010 (mtp180) cc_final: 0.7326 (mmt90) REVERT: E 458 TYR cc_start: 0.8436 (m-80) cc_final: 0.8229 (m-80) outliers start: 0 outliers final: 1 residues processed: 277 average time/residue: 0.8061 time to fit residues: 238.9826 Evaluate side-chains 196 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 451 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 234 ASN B 140 ASN B 234 ASN C 140 ASN C 234 ASN C 251 GLN D 140 ASN D 234 ASN E 140 ASN E 234 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113979 restraints weight = 12679.980| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.37 r_work: 0.3213 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14495 Z= 0.218 Angle : 0.670 5.525 19580 Z= 0.369 Chirality : 0.046 0.167 2210 Planarity : 0.005 0.038 2360 Dihedral : 7.018 68.364 2342 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.45 % Allowed : 10.10 % Favored : 88.45 % 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: 2.17 (0.20), residues: 1650 helix: 2.57 (0.23), residues: 535 sheet: 1.07 (0.25), residues: 390 loop : 0.92 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 313 TYR 0.018 0.002 TYR B 340 PHE 0.018 0.002 PHE C 356 TRP 0.015 0.002 TRP D 349 HIS 0.004 0.001 HIS E 126 Details of bonding type rmsd covalent geometry : bond 0.00369 (14495) covalent geometry : angle 0.66977 (19580) hydrogen bonds : bond 0.09754 ( 700) hydrogen bonds : angle 4.62218 ( 2085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.376 Fit side-chains REVERT: A 114 VAL cc_start: 0.8180 (t) cc_final: 0.7938 (m) REVERT: A 179 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.7948 (ttp80) REVERT: A 181 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: A 337 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7143 (mmt90) REVERT: B 178 LEU cc_start: 0.8708 (mt) cc_final: 0.8486 (tp) REVERT: B 179 ARG cc_start: 0.8261 (mtt-85) cc_final: 0.7924 (ttp80) REVERT: B 181 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: C 179 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.7843 (ttp80) REVERT: C 238 LYS cc_start: 0.8794 (mmtt) cc_final: 0.7859 (mppt) REVERT: C 241 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: C 337 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7152 (mmt90) REVERT: D 179 ARG cc_start: 0.8178 (mtt-85) cc_final: 0.7877 (ttp80) REVERT: D 227 MET cc_start: 0.8310 (tmt) cc_final: 0.8002 (tmm) REVERT: D 337 ARG cc_start: 0.7753 (mtp180) cc_final: 0.7171 (mmt90) REVERT: E 114 VAL cc_start: 0.8158 (t) cc_final: 0.7915 (m) REVERT: E 179 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7905 (ttp80) REVERT: E 337 ARG cc_start: 0.7731 (mtp180) cc_final: 0.7096 (mmt90) outliers start: 22 outliers final: 6 residues processed: 211 average time/residue: 0.8406 time to fit residues: 189.8822 Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 132 optimal weight: 0.4980 chunk 77 optimal weight: 0.0870 chunk 154 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS B 254 HIS C 181 GLN C 254 HIS D 254 HIS E 254 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119669 restraints weight = 12918.833| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.34 r_work: 0.3318 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14495 Z= 0.146 Angle : 0.509 4.930 19580 Z= 0.283 Chirality : 0.040 0.147 2210 Planarity : 0.004 0.038 2360 Dihedral : 6.001 39.115 2340 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.79 % Allowed : 11.75 % Favored : 87.46 % 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: 2.32 (0.21), residues: 1650 helix: 2.79 (0.23), residues: 540 sheet: 0.94 (0.22), residues: 465 loop : 1.06 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 278 TYR 0.016 0.002 TYR D 340 PHE 0.015 0.001 PHE E 356 TRP 0.012 0.001 TRP B 349 HIS 0.003 0.001 HIS E 126 Details of bonding type rmsd covalent geometry : bond 0.00231 (14495) covalent geometry : angle 0.50862 (19580) hydrogen bonds : bond 0.07047 ( 700) hydrogen bonds : angle 4.14196 ( 2085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 0.470 Fit side-chains