Starting phenix.real_space_refine on Tue May 20 22:21:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbg_21589/05_2025/6wbg_21589.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbg_21589/05_2025/6wbg_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/cci-nas-00/data/ceres_data/6wbg_21589/05_2025/6wbg_21589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbg_21589/05_2025/6wbg_21589.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbg_21589/05_2025/6wbg_21589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbg_21589/05_2025/6wbg_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-5687/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: 11.01, per 1000 atoms: 0.56 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: 5.16 Conformation dependent library (CDL) restraints added in 2.5 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: 2.06 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: 5.89 Time building geometry restraints manager: 5.92 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.760 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 42.190 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.080 ------------------------------------------------------------------------------- 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 20167 Z= 0.341 Angle : 0.827 10.103 27377 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 7) link_NAG-ASN : angle 0.88914 ( 21) hydrogen bonds : bond 0.14035 ( 1226) hydrogen bonds : angle 5.43804 ( 3531) SS BOND : bond 0.00249 ( 14) SS BOND : angle 0.73140 ( 28) covalent geometry : bond 0.00699 (20146) covalent geometry : angle 0.82747 (27328) *********************** 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 to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 2.216 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: 1.6628 time to fit residues: 391.1532 Evaluate side-chains 156 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 2.217 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.083526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.063857 restraints weight = 46884.086| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.43 r_work: 0.2900 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 20167 Z= 0.143 Angle : 0.632 13.611 27377 Z= 0.298 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 7) link_NAG-ASN : angle 1.44624 ( 21) hydrogen bonds : bond 0.03864 ( 1226) hydrogen bonds : angle 4.04644 ( 3531) SS BOND : bond 0.00348 ( 14) SS BOND : angle 0.70097 ( 28) covalent geometry : bond 0.00327 (20146) covalent geometry : angle 0.63090 (27328) *********************** 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 to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 2.203 Fit side-chains REVERT: A 5 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8527 (tm-30) REVERT: A 9 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 29 ARG cc_start: 0.8508 (mpt-90) cc_final: 0.7935 (mmt90) REVERT: A 337 GLU cc_start: 0.8678 (tp30) cc_final: 0.8336 (tm-30) REVERT: B 5 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: B 9 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8168 (tm-30) REVERT: B 138 ASP cc_start: 0.8852 (m-30) cc_final: 0.8642 (m-30) REVERT: B 337 GLU cc_start: 0.8831 (tp30) cc_final: 0.8441 (tm-30) REVERT: B 352 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8913 (tp30) REVERT: C 5 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 9 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8188 (tm-30) REVERT: C 29 ARG cc_start: 0.8642 (mmt90) cc_final: 0.8205 (mmm-85) REVERT: C 254 ARG cc_start: 0.8822 (tpp80) cc_final: 0.8587 (tpp80) REVERT: D 5 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8585 (tm-30) REVERT: D 29 ARG cc_start: 0.8527 (mpt-90) cc_final: 0.8313 (mmt90) REVERT: D 337 GLU cc_start: 0.8721 (tp30) cc_final: 0.8413 (tm-30) REVERT: E 5 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8283 (tm-30) REVERT: E 337 GLU cc_start: 0.8745 (tp30) cc_final: 0.8224 (tm-30) REVERT: F 5 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8189 (tm-30) REVERT: F 9 GLU cc_start: 0.8653 (tt0) cc_final: 0.8291 (tm-30) REVERT: F 29 ARG cc_start: 0.8664 (mmt90) cc_final: 0.8001 (mmt90) REVERT: F 254 ARG cc_start: 0.8866 (tpp80) cc_final: 0.8646 (tpp80) REVERT: F 337 GLU cc_start: 0.8733 (tp30) cc_final: 0.8178 (tm-30) REVERT: G 5 GLN cc_start: 0.8850 (mt0) cc_final: 0.8603 (tm-30) REVERT: G 29 ARG cc_start: 0.8501 (mpt-90) cc_final: 0.8034 (mmt90) REVERT: G 337 GLU cc_start: 0.8704 (tp30) cc_final: 0.8149 (tm-30) outliers