Starting phenix.real_space_refine on Sat Mar 16 10:47:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq6_17106/03_2024/8oq6_17106_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq6_17106/03_2024/8oq6_17106.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq6_17106/03_2024/8oq6_17106_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq6_17106/03_2024/8oq6_17106_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq6_17106/03_2024/8oq6_17106_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq6_17106/03_2024/8oq6_17106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq6_17106/03_2024/8oq6_17106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq6_17106/03_2024/8oq6_17106_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq6_17106/03_2024/8oq6_17106_updated.pdb" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 S 75 5.16 5 Cl 2 4.86 5 C 9485 2.51 5 N 2240 2.21 5 O 2665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14477 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2750 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2750 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2750 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2750 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2750 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 132 Unusual residues: {' CL': 2, '7P9': 2, 'D10': 3, 'NAG': 2, 'OCT': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 130 Unusual residues: {'7P9': 2, 'D10': 3, 'NAG': 2, 'OCT': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 130 Unusual residues: {'7P9': 2, 'D10': 3, 'NAG': 2, 'OCT': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 130 Unusual residues: {'7P9': 2, 'D10': 3, 'NAG': 2, 'OCT': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 130 Unusual residues: {'7P9': 2, 'D10': 3, 'NAG': 2, 'OCT': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 7.87, per 1000 atoms: 0.54 Number of scatterers: 14477 At special positions: 0 Unit cell: (93.6945, 94.359, 136.887, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 75 16.00 P 10 15.00 O 2665 8.00 N 2240 7.00 C 9485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM14178 O5 NAG D 503 .*. O " rejected from bonding due to valence issues. Atom "HETATM13776 O5 NAG A 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14308 O5 NAG E 503 .*. O " rejected from bonding due to valence issues. Atom "HETATM14048 O5 NAG C 503 .*. O " rejected from bonding due to valence issues. Atom "HETATM13918 O5 NAG B 503 .*. O " rejected from bonding due to valence issues. Atom "HETATM13762 O5 NAG A 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM13904 O5 NAG B 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14034 O5 NAG C 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14164 O5 NAG D 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14294 O5 NAG E 502 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 140 " " NAG A 502 " - " ASN A 234 " " NAG B 502 " - " ASN B 140 " " NAG B 503 " - " ASN B 234 " " NAG C 502 " - " ASN C 140 " " NAG C 503 " - " ASN C 234 " " NAG D 502 " - " ASN D 140 " " NAG D 503 " - " ASN D 234 " " NAG E 502 " - " ASN E 140 " " NAG E 503 " - " ASN E 234 " Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 2.5 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 30 sheets defined 37.5% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 147 through 152 removed outlier: 4.026A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 281 through 304 removed outlier: 4.263A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.553A pdb=" N TRP A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N PHE A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 334 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 343 through 379 removed outlier: 3.789A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 477 removed outlier: 3.930A 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 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 147 through 152 removed outlier: 4.026A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 281 through 304 removed outlier: 4.263A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.554A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP B 304 " --> pdb=" O TRP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 334 Proline residue: B 315 - end of helix Processing helix chain 'B' and resid 343 through 379 removed outlier: 3.789A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 477 removed