Starting phenix.real_space_refine on Thu Jun 12 21:23:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6plw_20378/06_2025/6plw_20378.cif Found real_map, /net/cci-nas-00/data/ceres_data/6plw_20378/06_2025/6plw_20378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6plw_20378/06_2025/6plw_20378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6plw_20378/06_2025/6plw_20378.map" model { file = "/net/cci-nas-00/data/ceres_data/6plw_20378/06_2025/6plw_20378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6plw_20378/06_2025/6plw_20378.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9180 2.51 5 N 2265 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14095 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.33, per 1000 atoms: 0.59 Number of scatterers: 14095 At special positions: 0 Unit cell: (106.99, 105.344, 135.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2560 8.00 N 2265 7.00 C 9180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.7 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 25 sheets defined 39.3% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 removed outlier: 3.880A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.195A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 105 through 109 removed outlier: 4.015A pdb=" N ILE A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.675A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 285 removed outlier: 3.823A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 removed outlier: 3.548A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.723A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.503A pdb=" N SER A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.577A pdb=" N PHE A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 34 removed outlier: 3.881A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.195A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 105 through 109 removed outlier: 4.015A pdb=" N ILE B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.675A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 285 removed outlier: 3.823A pdb=" N LEU B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 325 removed outlier: 3.548A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.722A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.503A pdb=" N SER B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.577A pdb=" N PHE B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 removed outlier: 3.881A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.194A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 105 through 109 removed outlier: 4.015A pdb=" N ILE C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.675A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 285 removed outlier: 3.823A pdb=" N LEU C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 325 removed outlier: 3.548A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 400 removed outlier: 3.723A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 removed outlier: 3.503A pdb=" N SER C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.577A pdb=" N PHE C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE C 423 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 34 removed outlier: 3.880A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.195A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 105 through 109 removed outlier: 4.016A pdb=" N ILE D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.675A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 285 removed outlier: 3.823A pdb=" N LEU D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 325 removed outlier: 3.548A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 400 removed outlier: 3.723A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS D 400 " --> pdb=" O ILE D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 removed outlier: 3.503A pdb=" N SER D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.577A pdb=" N PHE D 420 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 34 removed outlier: 3.880A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.195A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 