REVERT: A 114 VAL cc_start: 0.8074 (t) cc_final: 0.7818 (m) REVERT: A 179 ARG cc_start: 0.8203 (mtt-85) cc_final: 0.7888 (ttp80) REVERT: A 337 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7159 (mmt90) REVERT: B 179 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7878 (ttp80) REVERT: B 207 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8482 (mt) REVERT: B 287 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8180 (mm110) REVERT: B 337 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7170 (mmt90) REVERT: C 179 ARG cc_start: 0.8205 (mtt-85) cc_final: 0.7784 (ttp80) REVERT: C 337 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7107 (mmt90) REVERT: D 151 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7994 (mptt) REVERT: D 179 ARG cc_start: 0.8180 (mtt-85) cc_final: 0.7865 (ttp80) REVERT: D 251 GLN cc_start: 0.8839 (pt0) cc_final: 0.8571 (pm20) REVERT: D 337 ARG cc_start: 0.7670 (mtp180) cc_final: 0.7117 (mmt90) REVERT: E 131 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7472 (mm-30) REVERT: E 179 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7867 (ttp80) REVERT: E 337 ARG cc_start: 0.7583 (mtp180) cc_final: 0.7037 (mmt90) outliers start: 12 outliers final: 2 residues processed: 207 average time/residue: 0.8134 time to fit residues: 180.1213 Evaluate side-chains 190 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 186 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 301 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 199 ASN A 234 ASN B 140 ASN B 162 HIS B 234 ASN C 162 HIS C 181 GLN C 234 ASN D 162 HIS D 234 ASN D 251 GLN E 162 HIS E 234 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107711 restraints weight = 12543.717| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.33 r_work: 0.3122 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 14495 Z= 0.364 Angle : 0.912 7.120 19580 Z= 0.512 Chirality : 0.056 0.251 2210 Planarity : 0.008 0.072 2360 Dihedral : 9.116 58.154 2340 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.64 % Allowed : 10.36 % Favored : 87.00 % 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: 1.73 (0.20), residues: 1650 helix: 2.15 (0.22), residues: 535 sheet: 1.05 (0.25), residues: 385 loop : 0.56 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 191 TYR 0.022 0.003 TYR E 219 PHE 0.014 0.003 PHE B 356 TRP 0.021 0.003 TRP B 349 HIS 0.006 0.002 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00703 (14495) covalent geometry : angle 0.91196 (19580) hydrogen bonds : bond 0.13225 ( 700) hydrogen bonds : angle 4.92025 ( 2085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.689 Fit side-chains REVERT: A 178 LEU cc_start: 0.8851 (mt) cc_final: 0.8581 (tp) REVERT: A 179 ARG cc_start: 0.8311 (mtt-85) cc_final: 0.8001 (ttp80) REVERT: A 181 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: A 337 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7250 (mmt90) REVERT: A 457 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8049 (ttmt) REVERT: B 178 LEU cc_start: 0.8920 (mt) cc_final: 0.8630 (tp) REVERT: B 179 ARG cc_start: 0.8349 (mtt-85) cc_final: 0.7946 (ttp80) REVERT: B 181 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: B 207 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8527 (mt) REVERT: B 287 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8321 (mm110) REVERT: B 337 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7238 (mmt90) REVERT: C 179 ARG cc_start: 0.8378 (mtt-85) cc_final: 0.7980 (ttp80) REVERT: C 241 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: C 244 SER cc_start: 0.8720 (p) cc_final: 0.8348 (m) REVERT: C 337 ARG cc_start: 0.7899 (mtp180) cc_final: 0.7286 (mmt90) REVERT: D 179 ARG cc_start: 0.8383 (mtt-85) cc_final: 0.7992 (ttp80) REVERT: D 243 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7917 (tt) REVERT: D 244 SER cc_start: 0.8775 (p) cc_final: 0.8390 (m) REVERT: D 337 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7251 (mmt90) REVERT: E 114 VAL cc_start: 0.8316 (t) cc_final: 0.8090 (m) REVERT: E 179 ARG cc_start: 0.8307 (mtt-85) cc_final: 0.7981 (ttp80) REVERT: E 243 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.8035 (tt) REVERT: E 337 ARG cc_start: 0.7834 (mtp180) cc_final: 0.7194 (mmt90) outliers start: 40 outliers final: 15 residues processed: 217 average time/residue: 0.8984 time to fit residues: 208.4144 Evaluate side-chains 214 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN C 140 ASN C 181 GLN D 140 ASN D 181 GLN E 140 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114467 restraints weight = 12908.563| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.37 r_work: 0.3223 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14495 Z= 0.190 Angle : 0.593 4.936 19580 Z= 0.332 Chirality : 0.042 0.150 2210 Planarity : 0.005 0.047 2360 Dihedral : 8.065 58.733 2340 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.58 % Allowed : 12.34 % Favored : 86.07 % 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: 1.65 (0.21), residues: 1650 helix: 2.15 (0.23), residues: 570 sheet: 0.75 (0.24), residues: 415 loop : 0.54 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 89 TYR 0.017 0.002 TYR D 340 PHE 0.018 0.002 PHE C 356 TRP 0.017 0.002 TRP C 349 HIS 0.004 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00303 (14495) covalent geometry : angle 0.59275 (19580) hydrogen bonds : bond 0.08934 ( 700) hydrogen bonds : angle 4.37762 ( 2085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.654 Fit side-chains REVERT: A 179 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7858 (ttp80) REVERT: A 337 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7132 (mmt90) REVERT: B 178 LEU cc_start: 0.8659 (mt) cc_final: 0.8437 (tp) REVERT: B 179 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7812 (ttp80) REVERT: B 207 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8485 (mt) REVERT: B 287 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8175 (mm110) REVERT: B 337 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7117 (mmt90) REVERT: C 179 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.7810 (ttp80) REVERT: C 337 ARG cc_start: 0.7783 (mtp180) cc_final: 0.7188 (mmt90) REVERT: D 179 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7858 (ttp80) REVERT: D 251 GLN cc_start: 0.8867 (pt0) cc_final: 0.8562 (pm20) REVERT: D 337 ARG cc_start: 0.7633 (mtp180) cc_final: 0.7069 (mmt90) REVERT: E 114 VAL cc_start: 0.8108 (t) cc_final: 0.7877 (m) REVERT: E 179 ARG cc_start: 0.8226 (mtt-85) cc_final: 0.7852 (ttp80) REVERT: E 337 ARG cc_start: 0.7660 (mtp180) cc_final: 0.7041 (mmt90) outliers start: 24 outliers final: 10 residues processed: 209 average time/residue: 0.8618 time to fit residues: 192.9950 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115364 restraints weight = 12832.019| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.36 r_work: 0.3238 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14495 Z= 0.177 Angle : 0.567 4.911 19580 Z= 0.318 Chirality : 0.042 0.151 2210 Planarity : 0.004 0.044 2360 Dihedral : 7.483 57.350 2340 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.32 % Allowed : 13.00 % Favored : 85.68 % 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: 1.76 (0.21), residues: 1650 helix: 2.27 (0.23), residues: 570 sheet: 0.77 (0.24), residues: 415 loop : 0.58 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 89 TYR 0.016 0.002 TYR D 340 PHE 0.016 0.001 PHE B 356 TRP 0.015 0.001 TRP C 349 HIS 0.004 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00283 (14495) covalent geometry : angle 0.56733 (19580) hydrogen bonds : bond 0.08367 ( 700) hydrogen bonds : angle 4.24047 ( 2085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.597 Fit side-chains REVERT: A 179 ARG cc_start: 0.8237 (mtt-85) cc_final: 0.7858 (ttp80) REVERT: A 337 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7123 (mmt90) REVERT: B 178 LEU cc_start: 0.8641 (mt) cc_final: 0.8411 (tp) REVERT: B 179 ARG cc_start: 0.8226 (mtt-85) cc_final: 0.7817 (ttp80) REVERT: B 287 