Starting phenix.real_space_refine on Sat Sep 28 22:30:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/09_2024/6wbg_21589.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/09_2024/6wbg_21589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/09_2024/6wbg_21589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/09_2024/6wbg_21589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/09_2024/6wbg_21589.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbg_21589/09_2024/6wbg_21589.cif" } resolution = 2.97 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= 0.004 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 P 21 5.49 5 S 77 5.16 5 C 13321 2.51 5 N 2912 2.21 5 O 3381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "E" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "F" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "G" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.64, per 1000 atoms: 0.59 Number of scatterers: 19712 At special positions: 0 Unit cell: (107.73, 108.756, 121.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 21 15.00 O 3381 8.00 N 2912 7.00 C 13321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 407 " - " ASN A 255 " " NAG B 407 " - " ASN B 255 " " NAG C 407 " - " ASN C 255 " " NAG D 407 " - " ASN D 255 " " NAG E 407 " - " ASN E 255 " " NAG F 407 " - " ASN F 255 " " NAG G 407 " - " ASN G 255 " Time building additional restraints: 4.97 Conformation dependent library (CDL) restraints added in 2.7 seconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 70.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.630A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.949A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 131 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 162 Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.619A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix removed outlier: 3.717A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.830A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.681A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.630A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.947A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 131 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 162 Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.619A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix removed outlier: 3.718A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 304 through 312 removed outlier: 4.014A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.828A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.629A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.949A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 131 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 162 Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.620A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix removed outlier: 3.718A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 304 through 312 removed outlier: 4.014A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.829A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.681A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.630A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 99 through 108 removed outlier: 3.950A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 131 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 162 Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.618A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix removed outlier: 3.717A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 304 through 312 removed outlier: 4.014A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.829A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.629A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 99 through 108 removed outlier: 3.949A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 131 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 162 Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 250 through 254 removed outlier: 3.618A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix removed outlier: 3.718A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 304 through 312 removed outlier: 4.012A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.829A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.628A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 99 through 108 removed outlier: 3.948A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 131 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 