outlier: 3.929A 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 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 147 through 152 removed outlier: 4.026A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 281 through 304 removed outlier: 4.263A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.554A pdb=" N TRP C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N PHE C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP C 304 " --> pdb=" O TRP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 334 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 343 through 379 removed outlier: 3.789A pdb=" N TYR C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 477 removed outlier: 3.930A 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 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'D' and resid 147 through 152 removed outlier: 4.025A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 281 through 304 removed outlier: 4.263A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.553A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N PHE D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP D 304 " --> pdb=" O TRP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 334 Proline residue: D 315 - end of helix Processing helix chain 'D' and resid 343 through 379 removed outlier: 3.788A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 477 removed outlier: 3.929A 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 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 147 through 152 removed outlier: 4.025A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 236 Processing helix chain 'E' and resid 281 through 304 removed outlier: 4.263A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.554A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL E 301 " --> pdb=" O MET E 297 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N PHE E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP E 304 " --> pdb=" O TRP E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 334 Proline residue: E 315 - end of helix Processing helix chain 'E' and resid 343 through 379 removed outlier: 3.790A pdb=" N TYR E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 477 removed outlier: 3.929A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 226 through 230 removed outlier: 6.370A pdb=" N ILE A 97 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR A 229 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL A 99 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 105 Processing sheet with id= C, first strand: chain 'A' and resid 110 through 112 removed outlier: 3.957A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.653A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 254 through 262 Processing sheet with id= F, first strand: chain 'A' and resid 163 through 168 removed outlier: 6.941A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.476A 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) Processing sheet with id= G, first strand: chain 'B' and resid 226 through 230 removed outlier: 6.370A pdb=" N ILE B 97 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR B 229 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 99 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= I, first strand: chain 'B' and resid 110 through 112 removed outlier: 3.957A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.653A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 254 through 262 Processing sheet with id= L, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.941A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.476A 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) Processing sheet with id= M, first strand: chain 'C' and resid 226 through 230 removed outlier: 6.370A pdb=" N ILE C 97 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR C 229 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 99 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= O, first strand: chain 'C' and resid 110 through 112 removed outlier: 3.957A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.653A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 254 through 262 Processing sheet with id= R, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.942A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 226 through 230 removed outlier: 6.370A pdb=" N ILE D 97 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR D 229 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL D 99 " --> pdb=" O TYR D 229 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 103 through 105 Processing sheet with id= U, first strand: chain 'D' and resid 110 through 112 removed outlier: 3.957A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.653A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 254 through 262 Processing sheet with id= X, first strand: chain 'D' and resid 163 through 168 removed outlier: 6.941A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.476A 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) Processing sheet with id= Y, first strand: chain 'E' and resid 226 through 230 removed outlier: 6.371A pdb=" N ILE E 97 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR E 229 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL E 99 " --> pdb=" O TYR E 229 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 103 through 105 Processing sheet with id= AA, first strand: chain 'E' and resid 110 through 112 removed outlier: 3.957A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.653A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 254 through 262 Processing sheet with id= AD, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.941A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1935 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: 4.77 Time building geometry restraints manager: 5.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2120 1.31 - 1.44: 4365 1.44 - 1.56: 8095 1.56 - 1.69: 20 1.69 - 1.81: 140 Bond restraints: 14740 Sorted by residual: bond pdb=" O3 7P9 B 507 " pdb=" P1 7P9 B 507 " ideal model delta sigma weight residual 1.516 1.647 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" O3 7P9 E 508 " pdb=" P1 7P9 E 508 " ideal model delta sigma weight residual 1.516 1.647 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" O3 7P9 E 507 " pdb=" P1 7P9 E 507 " ideal model delta sigma weight residual 1.516 1.647 -0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" O3 7P9 A 506 " pdb=" P1 7P9 A 506 " ideal model delta sigma weight residual 1.516 1.647 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" O3 7P9 D 508 " pdb=" P1 7P9 D 508 " ideal model delta sigma weight residual 1.516 1.647 -0.131 2.00e-02 2.50e+03 4.29e+01 ... (remaining 14735 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.22: 458 107.22 - 113.92: 8566 113.92 - 120.63: 5708 120.63 - 127.33: 5003 127.33 - 134.04: 170 Bond angle restraints: 19905 Sorted by residual: angle pdb=" CA TYR C 362 " pdb=" CB TYR C 362 " pdb=" CG TYR C 362 " ideal model delta sigma weight residual 113.90 110.72 3.18 1.80e+00 3.09e-01 3.12e+00 angle pdb=" CA TYR B 362 " pdb=" CB TYR B 362 " pdb=" CG TYR B 362 " ideal model delta sigma weight residual 113.90 110.75 3.15 1.80e+00 3.09e-01 3.06e+00 angle pdb=" CA TYR A 362 " pdb=" CB TYR A 362 " pdb=" CG TYR A 362 " ideal model delta sigma weight residual 113.90 110.77 3.13 1.80e+00 3.09e-01 3.03e+00 angle pdb=" CA TYR D 362 " pdb=" CB TYR D 362 " pdb=" CG TYR D 362 " ideal model delta sigma weight residual 113.90 110.77 3.13 1.80e+00 3.09e-01 3.03e+00 angle pdb=" CA TYR E 362 " pdb=" CB TYR E 362 " pdb=" CG TYR E 362 " ideal model delta sigma weight residual 113.90 110.77 3.13 1.80e+00 3.09e-01 3.02e+00 ... (remaining 19900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.47: 8585 25.47 - 50.94: 205 50.94 - 76.41: 20 76.41 - 101.88: 0 101.88 - 127.35: 5 Dihedral angle restraints: 8815 sinusoidal: 3800 harmonic: 5015 Sorted by residual: dihedral pdb=" C11 7P9 B 507 " pdb=" C18 7P9 B 507 " pdb=" C19 7P9 B 507 " pdb=" C17 7P9 B 507 " ideal model delta sinusoidal sigma weight residual 196.17 68.82 127.35 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" C11 7P9 D 507 " pdb=" C18 7P9 D 507 " pdb=" C19 7P9 D 507 " pdb=" C17 7P9 D 507 " ideal model delta sinusoidal sigma weight residual 196.17 68.84 127.33 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" C11 7P9 A 506 " pdb=" C18 7P9 A 506 " pdb=" C19 7P9 A 506 " pdb=" C17 7P9 A 506 " ideal model delta sinusoidal sigma weight residual 196.17 68.86 127.31 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 8812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.271: 2240 0.271 - 0.542: 0 0.542 - 0.813: 0 0.813 - 1.084: 0 1.084 - 1.355: 5 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C1 NAG E 503 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 503 " pdb=" O5 NAG E 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.04 -1.36 2.00e-01 2.50e+01 4.59e+01 chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-01 2.50e+01 4.58e+01 chirality pdb=" C1 NAG B 503 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B 503 " pdb=" O5 NAG B 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-01 2.50e+01 4.58e+01 ... (remaining 2242 not shown) Planarity restraints: 2405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " 0.048 2.00e-02 2.50e+03 1.60e-01 3.19e+02 pdb=" CG ASN C 234 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " 0.100 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.283 2.00e-02 2.50e+03 pdb=" C1 NAG C 503 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.048 2.00e-02 2.50e+03 1.60e-01 3.18e+02 pdb=" CG ASN D 234 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " 0.100 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.283 2.00e-02 2.50e+03 pdb=" C1 NAG D 503 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.048 2.00e-02 2.50e+03 1.60e-01 3.18e+02 pdb=" CG ASN A 234 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.100 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.283 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.181 2.00e-02 2.50e+03 ... (remaining 2402 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3014 2.79 - 3.32: 12377 3.32 - 3.84: 22382 3.84 - 4.37: 26769 4.37 - 4.90: 48890 Nonbonded interactions: 113432 Sorted by model distance: nonbonded pdb=" OG SER D 166 " pdb=" O HOH D 601 " model vdw 2.259 2.440 nonbonded pdb=" OD1 ASP E 117 " pdb=" O HOH E 601 " model vdw 2.278 2.440 nonbonded pdb=" OD1 ASP B 117 " pdb=" O HOH B 601 " model vdw 2.278 2.440 nonbonded pdb=" OD1 ASP D 117 " pdb=" O HOH D 602 " model vdw 2.279 2.440 nonbonded pdb=" OD1 ASP A 117 " pdb=" O HOH A 601 " model vdw 2.279 2.440 ... (remaining 113427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 479 or resid 502 or resid 505 or resid 507)) selection = (chain 'B' and (resid 74 through 479 or resid 502 or resid 505 or resid 507)) selection = (chain 'C' and (resid 74 through 479 or resid 502 or resid 505 or resid 507)) selection = (chain 'D' and (resid 74 through 479 or resid 502 or resid 505 or resid 507)) selection = (chain 'E' and (resid 74 through 479 or resid 502 or resid 505 or resid 507)) } 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: 0.010 Normalize map: mean=0, sd=1: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.820 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 41.030 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 : 0.004 0.131 14740 Z= 0.287 Angle : 0.579 5.149 19905 Z= 0.266 Chirality : 0.075 1.355 2245 Planarity : 0.003 0.026 2395 Dihedral : 10.855 127.351 5540 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.21), residues: 1660 helix: 2.38 (0.23), residues: 570 sheet: 1.96 (0.25), residues: 440 loop : 1.26 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 349 HIS 0.004 0.001 HIS D 126 PHE 0.010 0.001 PHE E 290 TYR 0.012 0.002 TYR D 340 ARG 0.004 0.000 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.695 Fit side-chains REVERT: A 88 MET cc_start: 0.8016 (ptp) cc_final: 0.7794 (ptm) REVERT: A 148 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7795 (mtm-85) REVERT: A 157 ASP cc_start: 0.8533 (p0) cc_final: 0.8052 (p0) REVERT: A 238 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7542 (mtmm) REVERT: B 88 MET cc_start: 0.8111 (ptp) cc_final: 0.7887 (ptm) REVERT: B 238 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7197 (mtmm) REVERT: B 335 MET cc_start: 0.7180 (mtm) cc_final: 0.6948 (mmt) REVERT: C 129 LYS cc_start: 0.8721 (tttt) cc_final: 0.8447 (ttmt) REVERT: C 157 ASP cc_start: 0.8463 (p0) cc_final: 0.7844 (p0) REVERT: C 164 LYS cc_start: 0.8856 (mttt) cc_final: 0.8627 (mttm) REVERT: C 238 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7398 (mtmm) REVERT: C 247 GLN cc_start: 0.7964 (pm20) cc_final: 0.7759 (pt0) REVERT: C 335 MET cc_start: 0.6953 (mtm) cc_final: 0.6715 (mmt) REVERT: D 129 LYS cc_start: 0.8686 (tttt) cc_final: 0.8422 (ttmt) REVERT: D 148 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7842 (mtm-85) REVERT: D 157 ASP cc_start: 0.8418 (p0) cc_final: 0.7829 (p0) REVERT: D 238 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7322 (mtmm) REVERT: D 247 GLN cc_start: 0.7976 (pm20) cc_final: 0.7724 (pt0) REVERT: D 361 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8505 (tm-30) REVERT: E 129 LYS cc_start: 0.8598 (tttt) cc_final: 0.8386 (ttmt) REVERT: E 157 ASP cc_start: 0.8476 (p0) cc_final: 0.8025 (p0) REVERT: E 238 