start: 41 outliers final: 7 residues processed: 193 average time/residue: 1.3884 time to fit residues: 301.7798 Evaluate side-chains 163 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 2.142 ------------------------------------------------------------------------------- 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 5 GLN Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain D residue 5 GLN 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 58 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 138 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.0082 ------------------------------------------------------------------------------- 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 E 89 GLN E 134 HIS G 89 GLN G 134 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.084704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065299 restraints weight = 46944.374| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.45 r_work: 0.2938 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20167 Z= 0.121 Angle : 0.580 11.873 27377 Z= 0.275 Chirality : 0.039 0.135 3255 Planarity : 0.004 0.038 3178 Dihedral : 12.701 87.977 4522 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.28 % Allowed : 13.47 % Favored : 84.25 % 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: 0.92 (0.18), residues: 2380 helix: 1.79 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.18 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.002 0.001 HIS G 134 PHE 0.009 0.001 PHE G 12 TYR 0.009 0.001 TYR C 10 ARG 0.006 0.001 ARG C 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 7) link_NAG-ASN : angle 1.37382 ( 21) hydrogen bonds : bond 0.03494 ( 1226) hydrogen bonds : angle 3.79079 ( 3531) SS BOND : bond 0.00249 ( 14) SS BOND : angle 0.46145 ( 28) covalent geometry : bond 0.00268 (20146) covalent geometry : angle 0.57889 (27328) *********************** 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 208 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 2.355 Fit side-chains REVERT: A 5 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8368 (tm-30) REVERT: A 9 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: A 56 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8605 (pp30) REVERT: A 254 ARG cc_start: 0.8819 (tpp80) cc_final: 0.8534 (tpp80) REVERT: B 9 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8325 (tm-30) REVERT: B 337 GLU cc_start: 0.8850 (tp30) cc_final: 0.8521 (tm-30) REVERT: B 352 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8894 (tp30) REVERT: C 5 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 9 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8224 (tm-30) REVERT: C 29 ARG cc_start: 0.8548 (mmt90) cc_final: 0.8256 (mmt90) REVERT: C 56 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8316 (pp30) REVERT: C 89 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8719 (mm-40) REVERT: C 254 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8616 (tpp80) REVERT: C 337 GLU cc_start: 0.8778 (tp30) cc_final: 0.8506 (tp30) REVERT: D 5 GLN cc_start: 0.8771 (mt0) cc_final: 0.8568 (tm-30) REVERT: D 9 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8124 (tm-30) REVERT: D 56 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8595 (pp30) REVERT: D 337 GLU cc_start: 0.8658 (tp30) cc_final: 0.8360 (tm-30) REVERT: E 5 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8268 (tm-30) REVERT: E 9 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8259 (tm-30) REVERT: E 29 ARG cc_start: 0.8471 (mmt90) cc_final: 0.8229 (mmt90) REVERT: E 56 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8595 (pp30) REVERT: E 337 GLU cc_start: 0.8696 (tp30) cc_final: 0.8396 (tm-30) REVERT: F 9 GLU cc_start: 0.8780 (tt0) cc_final: 0.8449 (tm-30) REVERT: F 56 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8600 (pp30) REVERT: F 337 GLU cc_start: 0.8684 (tp30) cc_final: 0.8250 (tm-30) REVERT: G 5 GLN cc_start: 0.8809 (mt0) cc_final: 0.8579 (tm-30) REVERT: G 9 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: G 29 ARG cc_start: 0.8375 (mpt-90) cc_final: 0.7874 (mmt90) REVERT: G 337 GLU cc_start: 0.8620 (tp30) cc_final: 0.8070 (tm-30) outliers start: 42 outliers final: 9 residues processed: 197 average time/residue: 1.4369 time to fit residues: 317.8315 Evaluate side-chains 170 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 258 THR 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 Chi-restraints excluded: chain G residue 261 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 103 