162 Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 250 through 254 removed outlier: 3.618A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix removed outlier: 3.717A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 304 through 312 removed outlier: 4.014A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.830A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.632A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 99 through 108 removed outlier: 3.949A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 131 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 162 Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 250 through 254 removed outlier: 3.619A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix removed outlier: 3.717A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.830A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 1226 hydrogen bonds defined for protein. 3531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 5.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2908 1.32 - 1.44: 5034 1.44 - 1.57: 12071 1.57 - 1.69: 42 1.69 - 1.81: 91 Bond restraints: 20146 Sorted by residual: bond pdb=" N ASN A 369 " pdb=" CA ASN A 369 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.17e-02 7.31e+03 9.16e+00 bond pdb=" N ASN B 369 " pdb=" CA ASN B 369 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.17e-02 7.31e+03 8.74e+00 bond pdb=" N ASN F 369 " pdb=" CA ASN F 369 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.17e-02 7.31e+03 8.65e+00 bond pdb=" N ASN D 369 " pdb=" CA ASN D 369 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.17e-02 7.31e+03 8.54e+00 bond pdb=" N ASN C 369 " pdb=" CA ASN C 369 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.17e-02 7.31e+03 8.49e+00 ... (remaining 20141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 26497 2.02 - 4.04: 712 4.04 - 6.06: 91 6.06 - 8.08: 14 8.08 - 10.10: 14 Bond angle restraints: 27328 Sorted by residual: angle pdb=" C TYR E 10 " pdb=" N VAL E 11 " pdb=" CA VAL E 11 " ideal model delta sigma weight residual 122.77 118.81 3.96 1.05e+00 9.07e-01 1.42e+01 angle pdb=" C TYR F 10 " pdb=" N VAL F 11 " pdb=" CA VAL F 11 " ideal model delta sigma weight residual 122.77 118.88 3.89 1.05e+00 9.07e-01 1.37e+01 angle pdb=" C TYR D 10 " pdb=" N VAL D 11 " pdb=" CA VAL D 11 " ideal model delta sigma weight residual 122.77 118.89 3.88 1.05e+00 9.07e-01 1.37e+01 angle pdb=" C TYR A 10 " pdb=" N VAL A 11 " pdb=" CA VAL A 11 " ideal model delta sigma weight residual 122.77 118.91 3.86 1.05e+00 9.07e-01 1.35e+01 angle pdb=" C TYR B 10 " pdb=" N VAL B 11 " pdb=" CA VAL B 11 " ideal model delta sigma weight residual 122.77 118.92 3.85 1.05e+00 9.07e-01 1.35e+01 ... (remaining 27323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.68: 12375 29.68 - 59.37: 626 59.37 - 89.05: 32 89.05 - 118.73: 1 118.73 - 148.41: 14 Dihedral angle restraints: 13048 sinusoidal: 5873 harmonic: 7175 Sorted by residual: dihedral pdb=" N1 PTY A 401 " pdb=" C2 PTY A 401 " pdb=" C3 PTY A 401 " pdb=" O11 PTY A 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.08 148.41 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" N1 PTY E 401 " pdb=" C2 PTY E 401 " pdb=" C3 PTY E 401 " pdb=" O11 PTY E 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.07 148.40 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" N1 PTY D 401 " pdb=" C2 PTY D 401 " pdb=" C3 PTY D 401 " pdb=" O11 PTY D 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.06 148.39 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 13045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2266 0.039 - 0.077: 709 0.077 - 0.116: 223 0.116 - 0.154: 43 0.154 - 0.193: 14 Chirality restraints: 3255 Sorted by residual: chirality pdb=" CA ILE E 373 " pdb=" N ILE E 373 " pdb=" C ILE E 373 " pdb=" CB ILE E 373 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA ILE B 373 " pdb=" N ILE B 373 " pdb=" C ILE B 373 " pdb=" CB ILE B 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA ILE C 373 " pdb=" N ILE C 373 " pdb=" C ILE C 373 " pdb=" CB ILE C 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 3252 not shown) Planarity restraints: 3185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 407 " 0.090 2.00e-02 2.50e+03 7.42e-02 6.88e+01 pdb=" C7 NAG F 407 " -0.026 2.00e-02 2.50e+03 pdb=" C8 NAG F 407 " 0.069 2.00e-02 2.50e+03 pdb=" N2 NAG F 407 " -0.117 2.00e-02 2.50e+03 pdb=" O7 NAG F 407 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 407 " -0.090 2.00e-02 2.50e+03 