105 through 109 removed outlier: 4.015A pdb=" N ILE E 109 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.674A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 285 removed outlier: 3.822A pdb=" N LEU E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 325 removed outlier: 3.548A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 400 removed outlier: 3.723A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS E 400 " --> pdb=" O ILE E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 425 removed outlier: 3.503A pdb=" N SER E 406 " --> pdb=" O ILE E 402 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.577A pdb=" N PHE E 420 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE E 423 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.504A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.272A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.505A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 123 removed outlier: 6.272A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.504A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 123 removed outlier: 6.272A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.505A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 123 removed outlier: 6.272A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.505A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 6.271A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 720 hydrogen bonds defined for protein. 2070 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.72 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4350 1.35 - 1.47: 3927 1.47 - 1.60: 6013 1.60 - 1.73: 0 1.73 - 1.86: 150 Bond restraints: 14440 Sorted by residual: bond pdb=" CB ARG A 234 " pdb=" CG ARG A 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.70e+00 bond pdb=" CB ARG D 234 " pdb=" CG ARG D 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.70e+00 bond pdb=" CB ARG E 234 " pdb=" CG ARG E 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.69e+00 bond pdb=" CB ARG B 234 " pdb=" CG ARG B 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.66e+00 bond pdb=" CB ARG C 234 " pdb=" CG ARG C 234 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.57e+00 ... (remaining 14435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 19037 2.60 - 5.19: 487 5.19 - 7.79: 71 7.79 - 10.39: 10 10.39 - 12.99: 5 Bond angle restraints: 19610 Sorted by residual: angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 134.53 -12.99 1.91e+00 2.74e-01 4.62e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 134.51 -12.97 1.91e+00 2.74e-01 4.61e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 134.50 -12.96 1.91e+00 2.74e-01 4.60e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 134.50 -12.96 1.91e+00 2.74e-01 4.60e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 134.49 -12.95 1.91e+00 2.74e-01 4.60e+01 ... (remaining 19605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 8531 21.59 - 43.18: 194 43.18 - 64.77: 25 64.77 - 86.36: 35 86.36 - 107.95: 20 Dihedral angle restraints: 8805 sinusoidal: 3690 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual 93.00 49.65 43.35 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 49.67 43.33 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 49.67 43.33 1 1.00e+01 1.00e-02 2.62e+01 ... (remaining 8802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1606 0.059 - 0.118: 541 0.118 - 0.177: 88 0.177 - 0.236: 19 0.236 - 0.295: 6 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2257 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 128 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C THR B 128 " -0.040 2.00e-02 2.50e+03 pdb=" O THR B 128 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 129 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 128 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C THR E 128 " 0.040 2.00e-02 2.50e+03 pdb=" O THR E 128 " -0.015 2.00e-02 2.50e+03 pdb=" N THR E 129 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 128 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C THR A 128 