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8170 (mm110) REVERT: B 337 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7139 (mmt90) REVERT: C 179 ARG cc_start: 0.8254 (mtt-85) cc_final: 0.7819 (ttp80) REVERT: C 337 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7160 (mmt90) REVERT: D 179 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7849 (ttp80) REVERT: D 251 GLN cc_start: 0.8854 (pt0) cc_final: 0.8565 (pm20) REVERT: D 337 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7077 (mmt90) REVERT: E 114 VAL cc_start: 0.8111 (t) cc_final: 0.7885 (m) REVERT: E 131 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7337 (mm-30) REVERT: E 179 ARG cc_start: 0.8207 (mtt-85) cc_final: 0.7834 (ttp80) REVERT: E 337 ARG cc_start: 0.7656 (mtp180) cc_final: 0.7018 (mmt90) outliers start: 20 outliers final: 11 residues processed: 209 average time/residue: 0.8600 time to fit residues: 192.7662 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 43 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108417 restraints weight = 12542.825| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.33 r_work: 0.3154 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14495 Z= 0.268 Angle : 0.740 5.969 19580 Z= 0.416 Chirality : 0.047 0.158 2210 Planarity : 0.006 0.055 2360 Dihedral : 8.411 59.174 2340 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.24 % Allowed : 12.48 % Favored : 85.28 % 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: 1.77 (0.20), residues: 1650 helix: 2.36 (0.23), residues: 540 sheet: 0.94 (0.25), residues: 385 loop : 0.51 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.017 0.002 TYR B 219 PHE 0.017 0.002 PHE B 356 TRP 0.016 0.002 TRP D 349 HIS 0.005 0.001 HIS E 126 Details of bonding type rmsd covalent geometry : bond 0.00473 (14495) covalent geometry : angle 0.73955 (19580) hydrogen bonds : bond 0.11326 ( 700) hydrogen bonds : angle 4.66736 ( 2085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.572 Fit side-chains REVERT: A 178 LEU cc_start: 0.8783 (mt) cc_final: 0.8539 (tp) REVERT: A 179 ARG cc_start: 0.8319 (mtt-85) cc_final: 0.7956 (ttp80) REVERT: A 181 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: A 337 ARG cc_start: 0.7858 (mtp180) cc_final: 0.7197 (mmt90) REVERT: B 178 LEU cc_start: 0.8853 (mt) cc_final: 0.8582 (tp) REVERT: B 179 ARG cc_start: 0.8307 (mtt-85) cc_final: 0.7913 (ttp80) REVERT: B 181 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: B 243 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.8014 (tt) REVERT: B 287 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8257 (mm110) REVERT: B 337 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7221 (mmt90) REVERT: C 179 ARG cc_start: 0.8320 (mtt-85) cc_final: 0.7938 (ttp80) REVERT: C 241 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6915 (pm20) REVERT: C 337 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7287 (mmt90) REVERT: D 179 ARG cc_start: 0.8304 (mtt-85) cc_final: 0.7940 (ttp80) REVERT: D 251 GLN cc_start: 0.8922 (pt0) cc_final: 0.8582 (pm20) REVERT: D 337 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7231 (mmt90) REVERT: E 114 VAL cc_start: 0.8307 (t) cc_final: 0.8093 (m) REVERT: E 179 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.7946 (ttp80) REVERT: E 337 ARG cc_start: 0.7819 (mtp180) cc_final: 0.7173 (mmt90) outliers start: 34 outliers final: 17 residues processed: 213 average time/residue: 0.8707 time to fit residues: 198.5079 Evaluate side-chains 215 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109726 restraints weight = 12567.582| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.33 r_work: 0.3175 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14495 Z= 0.238 Angle : 0.687 5.289 19580 Z= 0.386 Chirality : 0.045 0.154 2210 Planarity : 0.006 0.054 2360 Dihedral : 8.385 59.966 2340 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.24 % Allowed : 12.54 % Favored : 85.21 % 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: 1.75 (0.20), residues: 1650 helix: 2.39 (0.23), residues: 540 sheet: 