7.39e-02 6.83e+01 pdb=" C7 NAG G 407 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG G 407 " -0.069 2.00e-02 2.50e+03 pdb=" N2 NAG G 407 " 0.116 2.00e-02 2.50e+03 pdb=" O7 NAG G 407 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 407 " -0.090 2.00e-02 2.50e+03 7.38e-02 6.81e+01 pdb=" C7 NAG B 407 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG B 407 " -0.069 2.00e-02 2.50e+03 pdb=" N2 NAG B 407 " 0.116 2.00e-02 2.50e+03 pdb=" O7 NAG B 407 " 0.016 2.00e-02 2.50e+03 ... (remaining 3182 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1406 2.73 - 3.27: 20895 3.27 - 3.81: 33193 3.81 - 4.36: 39549 4.36 - 4.90: 68923 Nonbonded interactions: 163966 Sorted by model distance: nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.183 3.040 nonbonded pdb=" O LEU A 52 " pdb=" OH TYR G 111 " model vdw 2.184 3.040 nonbonded pdb=" OH TYR B 111 " pdb=" O LEU C 52 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR F 111 " pdb=" O LEU G 52 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR E 111 " pdb=" O LEU F 52 " model vdw 2.193 3.040 ... (remaining 163961 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.080 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: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 42.040 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.007 0.049 20146 Z= 0.447 Angle : 0.827 10.103 27328 Z= 0.458 Chirality : 0.043 0.193 3255 Planarity : 0.005 0.074 3178 Dihedral : 16.592 148.414 8344 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.38 % Allowed : 5.76 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.48 (0.16), residues: 2380 helix: -0.10 (0.12), residues: 1603 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 104 HIS 0.002 0.001 HIS B 106 PHE 0.013 0.002 PHE B 54 TYR 0.015 0.001 TYR D 10 ARG 0.002 0.000 ARG E 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 2.352 Fit side-chains REVERT: A 29 ARG cc_start: 0.8631 (mpt-90) cc_final: 0.8279 (mmt90) REVERT: A 242 ASP cc_start: 0.8957 (p0) cc_final: 0.8716 (p0) REVERT: B 352 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8706 (tp30) REVERT: D 29 ARG cc_start: 0.8571 (mpt-90) cc_final: 0.8326 (mmt90) REVERT: G 29 ARG cc_start: 0.8571 (mpt-90) cc_final: 0.8351 (mmt90) outliers start: 7 outliers final: 0 residues processed: 213 average time/residue: 1.6503 time to fit residues: 388.2801 Evaluate side-chains 156 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 9.9990 chunk 180 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 138 optimal weight: 0.0020 chunk 216 optimal weight: 5.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 134 HIS A 274 GLN B 76 GLN B 274 GLN C 76 GLN C 274 GLN D 76 GLN D 274 GLN E 76 GLN E 274 GLN F 76 GLN F 274 GLN G 76 GLN G 274 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20146 Z= 0.211 Angle : 0.631 13.611 27328 Z= 0.297 Chirality : 0.040 0.138 3255 Planarity : 0.004 0.039 3178 Dihedral : 15.010 114.242 4522 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.23 % Allowed : 11.35 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.35 (0.18), residues: 2380 helix: 1.36 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -2.39 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.003 0.002 HIS E 134 PHE 0.009 0.001 PHE B 12 TYR 0.014 0.001 TYR A 10 ARG 0.007 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 2.163 Fit side-chains REVERT: A 5 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8204 (tm-30) REVERT: A 29 ARG cc_start: 0.8340 (mpt-90) cc_final: 0.7842 (mmt90) REVERT: A 337 GLU cc_start: 0.8537 (tp30) cc_final: 0.8257 (tm-30) REVERT: B 138 ASP cc_start: 0.8670 (m-30) cc_final: 0.8438 (m-30) REVERT: B 337 GLU cc_start: 0.8628 (tp30) cc_final: 0.8303 (tm-30) REVERT: B 352 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8683 (tp30) REVERT: C 5 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7908 (tm-30) REVERT: C 29 ARG cc_start: 0.8472 (mmt90) cc_final: 0.8134 (mmm-85) REVERT: C 138 ASP cc_start: 0.8680 (m-30) cc_final: 0.8471 (m-30) REVERT: D 336 GLU cc_start: 0.8544 (tt0) cc_final: 0.8343 (tt0) REVERT: D 337 GLU cc_start: 0.8537 (tp30) cc_final: 0.8296 (tm-30) REVERT: E 5 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7972 (tm-30) REVERT: E 337 GLU cc_start: 0.8598 (tp30) cc_final: 0.8145 (tm-30) REVERT: F 5 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7843 (tm-30) REVERT: F 29 ARG cc_start: 0.8484 (mmt90) cc_final: 0.7854 (mmt90) REVERT: F 337 GLU cc_start: 0.8573 (tp30) cc_final: 0.8114 (tm-30) REVERT: G 29 ARG cc_start: 