Starting phenix.real_space_refine on Wed Mar 4 14:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ply_20380/03_2026/6ply_20380.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ply_20380/03_2026/6ply_20380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ply_20380/03_2026/6ply_20380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ply_20380/03_2026/6ply_20380.map" model { file = "/net/cci-nas-00/data/ceres_data/6ply_20380/03_2026/6ply_20380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ply_20380/03_2026/6ply_20380.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.060 sd= 3.076 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 100 5.16 5 C 9230 2.51 5 N 2275 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 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14165 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP: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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'ABU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} Time building chain proxies: 3.30, per 1000 atoms: 0.23 Number of scatterers: 14165 At special positions: 0 Unit cell: (107.813, 104.521, 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 100 16.00 O 2560 8.00 N 2275 7.00 C 9230 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 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=2.04 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: 0.92 Conformation dependent library (CDL) restraints added in 599.6 milliseconds 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: 64 helices and 25 sheets defined 34.9% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.537A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.685A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.085A 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 238 through 243 Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 267 through 286 removed outlier: 3.531A pdb=" N THR A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 307 through 324 removed outlier: 3.858A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 3.976A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 409 through 428 removed outlier: 4.064A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.511A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.702A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 108 " --> pdb=" O MET B 105 " (cutoff:3.500A) removed outlier: 4.033A 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 238 through 243 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 256 through 259 Processing helix chain 'B' and resid 267 through 286 removed outlier: 3.770A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 324 removed outlier: 3.923A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 3.969A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 409 through 428 removed outlier: 4.089A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.545A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.721A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 108 " --> pdb=" O MET C 105 " (cutoff:3.500A) removed outlier: 4.048A 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 238 through 243 Processing helix chain 'C' and resid 244 through 255 removed outlier: 4.056A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 259 Processing helix chain 'C' and resid 267 through 286 removed outlier: 3.854A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 307 through 324 removed outlier: 3.990A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 3.986A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 405 Processing helix chain 'C' and resid 409 through 428 removed outlier: 4.016A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.568A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 109 removed outlier: 3.680A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 108 " --> pdb=" O MET D 105 " (cutoff:3.500A) removed outlier: 3.942A 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 238 through 243 Processing helix chain 'D' and resid 248 through 255 Processing helix chain 'D' and resid 256 through 259 Processing helix chain 'D' and resid 267 through 286 removed outlier: 3.785A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 307 through 324 removed outlier: 3.840A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 397 removed outlier: 3.968A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 405 Processing helix chain 'D' and resid 409 through 428 removed outlier: 4.052A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.600A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 109 removed outlier: 