0.81 (0.25), residues: 390 loop : 0.51 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 89 TYR 0.017 0.002 TYR D 340 PHE 0.018 0.002 PHE D 356 TRP 0.016 0.002 TRP A 349 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00408 (14495) covalent geometry : angle 0.68703 (19580) hydrogen bonds : bond 0.10474 ( 700) hydrogen bonds : angle 4.57479 ( 2085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.465 Fit side-chains REVERT: A 179 ARG cc_start: 0.8304 (mtt-85) cc_final: 0.7927 (ttp80) REVERT: A 181 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: A 337 ARG cc_start: 0.7871 (mtp180) cc_final: 0.7153 (mmt90) REVERT: B 178 LEU cc_start: 0.8809 (mt) cc_final: 0.8554 (tp) REVERT: B 179 ARG cc_start: 0.8311 (mtt-85) cc_final: 0.7895 (ttp80) REVERT: B 181 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: B 287 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8241 (mm110) REVERT: B 337 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7229 (mmt90) REVERT: C 179 ARG cc_start: 0.8306 (mtt-85) cc_final: 0.7910 (ttp80) REVERT: C 241 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: C 337 ARG cc_start: 0.7858 (mtp180) cc_final: 0.7249 (mmt90) REVERT: D 179 ARG cc_start: 0.8285 (mtt-85) cc_final: 0.7934 (ttp80) REVERT: D 207 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8583 (mt) REVERT: D 251 GLN cc_start: 0.8926 (pt0) cc_final: 0.8620 (pm20) REVERT: D 337 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7236 (mmt90) REVERT: E 114 VAL cc_start: 0.8249 (t) cc_final: 0.8031 (m) REVERT: E 179 ARG cc_start: 0.8271 (mtt-85) cc_final: 0.7930 (ttp80) REVERT: E 337 ARG cc_start: 0.7824 (mtp180) cc_final: 0.7149 (mmt90) outliers start: 34 outliers final: 22 residues processed: 214 average time/residue: 0.8725 time to fit residues: 200.2063 Evaluate side-chains 219 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111929 restraints weight = 12696.257| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.33 r_work: 0.3208 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14495 Z= 0.202 Angle : 0.617 4.932 19580 Z= 0.346 Chirality : 0.043 0.152 2210 Planarity : 0.005 0.046 2360 Dihedral : 7.896 58.356 2340 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.11 % Allowed : 12.61 % Favored : 85.28 % 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: 1.85 (0.20), residues: 1650 helix: 2.53 (0.23), residues: 540 sheet: 0.81 (0.23), residues: 440 loop : 0.54 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 242 TYR 0.017 0.002 TYR B 340 PHE 0.018 0.002 PHE C 356 TRP 0.018 0.002 TRP A 349 HIS 0.004 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00331 (14495) covalent geometry : angle 0.61699 (19580) hydrogen bonds : bond 0.09290 ( 700) hydrogen bonds : angle 4.39858 ( 2085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.654 Fit side-chains REVERT: A 179 ARG cc_start: 0.8277 (mtt-85) cc_final: 0.7909 (ttp80) REVERT: A 337 ARG cc_start: 0.7835 (mtp180) cc_final: 0.7145 (mmt90) REVERT: B 178 LEU cc_start: 0.8743 (mt) cc_final: 0.8505 (tp) REVERT: B 179 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.7875 (ttp80) REVERT: B 181 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: B 287 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8187 (mm110) REVERT: B 337 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7189 (mmt90) REVERT: C 179 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.7868 (ttp80) REVERT: C 241 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: C 337 ARG cc_start: 0.7838 (mtp180) cc_final: 0.7203 (mmt90) REVERT: D 179 ARG cc_start: 0.8280 (mtt-85) cc_final: 0.7906 (ttp80) REVERT: D 207 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8550 (mt) REVERT: D 251 GLN cc_start: 0.8867 (pt0) cc_final: 0.8531 (pm20) REVERT: D 337 ARG cc_start: 0.7781 (mtp180) cc_final: 0.7174 (mmt90) REVERT: E 114 VAL cc_start: 0.8204 (t) cc_final: 0.7988 (m) REVERT: E 131 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7342 (mm-30) REVERT: E 179 ARG cc_start: 0.8253 (mtt-85) cc_final: 0.7889 (ttp80) REVERT: E 337 ARG cc_start: 0.7788 (mtp180) cc_final: 0.7105 (mmt90) outliers start: 32 outliers final: 19 residues processed: 208 average time/residue: 0.8820 time to fit residues: 196.5746 Evaluate side-chains 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 48 optimal weight: 0.0060 chunk 72 optimal weight: 9.9990 chunk 133 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 107 optimal weight: 0.0050 overall best weight: 0.6212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119219 restraints weight = 12977.095| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.36 r_work: 0.3290 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14495 Z= 0.150 Angle : 0.522 5.603 19580 Z= 0.290 Chirality : 0.041 0.142 2210 Planarity : 0.004 0.044 2360 Dihedral : 6.972 55.130 2340 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.99 % Allowed : 13.86 % Favored : 85.15 % 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: 2.01 (0.21), residues: 1650 helix: 2.78 (0.23), residues: 540 sheet: 0.75 (0.23), residues: 470 loop : 0.64 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 242 TYR 0.017 0.002 TYR D 340 PHE 0.017 0.001 PHE E 356 TRP 0.021 0.001 TRP C 349 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00241 (14495) covalent geometry : angle 0.52151 (19580) hydrogen bonds : bond 0.07070 ( 700) hydrogen bonds : angle 4.01351 ( 2085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.599 Fit side-chains REVERT: A 179 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.7810 (ttp80) REVERT: A 337 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7081 (mmt90) REVERT: B 178 LEU cc_start: 0.8583 (mt) cc_final: 0.8370 (tp) REVERT: B 179 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7780 (ttp80) REVERT: B 287 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8137 (mm110) REVERT: B 337 ARG cc_start: 0.7881 (mtp180) cc_final: 0.7084 (mmt90) REVERT: C 179 ARG cc_start: 0.8231 (mtt-85) cc_final: 0.7745 (ttp80) REVERT: C 211 THR cc_start: 0.8518 (m) cc_final: 0.8305 (p) REVERT: C 241 GLU cc_start: 0.7203 (pm20) cc_final: 0.6904 (pm20) REVERT: C 337 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7095 (mmt90) REVERT: D 179 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7808 (ttp80) REVERT: D 207 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8498 (mt) REVERT: D 337 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7058 (mmt90) REVERT: E 114 VAL cc_start: 0.7969 (t) cc_final: 0.7732 (m) REVERT: E 179 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7730 (ttp80) REVERT: E 337 ARG cc_start: 0.7681 (mtp180) cc_final: 0.7008 (mmt90) outliers start: 15 outliers final: 9 residues processed: 200 average time/residue: 0.8764 time to fit residues: 188.0537 Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 11 optimal weight: 0.2980 chunk 137 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN D 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.146197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114683 restraints weight = 12778.740| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.36 r_work: 0.3248 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14495 Z= 0.170 Angle : 0.557 5.455 19580 Z= 0.311 Chirality : 0.041 0.149 2210 Planarity : 0.004 0.044 2360 Dihedral : 6.832 57.593 2340 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.86 % Allowed : 14.19 % Favored : 84.95 % 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: 2.06 (0.21), residues: 1650 helix: 2.75 (0.23), residues: 540 sheet: 0.91 (0.23), residues: 440 loop : 0.64 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 313 TYR 0.016 0.002 TYR B 340 PHE 0.016 0.001 PHE C 356 TRP 0.017 0.001 TRP B 349 HIS 0.003 0.001 HIS E 126 Details of bonding type rmsd covalent geometry : bond 0.00274 (14495) covalent geometry : angle 0.55738 (19580) hydrogen bonds : bond 0.07957 ( 700) hydrogen bonds : angle 4.12313 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6735.13 seconds wall clock time: 115 minutes 19.29 seconds (6919.29 seconds total)