0.8314 (mpt-90) cc_final: 0.7963 (mmt90) REVERT: G 138 ASP cc_start: 0.8639 (m-30) cc_final: 0.8423 (m-30) REVERT: G 337 GLU cc_start: 0.8523 (tp30) cc_final: 0.8078 (tm-30) outliers start: 41 outliers final: 7 residues processed: 193 average time/residue: 1.3447 time to fit residues: 292.2050 Evaluate side-chains 158 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain F residue 258 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 233 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 134 HIS C 89 GLN C 134 HIS D 134 HIS E 89 GLN E 134 HIS F 134 HIS G 89 GLN G 134 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20146 Z= 0.315 Angle : 0.646 13.178 27328 Z= 0.305 Chirality : 0.041 0.140 3255 Planarity : 0.004 0.039 3178 Dihedral : 13.132 91.583 4522 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.23 % Allowed : 13.85 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.72 (0.18), residues: 2380 helix: 1.63 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -2.23 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 104 HIS 0.002 0.001 HIS E 134 PHE 0.013 0.001 PHE F 54 TYR 0.012 0.001 TYR F 10 ARG 0.008 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 2.270 Fit side-chains REVERT: B 5 GLN cc_start: 0.8228 (tm-30) cc_final: 0.8014 (tm-30) REVERT: B 138 ASP cc_start: 0.8756 (m-30) cc_final: 0.8508 (m-30) REVERT: B 337 GLU cc_start: 0.8669 (tp30) cc_final: 0.8340 (tm-30) REVERT: B 352 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8674 (tp30) REVERT: C 5 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7985 (tm-30) REVERT: C 9 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7883 (tm-30) REVERT: C 29 ARG cc_start: 0.8489 (mmt90) cc_final: 0.8183 (mmm-85) REVERT: C 138 ASP cc_start: 0.8707 (m-30) cc_final: 0.8473 (m-30) REVERT: D 5 GLN cc_start: 0.8234 (tm-30) cc_final: 0.8011 (tm-30) REVERT: D 9 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7825 (tm-30) REVERT: D 337 GLU cc_start: 0.8527 (tp30) cc_final: 0.8025 (tm-30) REVERT: E 5 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7965 (tm-30) REVERT: E 9 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7903 (tm-30) REVERT: E 337 GLU cc_start: 0.8577 (tp30) cc_final: 0.8065 (tm-30) REVERT: F 5 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8128 (tm-30) REVERT: G 9 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: G 29 ARG cc_start: 0.8334 (mpt-90) cc_final: 0.7736 (mmt90) REVERT: G 138 ASP cc_start: 0.8597 (m-30) cc_final: 0.8357 (m-30) REVERT: G 337 GLU cc_start: 0.8548 (tp30) cc_final: 0.7852 (tm-30) outliers start: 41 outliers final: 14 residues processed: 190 average time/residue: 1.4915 time to fit residues: 319.5993 Evaluate side-chains 166 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 258 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 103 optimal weight: 0.2980 chunk 145 optimal weight: 0.0060 chunk 217 optimal weight: 5.9990 chunk 230 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN G 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20146 Z= 0.155 Angle : 0.564 12.079 27328 Z= 0.271 Chirality : 0.038 0.139 3255 Planarity : 0.004 0.038 3178 Dihedral : 12.236 87.901 4522 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.55 % Allowed : 14.29 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.06 (0.18), residues: 2380 helix: 1.93 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.21 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 104 HIS 0.002 0.001 HIS C 106 PHE 0.008 0.001 PHE B 12 TYR 0.010 0.001 TYR A 83 ARG 0.007 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 170 time to evaluate : 2.215 Fit side-chains REVERT: A 9 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 9 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: B 352 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8663 (tp30) REVERT: C 9 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7998 (tm-30) REVERT: C 29 ARG cc_start: 0.8276 (mmt90) cc_final: 0.8062 (mmt90) REVERT: C 261 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8258 (t0) REVERT: C 337 GLU cc_start: 0.8559 (tp30) cc_final: 0.8237 (tp30) REVERT: D 9 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7952 (tm-30) REVERT: E 337 GLU cc_start: 0.8536 (tp30) cc_final: 0.8068 (tm-30) REVERT: F 5 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8138 (tm-30) REVERT: F 9 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7949 (tm-30) REVERT: F 29 ARG cc_start: 0.8153 (mmt90) cc_final: 0.7725 (mmm-85) REVERT: F 31 