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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 C 134 HIS D 134 HIS E 89 GLN F 89 GLN F 134 HIS G 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.082544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.062828 restraints weight = 47001.996| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.43 r_work: 0.2876 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20167 Z= 0.178 Angle : 0.608 12.923 27377 Z= 0.288 Chirality : 0.040 0.135 3255 Planarity : 0.004 0.040 3178 Dihedral : 12.446 88.858 4522 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.10 % Allowed : 13.69 % Favored : 83.22 % 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: 0.97 (0.18), residues: 2380 helix: 1.85 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.23 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.001 0.001 HIS B 134 PHE 0.012 0.001 PHE F 54 TYR 0.011 0.001 TYR C 10 ARG 0.007 0.001 ARG F 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 7) link_NAG-ASN : angle 1.30537 ( 21) hydrogen bonds : bond 0.03604 ( 1226) hydrogen bonds : angle 3.79807 ( 3531) SS BOND : bond 0.00398 ( 14) SS BOND : angle 0.78480 ( 28) covalent geometry : bond 0.00424 (20146) covalent geometry : angle 0.60665 (27328) *********************** 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 218 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 161 time to evaluate : 2.155 Fit side-chains REVERT: A 9 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: A 29 ARG cc_start: 0.8495 (mmt90) cc_final: 0.8199 (mmt90) REVERT: A 56 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8607 (pp30) REVERT: A 254 ARG cc_start: 0.8885 (tpp80) cc_final: 0.8584 (tpp80) REVERT: A 337 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8108 (tm-30) REVERT: B 9 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: B 254 ARG cc_start: 0.8760 (tpp80) cc_final: 0.8529 (tpp80) REVERT: B 337 GLU cc_start: 0.8828 (tp30) cc_final: 0.8546 (tm-30) REVERT: B 352 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8919 (tp30) REVERT: C 5 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8365 (tm-30) REVERT: C 9 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: C 29 ARG cc_start: 0.8605 (mmt90) cc_final: 0.8203 (mmm-85) REVERT: C 254 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8673 (tpp80) REVERT: C 337 GLU cc_start: 0.8835 (tp30) cc_final: 0.8591 (tp30) REVERT: D 5 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: D 9 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8148 (tm-30) REVERT: D 56 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8593 (tm-30) REVERT: D 254 ARG cc_start: 0.8723 (tpp80) cc_final: 0.8361 (tpp80) REVERT: D 337 GLU cc_start: 0.8629 (tp30) cc_final: 0.8394 (tm-30) REVERT: E 5 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8341 (tm-30) REVERT: E 9 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8272 (tm-30) REVERT: E 337 GLU cc_start: 0.8668 (tp30) cc_final: 0.8058 (tm-30) REVERT: F 9 GLU cc_start: 0.8762 (tt0) cc_final: 0.8557 (tm-30) REVERT: F 56 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8644 (pp30) REVERT: F 337 GLU cc_start: 0.8731 (tp30) cc_final: 0.8249 (tm-30) REVERT: G 5 GLN cc_start: 0.8819 (mt0) cc_final: 0.8564 (tm-30) REVERT: G 9 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: G 337 GLU cc_start: 0.8703 (tp30) cc_final: 0.8490 (tm-30) outliers start: 57 outliers final: 24 residues processed: 200 average time/residue: 1.4294 time to fit residues: 320.6041 Evaluate side-chains 185 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 89 GLN 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 B residue 305 VAL Chi-restraints excluded: chain C residue 9 GLU 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 5 GLN 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 89 GLN Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 258 THR 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 258 THR 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 156 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 E 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.081350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.061414 restraints weight = 47412.713| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.42 r_work: 0.2839 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 20167 Z= 0.232 Angle : 0.644 11.858 27377 Z= 0.305 Chirality : 0.041 0.138 3255 Planarity : 0.004 0.042 3178 Dihedral : 12.408 84.516 4522 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.93 % Allowed : 14.94 % Favored : 82.13 % 