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7440 (mtmm) REVERT: E 361 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8521 (tm-30) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.3634 time to fit residues: 155.1503 Evaluate side-chains 240 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 50 optimal weight: 0.0050 chunk 78 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN B 251 GLN C 251 GLN C 287 GLN D 251 GLN E 251 GLN E 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14740 Z= 0.264 Angle : 0.552 5.772 19905 Z= 0.292 Chirality : 0.044 0.165 2245 Planarity : 0.004 0.029 2395 Dihedral : 11.434 112.589 2390 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.25 % Allowed : 7.02 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.22), residues: 1660 helix: 2.19 (0.23), residues: 575 sheet: 1.70 (0.26), residues: 440 loop : 1.13 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 349 HIS 0.005 0.002 HIS B 126 PHE 0.012 0.002 PHE D 159 TYR 0.025 0.002 TYR E 272 ARG 0.004 0.000 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 248 time to evaluate : 1.734 Fit side-chains REVERT: B 88 MET cc_start: 0.8144 (ptp) cc_final: 0.7930 (ptm) REVERT: C 129 LYS cc_start: 0.8706 (tttt) cc_final: 0.8456 (ttmt) outliers start: 19 outliers final: 17 residues processed: 264 average time/residue: 0.3401 time to fit residues: 122.9912 Evaluate side-chains 248 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 231 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14740 Z= 0.158 Angle : 0.454 5.214 19905 Z= 0.243 Chirality : 0.041 0.151 2245 Planarity : 0.003 0.028 2395 Dihedral : 10.394 102.009 2390 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.90 % Allowed : 7.28 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.22), residues: 1660 helix: 2.23 (0.23), residues: 580 sheet: 1.51 (0.25), residues: 440 loop : 1.22 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 349 HIS 0.004 0.001 HIS A 126 PHE 0.009 0.001 PHE D 159 TYR 0.022 0.002 TYR B 272 ARG 0.003 0.000 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 246 time to evaluate : 1.771 Fit side-chains REVERT: B 157 ASP cc_start: 0.8327 (p0) cc_final: 0.8023 (p0) REVERT: B 197 MET cc_start: 0.7536 (ptm) cc_final: 0.7335 (ptt) REVERT: B 278 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.7369 (ttm170) REVERT: C 278 ARG cc_start: 0.7580 (mtm-85) cc_final: 0.7378 (ttm170) REVERT: D 157 ASP cc_start: 0.8347 (p0) cc_final: 0.8068 (p0) outliers start: 29 outliers final: 21 residues processed: 272 average time/residue: 0.3242 time to fit residues: 121.0303 Evaluate side-chains 255 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 234 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14740 Z= 0.216 Angle : 0.496 5.254 19905 Z= 0.265 Chirality : 0.042 0.164 2245 Planarity : 0.004 0.030 2395 Dihedral : 9.612 79.033 2390 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.56 % Allowed : 7.74 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.22), residues: 1660 helix: 2.16 (0.23), residues: 580 sheet: 1.31 (0.25), residues: 440 loop : 1.13 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 349 HIS 0.005 0.001 HIS A 254 PHE 0.011 0.001 PHE A 159 TYR 0.022 0.002 TYR A 272 ARG 0.003 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 251 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 157 ASP cc_start: 0.8446 (p0) cc_final: 0.8189 (p0) REVERT: B 185 LYS cc_start: 0.8564 (mttt) cc_final: 0.8229 (mttp) REVERT: B 278 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.7361 (ttm170) REVERT: C 106 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: D 157 ASP cc_start: 0.8435 (p0) cc_final: 0.7803 (p0) REVERT: D 278 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.7206 (mtt90) outliers start: 39 outliers final: 34 residues processed: 284 average time/residue: 0.3167 time to fit residues: 122.7450 Evaluate side-chains 281 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 246 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 287 GLN E 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 14740 Z= 0.460 Angle : 0.656 7.486 19905 Z= 0.346 Chirality : 0.048 0.176 2245 Planarity : 0.005 0.038 2395 Dihedral : 10.598 62.778 2390 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.95 % Allowed : 9.38 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1660 helix: 1.75 (0.23), residues: 575 sheet: 0.47 (0.23), residues: 515 loop : 0.84 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 349 HIS 