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8197 (tt0) REVERT: F 337 GLU cc_start: 0.8591 (tp30) cc_final: 0.8063 (tm-30) REVERT: G 9 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8080 (tm-30) REVERT: G 29 ARG cc_start: 0.8071 (mpt-90) cc_final: 0.7694 (mmt90) REVERT: G 138 ASP cc_start: 0.8576 (m-30) cc_final: 0.8358 (m-30) REVERT: G 337 GLU cc_start: 0.8454 (tp30) cc_final: 0.8102 (tm-30) outliers start: 47 outliers final: 19 residues processed: 205 average time/residue: 1.4456 time to fit residues: 334.1770 Evaluate side-chains 173 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 3.9990 chunk 130 optimal weight: 0.0570 chunk 3 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20146 Z= 0.234 Angle : 0.584 10.305 27328 Z= 0.281 Chirality : 0.039 0.138 3255 Planarity : 0.004 0.037 3178 Dihedral : 11.988 84.599 4522 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.66 % Allowed : 15.86 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.15 (0.18), residues: 2380 helix: 1.96 (0.14), residues: 1638 sheet: None (None), residues: 0 loop : -2.13 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.001 0.001 HIS D 106 PHE 0.010 0.001 PHE C 54 TYR 0.009 0.001 TYR A 10 ARG 0.008 0.001 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 156 time to evaluate : 2.270 Fit side-chains REVERT: A 9 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8072 (tm-30) REVERT: A 337 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 352 GLU cc_start: 0.8730 (tp30) cc_final: 0.8323 (tm-30) REVERT: B 9 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8245 (tm-30) REVERT: B 337 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8126 (tm-30) REVERT: B 352 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8602 (tm-30) REVERT: C 9 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7972 (tm-30) REVERT: C 29 ARG cc_start: 0.8342 (mmt90) cc_final: 0.7965 (mmm-85) REVERT: C 89 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8491 (mm-40) REVERT: C 261 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8306 (t0) REVERT: C 337 GLU cc_start: 0.8604 (tp30) cc_final: 0.8015 (tm-30) REVERT: D 9 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7978 (tm-30) REVERT: E 9 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8134 (tm-30) REVERT: E 138 ASP cc_start: 0.8757 (m-30) cc_final: 0.8550 (m-30) REVERT: E 337 GLU cc_start: 0.8568 (tp30) cc_final: 0.8049 (tm-30) REVERT: E 352 GLU cc_start: 0.8734 (tp30) cc_final: 0.8407 (tm-30) REVERT: F 9 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8048 (tm-30) REVERT: F 29 ARG cc_start: 0.8279 (mmt90) cc_final: 0.7788 (mmm-85) REVERT: F 31 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8196 (tt0) REVERT: F 337 GLU cc_start: 0.8601 (tp30) cc_final: 0.8070 (tm-30) REVERT: G 9 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: G 138 ASP cc_start: 0.8598 (m-30) cc_final: 0.8365 (m-30) outliers start: 49 outliers final: 22 residues processed: 194 average time/residue: 1.3482 time to fit residues: 295.2249 Evaluate side-chains 176 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 191 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20146 Z= 0.176 Angle : 0.560 9.840 27328 Z= 0.272 Chirality : 0.038 0.135 3255 Planarity : 0.004 0.037 3178 Dihedral : 11.658 77.478 4522 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.23 % Allowed : 16.68 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.24 (0.18), residues: 2380 helix: 2.03 (0.14), residues: 1638 sheet: None (None), residues: 0 loop : -2.09 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 104 HIS 0.001 0.001 HIS D 106 PHE 0.008 0.001 PHE C 54 TYR 0.009 0.001 TYR E 345 ARG 0.008 0.001 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 155 time to evaluate : 2.525 Fit side-chains REVERT: A 9 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8019 (tm-30) REVERT: A 29 ARG cc_start: 0.8133 (mmt90) cc_final: 0.7740 (mmt90) REVERT: A 337 GLU cc_start: 0.8555 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 9 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: B 29 ARG cc_start: 0.8213 (mmt90) cc_final: 0.7740 (mmt90) REVERT: B 336 GLU cc_start: 0.8568 (tt0) cc_final: 0.8276 (tt0) REVERT: B 337 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8066 (tm-30) REVERT: B 352 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8606 (tm-30) REVERT: C 9 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8030 (tm-30) REVERT: C 29 ARG cc_start: 0.8261 (mmt90) cc_final: 0.7967 (mmm-85) REVERT: C 337 GLU