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 128 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 129 " -0.013 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4128 2.80 - 3.33: 12273 3.33 - 3.85: 23354 3.85 - 4.38: 27386 4.38 - 4.90: 45549 Nonbonded interactions: 112690 Sorted by model distance: nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.277 3.040 ... (remaining 112685 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.580 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.010 0.065 14465 Z= 0.437 Angle : 1.027 12.987 19675 Z= 0.528 Chirality : 0.060 0.295 2260 Planarity : 0.007 0.047 2435 Dihedral : 13.315 107.951 5455 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: -4.80 (0.15), residues: 1710 helix: -4.53 (0.10), residues: 600 sheet: -1.36 (0.24), residues: 345 loop : -2.80 (0.17), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 110 HIS 0.006 0.002 HIS D 231 PHE 0.023 0.003 PHE B 115 TYR 0.026 0.003 TYR C 425 ARG 0.011 0.001 ARG C 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 5) link_NAG-ASN : angle 1.93356 ( 15) link_BETA1-4 : bond 0.00322 ( 10) link_BETA1-4 : angle 2.29120 ( 30) hydrogen bonds : bond 0.28279 ( 575) hydrogen bonds : angle 9.40116 ( 2070) SS BOND : bond 0.00711 ( 10) SS BOND : angle 3.38826 ( 20) covalent geometry : bond 0.00997 (14440) covalent geometry : angle 1.01745 (19610) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8392 (ttp) cc_final: 0.7531 (ttt) REVERT: A 28 GLU cc_start: 0.8966 (tp30) cc_final: 0.8739 (tm-30) REVERT: A 105 MET cc_start: 0.8435 (mmp) cc_final: 0.8130 (mpp) REVERT: A 249 LEU cc_start: 0.9356 (mt) cc_final: 0.9012 (pp) REVERT: A 317 TYR cc_start: 0.8371 (t80) cc_final: 0.7818 (t80) REVERT: B 173 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7715 (mp0) REVERT: B 249 LEU cc_start: 0.9329 (mt) cc_final: 0.8999 (pp) REVERT: C 105 MET cc_start: 0.8458 (mmp) cc_final: 0.8231 (mpp) REVERT: C 249 LEU cc_start: 0.9315 (mt) cc_final: 0.9031 (pp) REVERT: D 72 MET cc_start: 0.8996 (mtm) cc_final: 0.8753 (mtm) REVERT: D 173 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7616 (mm-30) REVERT: D 249 LEU cc_start: 0.9290 (mt) cc_final: 0.8993 (pp) REVERT: D 292 LYS cc_start: 0.9260 (mttt) cc_final: 0.9004 (mmmm) REVERT: D 317 TYR cc_start: 0.8351 (t80) cc_final: 0.8087 (t80) REVERT: E 249 LEU cc_start: 0.9299 (mt) cc_final: 0.8934 (pp) REVERT: E 416 ILE cc_start: 0.9509 (tp) cc_final: 0.9292 (tp) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 1.2291 time to fit residues: 433.9155 Evaluate side-chains 176 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 82 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 77 ASN B 82 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 77 ASN C 82 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 77 ASN D 82 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 82 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.061955 restraints weight = 34044.238| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.63 r_work: 0.2787 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14465 Z= 0.155 Angle : 0.732 10.256 19675 Z= 0.368 Chirality : 0.045 0.200 2260 Planarity : 0.005 0.050 2435 Dihedral : 11.397 70.379 2195 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.78 % Allowed : 10.20 % Favored : 87.02 % 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: -3.39 (0.17), residues: 1710 helix: -2.79 (0.16), residues: 615 sheet: -0.74 (0.26), residues: 345 loop : -2.40 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 110 HIS 0.003 0.001 HIS D 125 PHE 0.021 0.001 PHE D 258 TYR 0.016 0.001 TYR C 425 ARG 0.010 0.001 ARG C 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00032 ( 5) link_NAG-ASN : angle 0.88919 ( 15) link_BETA1-4 : bond 0.00633 ( 10) link_BETA1-4 : angle 2.59272 ( 30) hydrogen bonds : bond 0.05051 ( 575) hydrogen bonds : angle 5.24063 ( 2070) SS BOND : bond 0.01074 ( 10) SS BOND : angle 1.67579 ( 20) covalent geometry : bond 0.00323 (14440) covalent geometry : angle 0.72328 (19610) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.8245 (mp0) cc_final: 0.7822 (mm-30) REVERT: A 241 