0.007 0.002 HIS B 254 PHE 0.015 0.002 PHE B 159 TYR 0.026 0.002 TYR A 272 ARG 0.006 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 248 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8737 (t80) cc_final: 0.8406 (t80) REVERT: A 111 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8628 (mt) REVERT: A 278 ARG cc_start: 0.7564 (mtt90) cc_final: 0.7045 (mtt90) REVERT: B 278 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7387 (ttm170) REVERT: C 106 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7423 (mt-10) outliers start: 45 outliers final: 32 residues processed: 282 average time/residue: 0.3090 time to fit residues: 120.4428 Evaluate side-chains 278 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN D 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14740 Z= 0.174 Angle : 0.466 5.215 19905 Z= 0.252 Chirality : 0.041 0.154 2245 Planarity : 0.004 0.032 2395 Dihedral : 9.800 59.204 2390 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.77 % Allowed : 10.69 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.22), residues: 1660 helix: 2.05 (0.23), residues: 580 sheet: 0.99 (0.25), residues: 440 loop : 0.91 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 349 HIS 0.004 0.001 HIS C 254 PHE 0.010 0.001 PHE E 356 TYR 0.020 0.002 TYR A 272 ARG 0.004 0.000 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 249 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ARG cc_start: 0.7466 (mtt90) cc_final: 0.6954 (mtt90) REVERT: B 185 LYS cc_start: 0.8627 (mttt) cc_final: 0.8288 (mttp) REVERT: B 278 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7306 (ttm170) REVERT: C 190 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8505 (pp) REVERT: D 157 ASP cc_start: 0.8321 (p0) cc_final: 0.7788 (p0) outliers start: 27 outliers final: 22 residues processed: 267 average time/residue: 0.3436 time to fit residues: 126.8397 Evaluate side-chains 269 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 246 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 89 optimal weight: 0.0470 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 287 GLN E 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14740 Z= 0.276 Angle : 0.527 5.212 19905 Z= 0.282 Chirality : 0.043 0.161 2245 Planarity : 0.004 0.034 2395 Dihedral : 9.868 58.765 2390 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.62 % Allowed : 10.62 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.22), residues: 1660 helix: 2.07 (0.23), residues: 575 sheet: 0.98 (0.26), residues: 420 loop : 0.58 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 349 HIS 0.005 0.002 HIS E 254 PHE 0.012 0.002 PHE A 159 TYR 0.024 0.002 TYR D 272 ARG 0.005 0.001 ARG E 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 242 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 157 ASP cc_start: 0.8466 (p0) cc_final: 0.8023 (p0) REVERT: C 157 ASP cc_start: 0.8516 (p0) cc_final: 0.7984 (p0) REVERT: C 278 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7129 (mtt90) REVERT: D 157 ASP cc_start: 0.8458 (p0) cc_final: 0.7925 (p0) REVERT: D 278 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.7030 (mtt90) REVERT: E 157 ASP cc_start: 0.8471 (p0) cc_final: 0.8012 (p0) REVERT: E 278 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7160 (mtt90) outliers start: 40 outliers final: 34 residues processed: 274 average time/residue: 0.3170 time to fit residues: 119.5685 Evaluate side-chains 277 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 125 optimal weight: 0.4980 chunk 144 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14740 Z= 0.237 Angle : 0.498 5.215 19905 Z= 0.268 Chirality : 0.042 0.158 2245 Planarity : 0.004 0.034 2395 Dihedral : 9.740 59.974 2390 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.30 % Allowed : 10.69 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.21), residues: 1660 helix: 2.09 (0.23), residues: 575 sheet: 0.93 (0.26), residues: 410 loop : 0.66 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 349 HIS 0.005 0.001 HIS C 254 PHE 0.012 0.001 PHE E 159 TYR 0.021 0.002 TYR D 272 ARG 0.005 0.000 ARG E 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 242 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.8354 (p0) cc_final: 0.7931 (p0) REVERT: A 278 ARG cc_start: 0.7457 (mtt90) cc_final: 0.6961 (mtt90) REVERT: B 157 ASP cc_start: 0.8446 (p0) cc_final: 0.7969 (p0) REVERT: B 185 LYS cc_start: 0.8639 (mttt) cc_final: 0.8295 (mttp) REVERT: B 278 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7438 (ttm170) REVERT: C 157 ASP cc_start: 0.8494 (p0) cc_final: 0.7938 (p0) REVERT: C 278 ARG cc_start: 0.7661 (mtm-85) cc_final: 0.7146 (mtt90) REVERT: D 157 ASP cc_start: 0.8360 (p0) cc_final: 0.7824 (p0) REVERT: D 278 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7244 (mtt90) outliers start: 35 outliers final: 34 residues processed: 269 average time/residue: 0.3250 time to fit residues: 119.9762 Evaluate side-chains 275 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 0.0070 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14740 Z= 0.135 Angle : 0.435 5.271 19905 Z= 0.234 Chirality : 0.040 0.149 2245 Planarity : 0.003 0.033 2395 Dihedral : 9.142 59.685 2390 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.77 % Allowed : 11.21 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.22), residues: 1660 helix: 2.21 (0.23), residues: 580 sheet: 1.14 (0.26), residues: 410 loop : 0.86 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 349 HIS 0.003 0.001 HIS A 254 PHE 0.010 0.001 PHE A 356 TYR 0.018 0.002 TYR D 272 ARG 0.006 0.000 ARG E 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 249 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ARG cc_start: 0.7480 (mtt90) cc_final: 0.7004 (mtt90) REVERT: B 152 LYS cc_start: 0.8506 (mttm) cc_final: 0.8235 (mtmt) REVERT: B 185 LYS cc_start: 0.8628 (mttt) cc_final: 0.8283 (mttp) REVERT: C 157 ASP cc_start: 0.8404 (p0) cc_final: 0.8121 (p0) REVERT: C 278 ARG cc_start: 0.7591 (mtm-85) cc_final: 0.7093 (mtt90) REVERT: D 157 ASP cc_start: 0.8302 (p0) cc_final: 0.8083 (p0) REVERT: E 278 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.7201 (mtt90) outliers start: 27 outliers final: 25 residues processed: 268 average time/residue: 0.3287 time to fit residues: 120.5678 Evaluate side-chains 269 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 244 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 GLN D 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14740 Z= 0.174 Angle : 0.459 5.246 19905 Z= 0.246 Chirality : 0.041 0.154 2245 Planarity : 0.003 0.031 2395 Dihedral : 8.987 58.820 2390 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.03 % Allowed : 11.02 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.22), residues: 1660 helix: 2.23 (0.23), residues: 580 sheet: 1.12 (0.26), residues: 410 loop : 0.88 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 349 HIS 0.004 0.001 HIS D 254 PHE 0.010 0.001 PHE C 159 TYR 0.020 0.002 TYR A 272 ARG 0.005 0.000 ARG E 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 244 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ARG cc_start: 0.7493 (mtt90) cc_final: 0.7006 (mtt90) REVERT: B 111 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8576 (mt) REVERT: B 185 LYS cc_start: 0.8632 (mttt) cc_final: 0.8295 (mttp) REVERT: C 157 ASP cc_start: 0.8450 (p0) cc_final: 0.8200 (p0) REVERT: C 278 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7109 (mtt90) REVERT: D 157 ASP cc_start: 0.8364 (p0) cc_final: 0.7804 (p0) REVERT: D 278 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7079 (mtt90) REVERT: E 278 ARG cc_start: 0.7634 (mtm-85) cc_final: 0.7157 (mtt90) REVERT: E 375 LYS cc_start: 0.7161 (ttmm) cc_final: 0.6939 (ttpp) outliers start: 31 outliers final: 30 residues processed: 267 average time/residue: 0.3399 time to fit residues: 125.0652 Evaluate side-chains 274 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 243 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0370 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 GLN D 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.133879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.098816 restraints weight = 14934.811| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.00 r_work: 0.2817 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14740 Z= 0.193 Angle : 0.473 5.248 19905 Z= 0.254 Chirality : 0.041 0.157 2245 Planarity : 0.004 0.032 2395 Dihedral : 8.824 57.793 2390 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.30 % Allowed : 11.02 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.22), residues: 1660 helix: 2.18 (0.23), residues: 580 sheet: 1.05 (0.26), residues: 410 loop : 0.86 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 349 HIS 0.004 0.001 HIS C 254 PHE 0.011 0.001 PHE A 159 TYR 0.021 0.002 TYR D 272 ARG 0.005 0.000 ARG E 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3558.55 seconds wall clock time: 64 minutes 30.42 seconds (3870.42 seconds total)