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: 0.92 (0.18), residues: 2380 helix: 1.80 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.22 (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 G 106 PHE 0.016 0.002 PHE F 54 TYR 0.012 0.002 TYR C 10 ARG 0.010 0.001 ARG D 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 7) link_NAG-ASN : angle 1.14143 ( 21) hydrogen bonds : bond 0.03770 ( 1226) hydrogen bonds : angle 3.89833 ( 3531) SS BOND : bond 0.00542 ( 14) SS BOND : angle 1.00200 ( 28) covalent geometry : bond 0.00551 (20146) covalent geometry : angle 0.64263 (27328) *********************** 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 215 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 2.170 Fit side-chains REVERT: A 9 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: A 254 ARG cc_start: 0.8932 (tpp80) cc_final: 0.8644 (tpp80) REVERT: B 9 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: B 31 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8366 (tt0) REVERT: B 337 GLU cc_start: 0.8796 (tp30) cc_final: 0.8400 (tm-30) REVERT: B 352 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8876 (tm-30) REVERT: C 5 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8388 (tm-30) REVERT: C 9 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: C 29 ARG cc_start: 0.8664 (mmt90) cc_final: 0.8218 (mmm-85) REVERT: C 254 ARG cc_start: 0.8897 (tpp80) cc_final: 0.8686 (tpp80) REVERT: D 5 GLN cc_start: 0.8813 (mt0) cc_final: 0.8575 (tm-30) REVERT: D 9 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8125 (tm-30) REVERT: D 337 GLU cc_start: 0.8636 (tp30) cc_final: 0.8072 (tm-30) REVERT: E 5 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8402 (tm-30) REVERT: E 9 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8191 (tm-30) REVERT: E 337 GLU cc_start: 0.8681 (tp30) cc_final: 0.8089 (tm-30) REVERT: E 352 GLU cc_start: 0.9158 (tp30) cc_final: 0.8800 (tm-30) REVERT: F 337 GLU cc_start: 0.8721 (tp30) cc_final: 0.8257 (tm-30) REVERT: G 5 GLN cc_start: 0.8832 (mt0) cc_final: 0.8578 (tm-30) REVERT: G 9 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: G 254 ARG cc_start: 0.8701 (tpp80) cc_final: 0.8469 (tpp80) REVERT: G 337 GLU cc_start: 0.8698 (tp30) cc_final: 0.8223 (tm-30) outliers start: 54 outliers final: 28 residues processed: 203 average time/residue: 1.3363 time to fit residues: 305.8559 Evaluate side-chains 186 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 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 B residue 305 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 258 THR 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 261 ASP 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 E residue 258 THR 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 258 THR Chi-restraints excluded: chain G residue 261 ASP 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 158 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 138 optimal weight: 0.0060 chunk 94 optimal weight: 0.9990 chunk 210 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 35 optimal weight: 0.0870 overall best weight: 0.5174 ------------------------------------------------------------------------------- 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 E 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.085299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066015 restraints weight = 46753.741| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.49 r_work: 0.2960 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20167 Z= 0.109 Angle : 0.552 9.370 27377 Z= 0.268 Chirality : 0.038 0.139 3255 Planarity : 0.004 0.044 3178 Dihedral : 11.684 74.635 4522 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.17 % Allowed : 16.40 % Favored : 81.42 % 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: 1.18 (0.18), residues: 2380 helix: 2.01 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.14 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.002 0.001 HIS E 106 PHE 0.010 0.001 PHE D 54 TYR 0.009 0.001 TYR G 111 ARG 0.009 0.001 ARG D 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 7) link_NAG-ASN : angle 1.17445 ( 21) hydrogen bonds : bond 0.03129 ( 1226) hydrogen bonds : angle 3.67790 ( 3531) SS BOND : bond 0.00198 ( 14) SS BOND : angle 0.50550 ( 28) covalent geometry : bond 0.00236 (20146) covalent geometry : angle 0.55125 (27328) *********************** 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 211 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 2.389 Fit side-chains REVERT: A 9 