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9009 (mp) REVERT: A 300 ASP cc_start: 0.9295 (m-30) cc_final: 0.8979 (m-30) REVERT: B 28 GLU cc_start: 0.8366 (mp0) cc_final: 0.8073 (mp0) REVERT: B 43 ARG cc_start: 0.9561 (mtm-85) cc_final: 0.9328 (mtm180) REVERT: B 173 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8129 (mp0) REVERT: B 235 GLN cc_start: 0.9339 (mm-40) cc_final: 0.9092 (mm110) REVERT: B 241 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8916 (mp) REVERT: B 243 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8559 (mmm) REVERT: B 317 TYR cc_start: 0.8615 (t80) cc_final: 0.8302 (t80) REVERT: C 43 ARG cc_start: 0.9560 (mtm-85) cc_final: 0.9331 (mtm180) REVERT: C 105 MET cc_start: 0.9067 (mmp) cc_final: 0.8861 (mmp) REVERT: C 173 GLU cc_start: 0.8228 (mp0) cc_final: 0.7642 (mm-30) REVERT: C 243 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8566 (mmm) REVERT: C 300 ASP cc_start: 0.9269 (m-30) cc_final: 0.8962 (m-30) REVERT: C 317 TYR cc_start: 0.8539 (t80) cc_final: 0.8064 (t80) REVERT: D 28 GLU cc_start: 0.8425 (mp0) cc_final: 0.8216 (mp0) REVERT: D 72 MET cc_start: 0.9266 (mtm) cc_final: 0.9060 (mtm) REVERT: D 105 MET cc_start: 0.9086 (mmp) cc_final: 0.8840 (mmp) REVERT: D 173 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8041 (mm-30) REVERT: D 235 GLN cc_start: 0.9286 (mm-40) cc_final: 0.9039 (mm110) REVERT: D 243 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8548 (mmm) REVERT: D 391 MET cc_start: 0.0288 (tpt) cc_final: -0.0024 (tpp) REVERT: E 72 MET cc_start: 0.9246 (mtm) cc_final: 0.9008 (mmm) REVERT: E 235 GLN cc_start: 0.9262 (mm-40) cc_final: 0.9018 (mm110) REVERT: E 236 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7881 (tmm) REVERT: E 243 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8724 (mmm) REVERT: E 300 ASP cc_start: 0.9273 (m-30) cc_final: 0.8982 (m-30) REVERT: E 317 TYR cc_start: 0.8575 (t80) cc_final: 0.8319 (t80) REVERT: E 391 MET cc_start: 0.0592 (tpt) cc_final: 0.0222 (tpp) outliers start: 42 outliers final: 14 residues processed: 246 average time/residue: 1.0815 time to fit residues: 296.2288 Evaluate side-chains 204 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 155 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS B 77 ASN B 166 GLN B 231 HIS C 62 ASN C 77 ASN C 231 HIS D 62 ASN D 77 ASN D 231 HIS E 231 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.091374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.061322 restraints weight = 33839.233| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.77 r_work: 0.2707 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14465 Z= 0.177 Angle : 0.682 9.298 19675 Z= 0.339 Chirality : 0.045 0.155 2260 Planarity : 0.004 0.028 2435 Dihedral : 8.550 58.547 2195 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.52 % Allowed : 11.19 % Favored : 86.29 % 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: -2.36 (0.19), residues: 1710 helix: -1.81 (0.18), residues: 620 sheet: -0.22 (0.28), residues: 345 loop : -1.91 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 186 HIS 0.002 0.001 HIS B 231 PHE 0.013 0.001 PHE D 258 TYR 0.014 0.001 TYR C 238 ARG 0.011 0.001 ARG A 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 5) link_NAG-ASN : angle 1.00584 ( 15) link_BETA1-4 : bond 0.00437 ( 10) link_BETA1-4 : angle 2.66236 ( 30) hydrogen bonds : bond 0.04118 ( 575) hydrogen bonds : angle 4.69133 ( 2070) SS BOND : bond 0.00496 ( 10) SS BOND : angle 2.43024 ( 20) covalent geometry : bond 0.00401 (14440) covalent geometry : angle 0.67029 (19610) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8336 (mp0) cc_final: 0.8068 (mp0) REVERT: A 241 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8886 (mp) REVERT: A 243 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8469 (mpp) REVERT: A 300 ASP cc_start: 0.9378 (m-30) cc_final: 0.9050 (m-30) REVERT: A 317 TYR cc_start: 0.8592 (t80) cc_final: 0.8370 (t80) REVERT: B 28 GLU cc_start: 0.8477 (mp0) cc_final: 0.8030 (mp0) REVERT: B 75 ARG cc_start: 0.9012 (ttm110) cc_final: 0.8753 (mtp-110) REVERT: B 156 MET cc_start: 0.9399 (mmt) cc_final: 0.9014 (mmt) REVERT: B 173 GLU cc_start: 0.8748 (mt-10) cc_final: 0.7882 (mp0) REVERT: B 243 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8348 (mpp) REVERT: B 262 MET cc_start: 0.7204 (mpt) cc_final: 0.6931 (pmm) REVERT: B 300 ASP cc_start: 0.9352 (m-30) cc_final: 0.8984 (m-30) REVERT: B 306 CYS cc_start: 0.8729 (m) cc_final: 0.8193 (t) REVERT: B 317 TYR cc_start: 0.8637 (t80) cc_final: 0.8371 (t80) REVERT: C 105 MET cc_start: 0.9195 (mmp) cc_final: 0.8946 (mmp) REVERT: C 163 MET cc_start: 0.8830 (mpp) cc_final: 0.8060 (mtp) REVERT: C 243 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8541 (mmm) REVERT: C 300 ASP cc_start: 0.9340 (m-30) cc_final: 0.9013 (m-30) REVERT: C 306 CYS cc_start: 0.8560 (m) cc_final: 0.8261 (t) REVERT: C 317 TYR cc_start: 0.8555 (t80) cc_final: 0.8148 (t80) REVERT: D 31 ASP cc_start: 0.9179 (m-30) cc_final: 0.8679 (m-30) REVERT: D 75 ARG cc_start: 0.9019 (ttm110) cc_final: 0.8787 (mtp-110) REVERT: D 173 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8027 (mp0) REVERT: D 243 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8562 (mmm) REVERT: D 262 MET cc_start: 0.7332 (mpt) cc_final: 0.7048 (pmm) REVERT: D 300 ASP cc_start: 0.9332 (m-30) cc_final: 0.8958 (m-30) REVERT: D 317 TYR cc_start: 0.8579 (t80) cc_final: 0.8367 (t80) REVERT: E 156 MET cc_start: 0.9431 (mmt) cc_final: 0.9202 (mmt) REVERT: E 163 MET cc_start: 0.9061 (mtm) cc_final: 0.8317 (mpp) REVERT: E 243 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8712 (mmm) REVERT: E 262 MET cc_start: 0.7192 (mmt) cc_final: 0.6961 (mpm) REVERT: E 300 ASP cc_start: 0.9342 (m-30) cc_final: 0.9024 (m-30) REVERT: E 317 TYR cc_start: 0.8571 (t80) cc_final: 0.8355 (t80) REVERT: E 391 MET cc_start: 0.0838 (tpt) cc_final: 0.0552 (tpp) outliers start: 38 outliers final: 18 residues processed: 218 average time/residue: 1.0305 time to fit residues: 252.2136 Evaluate side-chains 194 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 101 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.059764 restraints weight = 34130.855| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.80 r_work: 0.2665 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14465 Z= 0.225 Angle : 0.692 9.648 19675 Z= 0.345 Chirality : 0.046 0.202 2260 Planarity : 0.004 0.027 2435 Dihedral : 6.802 53.802 2195 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.38 % Allowed : 11.59 % Favored : 85.03 % 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: -1.70 (0.20), residues: 1710 helix: -1.11 (0.20), residues: 620 sheet: 0.16 (0.30), residues: 345 loop : -1.69 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 186 HIS 0.001 0.000 HIS D 231 PHE 0.010 0.001 PHE E 258 TYR 0.013 0.002 TYR E 144 ARG 0.005 0.001 ARG A 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 5) link_NAG-ASN : angle 1.06579 ( 15) link_BETA1-4 : bond 0.00366 ( 10) link_BETA1-4 : angle 2.53060 ( 30) hydrogen bonds : bond 0.03748 ( 575) hydrogen bonds : angle 4.52378 ( 2070) SS BOND : bond 0.00996 ( 10) SS BOND : angle 2.62083 ( 20) covalent geometry : bond 0.00510 (14440) covalent geometry : angle 0.68027 (19610) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9267 (mmm) cc_final: 0.9024 (tpt) REVERT: A 243 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8495 (mpp) REVERT: A 300 ASP cc_start: 0.9369 (m-30) cc_final: 0.9001 (m-30) REVERT: A 306 CYS cc_start: 0.8790 (m) cc_final: 0.8272 (t) REVERT: B 71 THR cc_start: 0.9568 (OUTLIER) cc_final: 0.9301 (p) REVERT: B 72 MET cc_start: 0.9260 (mtm) cc_final: 0.8867 (mmt) REVERT: B 75 ARG cc_start: 0.9019 (ttm110) cc_final: 0.8752 (mtp-110) REVERT: B 166 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8167 (tp40) REVERT: B 173 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8068 (mm-30) REVERT: B 241 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8813 (mp) REVERT: B 243 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8380 (mmm) REVERT: B 300 ASP cc_start: 0.9353 (m-30) cc_final: 0.8939 (m-30) REVERT: B 306 CYS cc_start: 0.8719 (m) cc_final: 0.8252 (t) REVERT: C 71 THR cc_start: 0.9464 (OUTLIER) cc_final: 0.9171 (p) REVERT: C 243 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8497 (mmm) REVERT: C 300 ASP cc_start: 0.9334 (m-30) cc_final: 0.9000 (m-30) REVERT: C 306 CYS cc_start: 0.8623 (m) cc_final: 0.8298 (t) REVERT: D 72 MET cc_start: 0.9226 (mtm) cc_final: 0.8802 (mmm) REVERT: D 75 ARG cc_start: 0.9036 (ttm110) cc_final: 0.8790 (mtp-110) REVERT: D 105 MET cc_start: 0.9212 (mmp) cc_final: 0.8830 (mmp) REVERT: D 156 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8810 (tpp) REVERT: D 166 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7866 (tp40) REVERT: D 173 GLU cc_start: 0.8689 (mt-10) cc_final: 0.7984 (mp0) REVERT: D 242 GLN cc_start: 0.8825 (tp40) cc_final: 0.8488 (tm-30) REVERT: D 243 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8842 (mmm) REVERT: D 262 MET cc_start: 0.7318 (mpt) cc_final: 0.7048 (pmm) REVERT: D 292 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.8857 (mmmm) REVERT: D 300 ASP cc_start: 0.9304 (m-30) cc_final: 0.8909 (m-30) REVERT: E 72 MET cc_start: 0.9297 (mtm) cc_final: 0.8978 (mmt) REVERT: E 156 MET cc_start: 0.9485 (mmt) cc_final: 0.9056 (mmt) REVERT: E 163 MET cc_start: 0.9013 (mtm) cc_final: 0.8811 (mpp) REVERT: E 243 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8684 (mmm) REVERT: E 262 MET cc_start: 0.7193 (mmt) cc_final: 0.6987 (mpm) REVERT: E 300 ASP cc_start: 0.9340 (m-30) cc_final: 0.9028 (m-30) REVERT: E 306 CYS cc_start: 0.8595 (m) cc_final: 0.8265 (t) outliers start: 51 outliers final: 20 residues processed: 206 average time/residue: 1.0130 time to fit residues: 234.9179 Evaluate side-chains 202 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 149 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 202 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.092098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.062545 restraints weight = 34375.626| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.80 r_work: 0.2744 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14465 Z= 0.115 Angle : 0.640 10.151 19675 Z= 0.316 Chirality : 0.044 0.200 2260 Planarity : 0.003 0.028 2435 Dihedral : 5.881 42.450 2195 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.78 % Allowed : 13.58 % Favored : 83.64 % 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: -1.31 (0.20), residues: 1710 helix: -0.73 (0.21), residues: 615 sheet: 0.31 (0.30), residues: 345 loop : -1.48 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 259 HIS 0.001 0.000 HIS B 231 PHE 0.011 0.001 PHE E 258 TYR 0.024 0.001 TYR B 317 ARG 0.004 0.000 ARG A 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 5) link_NAG-ASN : angle 0.60492 ( 15) link_BETA1-4 : bond 0.00362 ( 10) link_BETA1-4 : angle 1.94730 ( 30) hydrogen bonds : bond 0.03502 ( 575) hydrogen bonds : angle 4.20099 ( 2070) SS BOND : bond 0.00332 ( 10) SS BOND : angle 2.01135 ( 20) covalent geometry : bond 0.00254 (14440) covalent geometry : angle 0.63348 (19610) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 1.622 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.9252 (mmm) cc_final: 0.8614 (mpm) REVERT: A 156 MET cc_start: 0.9357 (mmm) cc_final: 0.9090 (tpp) REVERT: A 202 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8837 (mp10) REVERT: A 241 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8825 (mp) REVERT: A 243 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8475 (mpp) REVERT: A 300 ASP cc_start: 0.9315 (m-30) cc_final: 0.8983 (m-30) REVERT: A 306 CYS cc_start: 0.8642 (m) cc_final: 0.8304 (t) REVERT: A 317 TYR cc_start: 0.8487 (t80) cc_final: 0.8253 (t80) REVERT: B 43 ARG cc_start: 0.9430 (mtm-85) cc_final: 0.9221 (mtp-110) REVERT: B 72 MET cc_start: 0.9201 (mtm) cc_final: 0.8821 (mmt) REVERT: B 75 ARG cc_start: 0.9065 (ttm110) cc_final: 0.8825 (ttm110) REVERT: B 105 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8524 (mpm) REVERT: B 166 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8291 (tp40) REVERT: B 173 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8047 (mm-30) REVERT: B 243 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8340 (mpp) REVERT: B 300 ASP cc_start: 0.9313 (m-30) cc_final: 0.8915 (m-30) REVERT: B 306 CYS cc_start: 0.8661 (m) cc_final: 0.8216 (t) REVERT: B 317 TYR