3.716A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 108 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 3.973A 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 238 through 243 Processing helix chain 'E' and resid 248 through 255 Processing helix chain 'E' and resid 256 through 259 Processing helix chain 'E' and resid 267 through 286 removed outlier: 3.826A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 307 through 324 removed outlier: 3.930A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 397 removed outlier: 3.984A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 405 Processing helix chain 'E' and resid 409 through 428 removed outlier: 4.127A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.626A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.334A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.289A 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 removed outlier: 3.506A pdb=" N ILE A 226 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.506A pdb=" N ILE A 226 " --> pdb=" O LEU A 172 " (cutoff:3.500A) 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: 4.643A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.273A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.259A 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: 4.663A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.627A 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 124 removed outlier: 6.336A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.255A 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: 4.615A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.299A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.232A 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: 4.593A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.313A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.219A 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 217 664 hydrogen bonds defined for protein. 1914 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4280 1.34 - 1.46: 3608 1.46 - 1.58: 6452 1.58 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 14510 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 14505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 18883 2.25 - 4.49: 629 4.49 - 6.74: 118 6.74 - 8.99: 41 8.99 - 11.23: 9 Bond angle restraints: 19680 Sorted by residual: angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 132.58 -11.04 1.91e+00 2.74e-01 3.34e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 132.56 -11.02 1.91e+00 2.74e-01 3.33e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 132.31 -10.77 1.91e+00 2.74e-01 3.18e+01 angle pdb=" N VAL E 37 " pdb=" CA VAL E 37 " pdb=" C VAL E 37 " ideal model delta sigma weight residual 113.71 108.92 4.79 9.50e-01 1.11e+00 2.54e+01 ... (remaining 19675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 8413 16.54 - 33.07: 350 33.07 - 49.61: 47 49.61 - 66.15: 36 66.15 - 82.69: 29 Dihedral angle restraints: 8875 sinusoidal: 3760 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASN A 160 " pdb=" C ASN A 160 " pdb=" N PHE A 161 " pdb=" CA PHE A 161 " ideal model delta harmonic sigma weight residual -180.00 -153.29 -26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N PHE C 161 " pdb=" CA PHE C 161 " ideal model delta harmonic sigma weight residual -180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 48.59 44.41 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 8872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1509 0.052 - 0.104: 588 0.104 - 0.156: 122 0.156 - 0.208: 29 0.208 - 0.260: 12 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.50e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+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 -2.53 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2257 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 410 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.56e+00 pdb=" N PRO E 411 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 411 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 411 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 410 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO B 411 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO A 411 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " -0.039 5.00e-02 4.00e+02 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4565 2.84 - 3.36: 12138 3.36 - 3.87: 22492 3.87 - 4.39: 26798 4.39 - 4.90: 45359 Nonbonded interactions: 111352 Sorted by model distance: nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.330 3.040 nonbonded pdb=" OE2 GLU A 69 " pdb=" NH2 ARG A 234 " model vdw 2.335 3.120 