cc_start: 0.8579 (tp30) cc_final: 0.8032 (tm-30) REVERT: D 9 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7999 (tm-30) REVERT: D 337 GLU cc_start: 0.8478 (tp30) cc_final: 0.7787 (tm-30) REVERT: E 9 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8246 (tm-30) REVERT: E 138 ASP cc_start: 0.8752 (m-30) cc_final: 0.8516 (m-30) REVERT: E 337 GLU cc_start: 0.8555 (tp30) cc_final: 0.8081 (tm-30) REVERT: F 9 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8058 (tm-30) REVERT: F 29 ARG cc_start: 0.8139 (mmt90) cc_final: 0.7756 (mmt90) REVERT: F 31 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8142 (tt0) REVERT: F 337 GLU cc_start: 0.8584 (tp30) cc_final: 0.8059 (tm-30) REVERT: G 9 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8092 (tm-30) REVERT: G 29 ARG cc_start: 0.8143 (mmt90) cc_final: 0.7864 (mmt90) REVERT: G 138 ASP cc_start: 0.8598 (m-30) cc_final: 0.8373 (m-30) REVERT: G 337 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7759 (tm-30) outliers start: 41 outliers final: 21 residues processed: 186 average time/residue: 1.3640 time to fit residues: 285.5995 Evaluate side-chains 168 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20146 Z= 0.188 Angle : 0.569 8.349 27328 Z= 0.275 Chirality : 0.038 0.135 3255 Planarity : 0.004 0.037 3178 Dihedral : 11.449 73.367 4522 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.85 % Allowed : 17.54 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.34 (0.18), residues: 2380 helix: 2.09 (0.14), residues: 1638 sheet: None (None), residues: 0 loop : -2.01 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.001 0.001 HIS D 106 PHE 0.008 0.001 PHE A 54 TYR 0.009 0.001 TYR B 345 ARG 0.008 0.001 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 2.480 Fit side-chains REVERT: A 9 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8068 (tm-30) REVERT: A 29 ARG cc_start: 0.8124 (mmt90) cc_final: 0.7746 (mmt90) REVERT: A 337 GLU cc_start: 0.8560 (tm-30) cc_final: 0.7927 (tm-30) REVERT: B 9 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8308 (tm-30) REVERT: B 29 ARG cc_start: 0.8193 (mmt90) cc_final: 0.7724 (mmt90) REVERT: B 336 GLU cc_start: 0.8563 (tt0) cc_final: 0.8304 (tt0) REVERT: B 337 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7866 (tm-30) REVERT: B 352 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8615 (tm-30) REVERT: C 9 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 29 ARG cc_start: 0.8219 (mmt90) cc_final: 0.7866 (mmm-85) REVERT: C 337 GLU cc_start: 0.8627 (tp30) cc_final: 0.8057 (tm-30) REVERT: D 9 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8073 (tm-30) REVERT: D 337 GLU cc_start: 0.8488 (tp30) cc_final: 0.7889 (tm-30) REVERT: E 9 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8278 (tm-30) REVERT: E 337 GLU cc_start: 0.8556 (tp30) cc_final: 0.8078 (tm-30) REVERT: E 352 GLU cc_start: 0.8761 (tp30) cc_final: 0.8454 (tm-30) REVERT: F 9 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8097 (tm-30) REVERT: F 29 ARG cc_start: 0.8129 (mmt90) cc_final: 0.7740 (mmt90) REVERT: F 31 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8120 (tt0) REVERT: F 337 GLU cc_start: 0.8590 (tp30) cc_final: 0.8051 (tm-30) REVERT: G 9 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: G 29 ARG cc_start: 0.8092 (mmt90) cc_final: 0.7754 (mmt90) REVERT: G 138 ASP cc_start: 0.8603 (m-30) cc_final: 0.8376 (m-30) REVERT: G 337 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7771 (tm-30) outliers start: 34 outliers final: 21 residues processed: 181 average time/residue: 1.3830 time to fit residues: 280.9941 Evaluate side-chains 171 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 69 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN E 208 ASN E 264 GLN G 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20146 Z= 0.154 Angle : 0.555 7.511 27328 Z= 0.270 Chirality : 0.038 0.134 3255 Planarity : 0.004 0.040 3178 Dihedral : 11.136 81.343 4522 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.01 % Allowed : 17.93 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.47 (0.19), residues: 2380 helix: 2.19 (0.14), residues: 1638 sheet: None (None), residues: 0 loop : -1.97 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.001 0.001 HIS C 106 PHE 0.008 0.001 PHE E 263 TYR 0.008 0.001 TYR B 345 ARG 0.010 0.001 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 2.391 Fit side-chains REVERT: A 9 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 29 ARG cc_start: 0.7845 (mmt90) cc_final: 0.7604 (mmt90) REVERT: A 336 GLU cc_start: 0.8686 (tt0) cc_final: 0.8479 (pt0) REVERT: A 337 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 352 GLU cc_start: 0.8698 (tp30) cc_final: 0.8426 (tm-30) REVERT: B 9 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: B 29 ARG cc_start: 0.8039 (mmt90) cc_final: 0.7737 (mmt90) REVERT: B 336 GLU cc_start: 0.8538 (tt0) cc_final: 0.8230 (tt0) REVERT: B 337 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 352 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8622 (tm-30) REVERT: C 9 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8052 (tm-30) REVERT: C 29 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7832 (mmm-85) REVERT: C 337 GLU cc_start: 0.8622 (tp30) cc_final: 0.8039 (tm-30) REVERT: C 352 GLU cc_start: 0.8701 (tp30) cc_final: 0.8389 (tm-30) REVERT: D 9 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8117 (tm-30) REVERT: D 29 ARG cc_start: 0.8108 (mmt90) cc_final: 0.7849 (mmt90) REVERT: D 337 GLU cc_start: 0.8499 (tp30) cc_final: 0.8289 (tp30) REVERT: D 352 GLU cc_start: 0.8720 (tp30) cc_final: 0.8315 (tm-30) REVERT: E 9 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8296 (tm-30) REVERT: E 29 ARG cc_start: 0.8142 (mmt90) cc_final: 0.7675 (mmt90) REVERT: E 254 ARG cc_start: 0.8562 (tpp80) cc_final: 0.8282 (tpp80) REVERT: E 337 GLU cc_start: 0.8517 (tp30) cc_final: 0.7957 (tm-30) REVERT: E 352 GLU cc_start: 0.8695 (tp30) cc_final: 0.8438 (tm-30) REVERT: F 9 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8151 (tm-30) REVERT: F 29 ARG cc_start: 0.8053 (mmt90) cc_final: 0.7689 (mmt90) REVERT: F 337 GLU cc_start: 0.8633 (tp30) cc_final: 0.8077 (tm-30) REVERT: G 9 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8123 (tm-30) REVERT: G 56 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7452 (pp30) REVERT: G 138 ASP cc_start: 0.8603 (m-30) cc_final: 0.8383 (m-30) REVERT: G 336 GLU cc_start: 0.8434 (tt0) cc_final: 0.8213 (tt0) REVERT: G 337 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7784 (tm-30) REVERT: G 352 GLU cc_start: 0.8689 (tp30) cc_final: 0.8444 (tm-30) outliers start: 37 outliers final: 18 residues processed: 186 average time/residue: 1.2855 time to fit residues: 271.2268 Evaluate side-chains 170 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 213 optimal weight: 0.1980 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20146 Z= 0.181 Angle : 0.565 8.079 27328 Z= 0.274 Chirality : 0.038 0.143 3255 Planarity : 0.004 0.037 3178 Dihedral : 11.060 85.609 4522 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.85 % Allowed : 18.31 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.50 (0.19), residues: 2380 helix: 2.21 (0.14), residues: 1638 sheet: None (None), residues: 0 loop : -1.96 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 104 HIS 0.001 0.000 HIS D 106 PHE 0.007 0.001 PHE F 263 TYR 0.008 0.001 TYR D 345 ARG 0.008 0.001 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 2.126 Fit side-chains REVERT: A 9 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 29 ARG cc_start: 0.7955 (mmt90) cc_final: 0.7634 (mmt90) REVERT: A 337 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8049 (tm-30) REVERT: A 352 GLU cc_start: 0.8736 (tp30) cc_final: 0.8460 (tm-30) REVERT: B 9 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: B 29 ARG cc_start: 0.8079 (mmt90) cc_final: 0.7771 (mmt90) REVERT: B 336 GLU cc_start: 0.8567 (tt0) cc_final: 0.8290 (tt0) REVERT: B 337 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: B 352 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 9 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8081 (tm-30) REVERT: C 29 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7896 (mmm-85) REVERT: C 337 GLU cc_start: 0.8648 (tp30) cc_final: 0.8078 (tm-30) REVERT: D 9 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8181 (tm-30) REVERT: D 29 ARG cc_start: 0.8158 (mmt90) cc_final: 0.7892 (mmt90) REVERT: D 337 GLU cc_start: 0.8535 (tp30) cc_final: 0.8294 (tp30) REVERT: D 352 GLU cc_start: 0.8704 (tp30) cc_final: 0.8365 (tm-30) REVERT: E 9 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8318 (tm-30) REVERT: E 29 ARG cc_start: 0.8183 (mmt90) cc_final: 0.7715 (mmt90) REVERT: E 337 GLU cc_start: 0.8539 (tp30) cc_final: 0.7968 (tm-30) REVERT: E 352 GLU cc_start: 0.8719 (tp30) cc_final: 0.8488 (tm-30) REVERT: F 9 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8150 (tm-30) REVERT: F 29 ARG cc_start: 0.8110 (mmt90) cc_final: 0.7786 (mmt90) REVERT: F 337 GLU cc_start: 0.8655 (tp30) cc_final: 