cc_start: 0.8401 (t80) cc_final: 0.8101 (t80) REVERT: C 71 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9120 (p) REVERT: C 163 MET cc_start: 0.8635 (mpp) cc_final: 0.8153 (mtp) REVERT: C 243 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8585 (mmm) REVERT: C 300 ASP cc_start: 0.9302 (m-30) cc_final: 0.8962 (m-30) REVERT: C 306 CYS cc_start: 0.8550 (m) cc_final: 0.8262 (t) REVERT: C 317 TYR cc_start: 0.8471 (t80) cc_final: 0.8235 (t80) REVERT: D 43 ARG cc_start: 0.9552 (mtm-85) cc_final: 0.9266 (mtm-85) REVERT: D 75 ARG cc_start: 0.9079 (ttm110) cc_final: 0.8815 (mtp-110) REVERT: D 173 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8037 (mm-30) REVERT: D 214 CYS cc_start: 0.6903 (p) cc_final: 0.6667 (p) REVERT: D 242 GLN cc_start: 0.8850 (tp40) cc_final: 0.8525 (tm-30) REVERT: D 243 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8539 (mpp) REVERT: D 262 MET cc_start: 0.7284 (mpt) cc_final: 0.7067 (pmm) REVERT: D 300 ASP cc_start: 0.9272 (m-30) cc_final: 0.8899 (m-30) REVERT: D 317 TYR cc_start: 0.8557 (t80) cc_final: 0.8286 (t80) REVERT: D 391 MET cc_start: 0.0476 (tpt) cc_final: 0.0149 (tpp) REVERT: E 72 MET cc_start: 0.9236 (mtm) cc_final: 0.8963 (mmt) REVERT: E 156 MET cc_start: 0.9447 (mmt) cc_final: 0.8939 (mmt) REVERT: E 163 MET cc_start: 0.8928 (mtm) cc_final: 0.8675 (mpp) REVERT: E 243 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8632 (mmm) REVERT: E 300 ASP cc_start: 0.9297 (m-30) cc_final: 0.9015 (m-30) REVERT: E 306 CYS cc_start: 0.8663 (m) cc_final: 0.8302 (t) REVERT: E 317 TYR cc_start: 0.8469 (t80) cc_final: 0.8240 (t80) outliers start: 42 outliers final: 19 residues processed: 216 average time/residue: 1.1918 time to fit residues: 290.2706 Evaluate side-chains 208 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 169 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 143 optimal weight: 0.0970 chunk 150 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN E 62 ASN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.092350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.063002 restraints weight = 34582.954| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.80 r_work: 0.2749 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14465 Z= 0.119 Angle : 0.639 9.736 19675 Z= 0.315 Chirality : 0.045 0.226 2260 Planarity : 0.003 0.032 2435 Dihedral : 5.544 30.386 2195 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.38 % Allowed : 15.36 % Favored : 82.25 % 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 (0.20), residues: 1710 helix: -0.31 (0.21), residues: 595 sheet: 0.38 (0.29), residues: 345 loop : -1.26 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 259 HIS 0.001 0.000 HIS C 125 PHE 0.017 0.001 PHE A 203 TYR 0.016 0.001 TYR B 317 ARG 0.003 0.000 ARG A 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00042 ( 5) link_NAG-ASN : angle 0.63640 ( 15) link_BETA1-4 : bond 0.00344 ( 10) link_BETA1-4 : angle 1.74032 ( 30) hydrogen bonds : bond 0.03339 ( 575) hydrogen bonds : angle 4.08905 ( 2070) SS BOND : bond 0.00380 ( 10) SS BOND : angle 1.82855 ( 20) covalent geometry : bond 0.00270 (14440) covalent geometry : angle 0.63346 (19610) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 1.643 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.9145 (mmm) cc_final: 0.8623 (mpm) REVERT: A 202 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8891 (mm110) REVERT: A 243 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8464 (mpp) REVERT: A 300 ASP cc_start: 0.9305 (m-30) cc_final: 0.8976 (m-30) REVERT: A 317 TYR cc_start: 0.8569 (t80) cc_final: 0.8359 (t80) REVERT: B 43 ARG cc_start: 0.9415 (mtm-85) cc_final: 0.9148 (mtm180) REVERT: B 72 MET cc_start: 0.9152 (mtm) cc_final: 0.8795 (mmt) REVERT: B 75 ARG cc_start: 0.9096 (ttm110) cc_final: 0.8854 (mtp-110) REVERT: B 105 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8537 (mpm) REVERT: B 166 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8246 (tp40) REVERT: B 173 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8100 (mm-30) REVERT: B 202 GLN cc_start: 0.9172 (mt0) cc_final: 0.8969 (mt0) REVERT: B 243 