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: A 29 ARG cc_start: 0.8326 (mmt90) cc_final: 0.7945 (mmt90) REVERT: A 56 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8517 (pp30) REVERT: A 254 ARG cc_start: 0.8942 (tpp80) cc_final: 0.8677 (tpp80) REVERT: A 337 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7872 (tm-30) REVERT: B 9 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: B 31 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8362 (tt0) REVERT: B 337 GLU cc_start: 0.8783 (tp30) cc_final: 0.8523 (tm-30) REVERT: B 352 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8858 (tm-30) REVERT: C 5 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8425 (tm-30) REVERT: C 9 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8062 (tm-30) REVERT: C 29 ARG cc_start: 0.8422 (mmt90) cc_final: 0.7844 (mmm-85) REVERT: C 261 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8811 (t0) REVERT: C 337 GLU cc_start: 0.8817 (tp30) cc_final: 0.8050 (tm-30) REVERT: D 9 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8121 (tm-30) REVERT: D 56 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8473 (pp30) REVERT: D 254 ARG cc_start: 0.8622 (tpp80) cc_final: 0.8365 (tpp80) REVERT: D 261 ASP cc_start: 0.9182 (OUTLIER) cc_final: 0.8962 (t0) REVERT: D 337 GLU cc_start: 0.8579 (tp30) cc_final: 0.7935 (tm-30) REVERT: E 5 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8378 (tm-30) REVERT: E 9 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8299 (tm-30) REVERT: E 254 ARG cc_start: 0.8920 (tpp80) cc_final: 0.8704 (tpp80) REVERT: E 337 GLU cc_start: 0.8643 (tp30) cc_final: 0.8109 (tm-30) REVERT: F 337 GLU cc_start: 0.8712 (tp30) cc_final: 0.8111 (tm-30) REVERT: G 9 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8293 (tm-30) REVERT: G 254 ARG cc_start: 0.8676 (tpp80) cc_final: 0.8456 (tpp80) REVERT: G 261 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8783 (t0) REVERT: G 337 GLU cc_start: 0.8655 (tp30) cc_final: 0.8416 (tm-30) outliers start: 40 outliers final: 19 residues processed: 194 average time/residue: 1.3796 time to fit residues: 301.1241 Evaluate side-chains 181 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 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 C residue 31 GLU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 261 ASP 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 261 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E 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 261 ASP 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.4026 > 50: distance: 26 - 45: 6.151 distance: 32 - 53: 7.432 distance: 37 - 58: 9.514 distance: 41 - 45: 3.590 distance: 42 - 65: 28.362 distance: 45 - 46: 5.785 distance: 46 - 47: 6.234 distance: 46 - 49: 7.912 distance: 47 - 48: 6.286 distance: 47 - 53: 5.384 distance: 48 - 69: 10.673 distance: 49 - 50: 5.221 distance: 49 - 51: 8.514 distance: 50 - 52: 12.634 distance: 53 - 54: 9.310 distance: 54 - 55: 10.159 distance: 54 - 57: 11.082 distance: 55 - 56: 17.692 distance: 58 - 59: 6.214 distance: 59 - 60: 11.816 distance: 59 - 62: 8.654 distance: 60 - 61: 32.662 distance: 60 - 65: 30.595 distance: 62 - 63: 6.389 distance: 62 - 64: 5.048 distance: 65 - 66: 54.256 distance: 66 - 67: 27.006 distance: 67 - 68: 5.835 distance: 67 - 69: 17.737 distance: 69 - 70: 15.592 distance: 70 - 71: 9.844 distance: 70 - 73: 10.262 distance: 71 - 72: 10.709 distance: 71 - 77: 13.405 distance: 72 - 100: 11.892 distance: 73 - 74: 3.478 distance: 74 - 75: 7.276 distance: 74 - 76: 7.789 distance: 77 - 78: 6.675 distance: 77 - 83: 8.224 distance: 78 - 79: 6.499 distance: 78 - 81: 9.630 distance: 79 - 80: 8.749 distance: 79 - 84: 9.102 distance: 80 - 108: 12.721 distance: 81 - 82: 8.348 distance: 82 - 83: 8.211 distance: 84 - 85: 10.566 distance: 85 - 86: 6.277 distance: 85 - 88: 11.146 distance: 86 - 87: 8.232 distance: 86 - 92: 3.766 distance: 87 - 116: 12.015 distance: 88 - 89: 3.197 distance: 89 - 90: 11.169 distance: 89 - 91: 20.810 distance: 92 - 93: 7.456 distance: 93 - 94: 8.141 distance: 93 - 96: 5.700 distance: 94 - 95: 4.898 distance: 94 - 100: 3.657 distance: 95 - 122: 5.551 distance: 97 - 98: 8.916 distance: 97 - 99: 6.602 distance: 100 - 101: 4.731 distance: 101 - 102: 7.243 distance: 101 - 104: 8.037 distance: 102 - 103: 5.139 distance: 102 - 108: 7.968 distance: 103 - 130: 4.244 distance: 104 - 105: 9.283 distance: 105 - 106: 10.182 distance: 108 - 109: 7.740 distance: 109 - 110: 3.827 distance: 110 - 111: 6.963 distance: 112 - 113: 10.902 distance: 112 - 114: 6.320 distance: 113 - 115: 3.754