0.8103 (tm-30) REVERT: F 352 GLU cc_start: 0.8731 (tp30) cc_final: 0.8494 (tm-30) REVERT: G 9 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8163 (tm-30) REVERT: G 29 ARG cc_start: 0.7973 (mmt90) cc_final: 0.7534 (mmt90) REVERT: G 138 ASP cc_start: 0.8604 (m-30) cc_final: 0.8377 (m-30) REVERT: G 337 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7712 (tm-30) outliers start: 34 outliers final: 19 residues processed: 178 average time/residue: 1.3247 time to fit residues: 266.5622 Evaluate side-chains 171 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 107 optimal weight: 0.0020 chunk 157 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20146 Z= 0.167 Angle : 0.562 7.712 27328 Z= 0.274 Chirality : 0.038 0.132 3255 Planarity : 0.004 0.037 3178 Dihedral : 10.951 89.970 4522 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.14 % Allowed : 18.96 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.84 (0.19), residues: 2380 helix: 2.45 (0.14), residues: 1596 sheet: None (None), residues: 0 loop : -1.52 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.001 0.001 HIS D 106 PHE 0.007 0.001 PHE F 263 TYR 0.008 0.001 TYR D 345 ARG 0.009 0.001 ARG E 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 2.163 Fit side-chains REVERT: A 9 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 29 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7629 (mmt90) REVERT: A 336 GLU cc_start: 0.8768 (tt0) cc_final: 0.8531 (pt0) REVERT: A 337 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8064 (tm-30) REVERT: A 352 GLU cc_start: 0.8717 (tp30) cc_final: 0.8507 (tm-30) REVERT: B 9 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: B 29 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7764 (mmt90) REVERT: B 336 GLU cc_start: 0.8561 (tt0) cc_final: 0.8284 (tt0) REVERT: B 337 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: B 352 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8588 (tm-30) REVERT: C 9 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8078 (tm-30) REVERT: C 29 ARG cc_start: 0.8202 (mmt90) cc_final: 0.7918 (mmm-85) REVERT: C 337 GLU cc_start: 0.8646 (tp30) cc_final: 0.8046 (tm-30) REVERT: C 352 GLU cc_start: 0.8705 (tp30) cc_final: 0.8435 (tm-30) REVERT: D 9 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8197 (tm-30) REVERT: D 29 ARG cc_start: 0.8112 (mmt90) cc_final: 0.7856 (mmt90) REVERT: D 337 GLU cc_start: 0.8529 (tp30) cc_final: 0.8296 (tp30) REVERT: D 352 GLU cc_start: 0.8706 (tp30) cc_final: 0.8433 (tm-30) REVERT: E 9 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8320 (tm-30) REVERT: E 29 ARG cc_start: 0.8128 (mmt90) cc_final: 0.7687 (mmt90) REVERT: E 337 GLU cc_start: 0.8522 (tp30) cc_final: 0.7967 (tm-30) REVERT: E 352 GLU cc_start: 0.8722 (tp30) cc_final: 0.8488 (tm-30) REVERT: F 9 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8193 (tm-30) REVERT: F 29 ARG cc_start: 0.8022 (mmt90) cc_final: 0.7708 (mmt90) REVERT: F 337 GLU cc_start: 0.8643 (tp30) cc_final: 0.8080 (tm-30) REVERT: F 352 GLU cc_start: 0.8733 (tp30) cc_final: 0.8489 (tm-30) REVERT: G 9 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8169 (tm-30) REVERT: G 29 ARG cc_start: 0.7904 (mmt90) cc_final: 0.7556 (mmt90) REVERT: G 138 ASP cc_start: 0.8601 (m-30) cc_final: 0.8376 (m-30) REVERT: G 337 GLU cc_start: 0.8549 (tm-30) cc_final: 0.7664 (tm-30) outliers start: 21 outliers final: 18 residues processed: 166 average time/residue: 1.3959 time to fit residues: 261.0678 Evaluate side-chains 170 residues out of total 2177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN F 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.084539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.065269 restraints weight = 47042.073| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.51 r_work: 0.2944 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20146 Z= 0.190 Angle : 0.570 7.674 27328 Z= 0.277 Chirality : 0.038 0.131 3255 Planarity : 0.004 0.037 3178 Dihedral : 10.873 86.754 4522 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.52 % Allowed : 18.58 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.87 (0.19), residues: 2380 helix: 2.47 (0.14), residues: 1596 sheet: None (None), residues: 0 loop : -1.49 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 104 HIS 0.001 0.000 HIS D 106 PHE 0.007 0.001 PHE A 54 TYR 0.008 0.001 TYR D 10 ARG 0.008 0.001 ARG E 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5287.00 seconds wall clock time: 94 minutes 26.34 seconds (5666.34 seconds total)