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8254 (mpp) REVERT: B 292 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9085 (mtmm) REVERT: B 300 ASP cc_start: 0.9333 (m-30) cc_final: 0.8940 (m-30) REVERT: B 306 CYS cc_start: 0.8605 (m) cc_final: 0.8231 (t) REVERT: B 317 TYR cc_start: 0.8418 (t80) cc_final: 0.8140 (t80) REVERT: C 71 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9115 (p) REVERT: C 163 MET cc_start: 0.8599 (mpp) cc_final: 0.8157 (mtp) REVERT: C 202 GLN cc_start: 0.9132 (mt0) cc_final: 0.8860 (mm-40) REVERT: C 243 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8380 (mmm) REVERT: C 300 ASP cc_start: 0.9314 (m-30) cc_final: 0.8974 (m-30) REVERT: C 306 CYS cc_start: 0.8495 (m) cc_final: 0.8269 (t) REVERT: C 317 TYR cc_start: 0.8518 (t80) cc_final: 0.8274 (t80) REVERT: D 31 ASP cc_start: 0.9135 (m-30) cc_final: 0.8615 (m-30) REVERT: D 72 MET cc_start: 0.9256 (mtm) cc_final: 0.8951 (mmm) REVERT: D 75 ARG cc_start: 0.9096 (ttm110) cc_final: 0.8827 (mtp-110) REVERT: D 173 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8046 (mm-30) REVERT: D 202 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8914 (mt0) REVERT: D 242 GLN cc_start: 0.8851 (tp40) cc_final: 0.8517 (tm-30) REVERT: D 243 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8532 (mpp) REVERT: D 300 ASP cc_start: 0.9271 (m-30) cc_final: 0.8903 (m-30) REVERT: D 317 TYR cc_start: 0.8589 (t80) cc_final: 0.8363 (t80) REVERT: D 391 MET cc_start: 0.0501 (tpt) cc_final: 0.0227 (tpp) REVERT: E 72 MET cc_start: 0.9239 (mtm) cc_final: 0.8999 (mmt) REVERT: E 156 MET cc_start: 0.9457 (mmt) cc_final: 0.8947 (mmt) REVERT: E 163 MET cc_start: 0.8889 (mtm) cc_final: 0.8613 (mpp) REVERT: E 202 GLN cc_start: 0.9221 (mt0) cc_final: 0.8905 (mt0) REVERT: E 243 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8614 (mmm) REVERT: E 300 ASP cc_start: 0.9286 (m-30) cc_final: 0.9027 (m-30) REVERT: E 306 CYS cc_start: 0.8639 (m) cc_final: 0.8349 (t) REVERT: E 317 TYR cc_start: 0.8487 (t80) cc_final: 0.8272 (t80) outliers start: 36 outliers final: 17 residues processed: 197 average time/residue: 1.0324 time to fit residues: 228.5737 Evaluate side-chains 200 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 50.7349 > 50: distance: 40 - 57: 11.407 distance: 44 - 66: 5.347 distance: 48 - 72: 3.441 distance: 52 - 57: 10.365 distance: 53 - 78: 8.628 distance: 57 - 58: 7.915 distance: 58 - 59: 6.391 distance: 58 - 61: 6.280 distance: 59 - 60: 11.637 distance: 59 - 66: 7.696 distance: 61 - 62: 7.616 distance: 62 - 63: 6.403 distance: 63 - 64: 5.892 distance: 63 - 65: 5.724 distance: 66 - 67: 7.060 distance: 67 - 68: 10.994 distance: 67 - 70: 7.983 distance: 68 - 69: 15.123 distance: 68 - 72: 8.355 distance: 70 - 71: 10.273 distance: 72 - 73: 10.889 distance: 73 - 74: 16.223 distance: 73 - 76: 15.660 distance: 74 - 75: 15.698 distance: 74 - 78: 8.295 distance: 76 - 77: 23.456 distance: 78 - 79: 18.778 distance: 79 - 80: 24.710 distance: 80 - 81: 13.995 distance: 80 - 82: 14.828 distance: 82 - 83: 5.456 distance: 83 - 84: 4.404 distance: 83 - 86: 25.512 distance: 84 - 85: 8.698 distance: 84 - 88: 9.355 distance: 86 - 87: 6.304 distance: 88 - 89: 11.583 distance: 89 - 90: 14.435 distance: 89 - 92: 3.997 distance: 90 - 91: 11.433 distance: 90 - 99: 9.170 distance: 92 - 93: 10.403 distance: 94 - 95: 3.448 distance: 95 - 96: 3.780 distance: 96 - 97: 3.352 distance: 96 - 98: 3.095 distance: 99 - 100: 21.423 distance: 100 - 101: 22.633 distance: 100 - 103: 17.399 distance: 101 - 102: 7.263 distance: 101 - 104: 35.103 distance: 104 - 105: 16.199 distance: 105 - 106: 5.398 distance: 105 - 108: 13.444 distance: 106 - 107: 38.413 distance: 106 - 110: 14.674 distance: 108 - 109: 16.979 distance: 110 - 111: 17.984 distance: 111 - 112: 11.188 distance: 111 - 114: 14.606 distance: 112 - 113: 8.347 distance: 112 - 118: 13.347 distance: 114 - 115: 9.299 distance: 115 - 116: 10.735 distance: 115 - 117: 25.198 distance: 118 - 119: 12.563 distance: 118 - 124: 6.461 distance: 119 - 120: 10.230 distance: 119 - 122: 10.069 distance: 120 - 121: 22.103 distance: 120 - 125: 6.743 distance: 122 - 123: 5.483 distance: 123 - 124: 12.774