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.342 3.040 nonbonded pdb=" OE2 GLU D 69 " pdb=" NH2 ARG D 234 " model vdw 2.343 3.120 ... (remaining 111347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 23 through 428) selection = (chain 'B' and resid 23 through 428) selection = (chain 'C' and resid 23 through 428) selection = (chain 'D' and resid 23 through 428) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 2.050 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: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.130 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 14535 Z= 0.301 Angle : 1.034 11.234 19745 Z= 0.528 Chirality : 0.058 0.260 2260 Planarity : 0.007 0.073 2435 Dihedral : 11.636 82.687 5525 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.21 (0.14), residues: 1710 helix: -4.84 (0.08), residues: 560 sheet: -2.43 (0.22), residues: 390 loop : -2.73 (0.17), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 147 TYR 0.028 0.003 TYR A 425 PHE 0.023 0.003 PHE D 115 TRP 0.019 0.003 TRP B 110 HIS 0.004 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00725 (14510) covalent geometry : angle 1.02600 (19680) SS BOND : bond 0.01124 ( 10) SS BOND : angle 3.54137 ( 20) hydrogen bonds : bond 0.25368 ( 520) hydrogen bonds : angle 9.43034 ( 1914) link_BETA1-4 : bond 0.00566 ( 10) link_BETA1-4 : angle 2.08469 ( 30) link_NAG-ASN : bond 0.00109 ( 5) link_NAG-ASN : angle 0.79945 ( 15) *********************** 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 451 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.537 Fit side-chains REVERT: A 43 ARG cc_start: 0.8925 (mtm-85) cc_final: 0.8385 (mtm180) REVERT: A 97 ASP cc_start: 0.8116 (m-30) cc_final: 0.7368 (t0) REVERT: A 105 MET cc_start: 0.8044 (mmp) cc_final: 0.7838 (mmm) REVERT: A 126 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 138 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8280 (mttm) REVERT: A 181 ASP cc_start: 0.8159 (m-30) cc_final: 0.7919 (m-30) REVERT: A 206 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7601 (mttm) REVERT: A 210 ASP cc_start: 0.8100 (m-30) cc_final: 0.7477 (m-30) REVERT: A 227 GLU cc_start: 0.8340 (pt0) cc_final: 0.7965 (pt0) REVERT: A 233 GLU cc_start: 0.7087 (tt0) cc_final: 0.6725 (tt0) REVERT: A 420 PHE cc_start: 0.7620 (t80) cc_final: 0.7404 (t80) REVERT: B 28 GLU cc_start: 0.8571 (tp30) cc_final: 0.8353 (mt-10) REVERT: B 43 ARG cc_start: 0.9082 (mtm-85) cc_final: 0.8717 (mtm180) REVERT: B 75 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.6928 (mtp-110) REVERT: B 93 GLU cc_start: 0.8698 (pp20) cc_final: 0.8461 (pp20) REVERT: B 97 ASP cc_start: 0.8178 (m-30) cc_final: 0.7471 (t0) REVERT: B 105 MET cc_start: 0.8038 (mmp) cc_final: 0.7797 (mmm) REVERT: B 113 ASP cc_start: 0.8407 (p0) cc_final: 0.7928 (p0) REVERT: B 126 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7243 (mt-10) REVERT: B 138 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8354 (mttt) REVERT: B 227 GLU cc_start: 0.8427 (pt0) cc_final: 0.8072 (pt0) REVERT: B 246 PRO cc_start: 0.7756 (Cg_exo) cc_final: 0.7547 (Cg_endo) REVERT: C 28 GLU cc_start: 0.8517 (tp30) cc_final: 0.8277 (tt0) REVERT: C 43 ARG cc_start: 0.8992 (mtm-85) cc_final: 0.8697 (mtp180) REVERT: C 75 ARG cc_start: 0.7232 (ttm-80) cc_final: 0.6889 (mtp-110) REVERT: C 97 ASP cc_start: 0.8055 (m-30) cc_final: 0.7483 (t0) REVERT: C 113 ASP cc_start: 0.8457 (p0) cc_final: 0.7925 (p0) REVERT: C 126 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7217 (mt-10) REVERT: C 130 ASP cc_start: 0.7824 (m-30) cc_final: 0.7568 (m-30) REVERT: C 181 ASP cc_start: 0.8116 (m-30) cc_final: 0.7738 (m-30) REVERT: C 206 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7485 (mttm) REVERT: C 210 ASP cc_start: 0.7964 (m-30) cc_final: 0.7649 (m-30) REVERT: C 227 GLU cc_start: 0.8276 (pt0) cc_final: 0.7934 (pt0) REVERT: C 246 PRO cc_start: 0.7945 (Cg_exo) cc_final: 0.7705 (Cg_endo) REVERT: D 27 SER cc_start: 0.7970 (t) cc_final: 0.7747 (t) REVERT: D 43 ARG cc_start: 0.9036 (mtm-85) cc_final: 0.8539 (mtm180) REVERT: D 72 MET cc_start: 0.8691 (mtm) cc_final: 0.8448 (mtt) REVERT: D 75 ARG cc_start: 0.7141 (ttm-80) cc_final: 0.6826 (mtp-110) REVERT: D 97 ASP cc_start: 0.8124 (m-30) cc_final: 0.7389 (t0) REVERT: D 126 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7255 (mt-10) REVERT: D 138 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8238 (mttm) REVERT: D 206 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7853 (mtmt) REVERT: D 210 ASP cc_start: 0.8085 (m-30) cc_final: 0.7571 (m-30) REVERT: D 303 MET cc_start: 0.9210 (mmm) cc_final: 0.8711 (mmt) REVERT: E 28 GLU cc_start: 0.8582 (tp30) cc_final: 0.8285 (tt0) REVERT: E 43 ARG cc_start: 0.9028 (mtm-85) cc_final: 0.8590 (mtm180) REVERT: E 97 ASP cc_start: 0.7961 (m-30) cc_final: 0.7229 (t0) REVERT: E 126 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7135 (pm20) REVERT: E 210 ASP cc_start: 0.8079 (m-30) cc_final: 0.7573 (m-30) REVERT: E 227 GLU cc_start: 0.8355 (pt0) cc_final: 0.7978 (pt0) REVERT: E 233 GLU cc_start: 0.7081 (tt0) cc_final: 0.6783 (tt0) REVERT: E 246 PRO cc_start: 0.7798 (Cg_exo) cc_final: 0.7572 (Cg_endo) REVERT: E 419 ILE cc_start: 0.8102 (mt) cc_final: 0.7825 (mt) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.5541 time to fit residues: 274.6384 Evaluate side-chains 319 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN B 180 ASN B 231 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 282 GLN D 62 ASN D 123 ASN D 282 GLN E 62 ASN E 180 ASN E 282 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.145992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108990 restraints weight = 16933.552| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.24 r_work: 0.3116 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14535 Z= 0.170 Angle : 0.736 7.421 19745 Z= 0.372 Chirality : 0.048 0.185 2260 Planarity : 0.005 0.046 2435 Dihedral : 9.961 52.682 2195 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.40 % Allowed : 13.92 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.16), residues: 1710 helix: -3.37 (0.16), residues: 565 sheet: -1.51 (0.26), residues: 345 loop : -2.54 (0.17), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 407 TYR 0.016 0.002 TYR B 317 PHE 0.016 0.002 PHE A 322 TRP 0.012 0.002 TRP A 259 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00398 (14510) covalent geometry : angle 0.72638 (19680) SS BOND : bond 0.00564 ( 10) SS BOND : angle 1.73596 ( 20) hydrogen bonds : bond 0.05132 ( 520) hydrogen bonds : angle 5.64662 ( 1914) link_BETA1-4 : bond 0.00399 ( 10) link_BETA1-4 : angle 2.85890 ( 30) link_NAG-ASN : bond 0.00102 ( 5) link_NAG-ASN : angle 0.42290 ( 15) *********************** 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 393 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 341 time to evaluate : 0.574 Fit side-chains REVERT: A 43 ARG cc_start: 0.8997 (mtm-85) cc_final: 0.8598 (mtm180) REVERT: A 97 ASP cc_start: 0.8250 (m-30) cc_final: 0.7464 (t0) REVERT: A 126 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 130 ASP cc_start: 0.8336 (m-30) cc_final: 0.7929 (m-30) REVERT: A 138 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8421 (mttm) REVERT: A 206 LYS cc_start: 0.8541 (mtpt) cc_final: 0.7866 (mttm) REVERT: A 210 ASP cc_start: 0.8388 (m-30) cc_final: 0.8059 (m-30) REVERT: A 229 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8253 (mtp85) REVERT: A 391 MET cc_start: 0.5901 (tpt) cc_final: 0.5675 (tpt) REVERT: A 423 ILE cc_start: 0.9164 (mt) cc_final: 0.8946 (mt) REVERT: B 28 GLU cc_start: 0.8634 (tp30) cc_final: 0.8293 (tt0) REVERT: B 43 ARG cc_start: 0.9178 (mtm-85) cc_final: 0.8898 (mtm180) REVERT: B 75 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7454 (mtp-110) REVERT: B 97 ASP cc_start: 0.8222 (m-30) cc_final: 0.7524 (t0) REVERT: B 113 ASP cc_start: 0.8597 (p0) cc_final: 0.8214 (p0) REVERT: B 126 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7721 (mt-10) REVERT: B 235 GLN cc_start: 0.8365 (mm110) cc_final: 0.7995 (mt0) REVERT: B 418 ASN cc_start: 0.8348 (m-40) cc_final: 0.7971 (m-40) REVERT: B 423 ILE cc_start: 0.9204 (mt) cc_final: 0.8978 (mp) REVERT: C 28 GLU cc_start: 0.8637 (tp30) cc_final: 0.8320 (tt0) REVERT: C 43 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8880 (mtm180) REVERT: C 72 MET cc_start: 0.8963 (mtt) cc_final: 0.8756 (mtt) REVERT: C 75 ARG cc_start: 0.7902 (ttm-80) cc_final: 0.7396 (mtp-110) REVERT: C 97 ASP cc_start: 0.8241 (m-30) cc_final: 0.7571 (t0) REVERT: C 113 ASP cc_start: 0.8629 (p0) cc_final: 0.8238 (p0) REVERT: C 126 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 130 ASP cc_start: 0.8144 (m-30) cc_final: 0.7894 (m-30) REVERT: C 206 LYS cc_start: 0.8411 (mtpt) cc_final: 0.7942 (mttm) REVERT: C 210 ASP cc_start: 0.8314 (m-30) cc_final: 0.8080 (m-30) REVERT: C 243 MET cc_start: 0.7879 (tpp) cc_final: 0.7523 (mtt) REVERT: D 28 GLU cc_start: 0.8750 (tp30) cc_final: 0.8332 (tt0) REVERT: D 72 MET cc_start: 0.8891 (mtm) cc_final: 0.8642 (mtt) REVERT: D 75 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7369 (mtp-110) REVERT: D 97 ASP cc_start: 0.8143 (m-30) cc_final: 0.7425 (t0) REVERT: D 126 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7730 (mt-10) REVERT: D 138 LYS cc_start: 0.8678 (mtpt) cc_final: 0.8416 (mttm) REVERT: D 210 ASP cc_start: 0.8362 (m-30) cc_final: 0.8098 (m-30) REVERT: D 243 MET cc_start: 0.8089 (tpp) cc_final: 0.7557 (mtt) REVERT: D 303 MET cc_start: 0.9238 (mmm) cc_final: 0.8860 (mmt) REVERT: D 419 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7459 (mt) REVERT: E 28 GLU cc_start: 0.8626 (tp30) cc_final: 0.8229 (tt0) REVERT: E 43 ARG cc_start: 0.9084 (mtm-85) cc_final: 0.8840 (mtm180) REVERT: E 97 ASP cc_start: 0.8226 (m-30) cc_final: 0.7403 (t0) REVERT: E 126 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7880 (mt-10) REVERT: E 208 GLU cc_start: 0.8415 (tp30) cc_final: 0.8205 (tp30) REVERT: E 210 ASP cc_start: 0.8425 (m-30) cc_final: 0.8043 (m-30) REVERT: E 243 MET cc_start: 0.8076 (tpp) cc_final: 0.7345 (mpp) REVERT: E 322 PHE cc_start: 0.7955 (t80) cc_final: 0.7505 (t80) REVERT: E 423 ILE cc_start: 0.8959 (mt) cc_final: 0.8745 (mp) outliers start: 52 outliers final: 13 residues processed: 372 average time/residue: 0.5375 time to fit residues: 221.2116 Evaluate side-chains 306 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 291 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 316 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 120 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.146247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108095 restraints weight = 16638.751| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.32 r_work: 0.3072 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14535 Z= 0.186 Angle : 0.710 8.722 19745 Z= 0.356 Chirality : 0.048 0.171 2260 Planarity : 0.004 0.045 2435 Dihedral : 8.736 45.257 2195 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.53 % Allowed : 17.25 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.17), residues: 1710 helix: -2.61 (0.18), residues: 565 sheet: -0.97 (0.27), residues: 345 loop : -2.45 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 75 TYR 0.015 0.002 TYR A 317 PHE 0.019 0.002 PHE A 322 TRP 0.011 0.002 TRP A 259 HIS 0.002 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00447 (14510) covalent geometry : angle 0.70022 (19680) SS BOND : bond 0.00644 ( 10) SS BOND : angle 1.87681 ( 20) hydrogen bonds : bond 0.04425 ( 520) hydrogen bonds : angle 5.09632 ( 1914) link_BETA1-4 : bond 0.00381 ( 10) link_BETA1-4 : angle 2.82470 ( 30) link_NAG-ASN : bond 0.00070 ( 5) link_NAG-ASN : angle 0.63530 ( 15) *********************** 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 354 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 300 time to evaluate : 0.550 Fit side-chains REVERT: A 28 GLU cc_start: 0.8415 (tp30) cc_final: 0.8192 (tt0) REVERT: A 43 ARG cc_start: 0.8966 (mtm-85) cc_final: 0.8700 (mtm180) REVERT: A 72 MET cc_start: 0.8756 (mtm) cc_final: 0.8429 (mtt) REVERT: A 97 ASP cc_start: 0.8246 (m-30) cc_final: 0.7483 (t0) REVERT: A 126 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7589 (mt-10) REVERT: A 138 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8241 (mttm) REVERT: A 163 MET cc_start: 0.8452 (mpp) cc_final: 0.8024 (mtp) REVERT: A 206 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8172 (mttt) REVERT: A 210 ASP cc_start: 0.8323 (m-30) cc_final: 0.7975 (m-30) REVERT: A 227 GLU cc_start: 0.8534 (pt0) cc_final: 0.8307 (pt0) REVERT: B 28 GLU cc_start: 0.8571 (tp30) cc_final: 0.8223 (tt0) REVERT: B 43 ARG cc_start: 0.9060 (mtm-85) cc_final: 0.8771 (mtm180) REVERT: B 97 ASP cc_start: 0.8291 (m-30) cc_final: 0.7535 (t0) REVERT: B 113 ASP cc_start: 0.8598 (p0) cc_final: 0.8253 (p0) REVERT: B 126 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7718 (mt-10) REVERT: B 207 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8416 (tt0) REVERT: B 229 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8114 (mtp85) REVERT: B 235 GLN cc_start: 0.8399 (mm110) cc_final: 0.8040 (mt0) REVERT: B 243 MET cc_start: 0.8071 (tpp) cc_final: 0.7842 (mtt) REVERT: B 419 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7524 (mp) REVERT: B 420 PHE cc_start: 0.8565 (t80) cc_final: 0.8171 (m-80) REVERT: C 28 GLU cc_start: 0.8572 (tp30) cc_final: 0.8260 (tt0) REVERT: C 31 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8389 (m-30) REVERT: C 72 MET cc_start: 0.8841 (mtt) cc_final: 0.8616 (mtt) REVERT: C 97 ASP cc_start: 0.8248 (m-30) cc_final: 0.7589 (t0) REVERT: C 113 ASP cc_start: 0.8630 (p0) cc_final: 0.8265 (p0) REVERT: C 126 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7458 (mt-10) REVERT: C 130 ASP cc_start: 0.8075 (m-30) cc_final: 0.7796 (m-30) REVERT: C 206 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7883 (mttm) REVERT: C 210 ASP cc_start: 0.8242 (m-30) cc_final: 0.7986 (m-30) REVERT: C 243 MET cc_start: 0.7929 (tpp) cc_final: 0.7603 (mtt) REVERT: D 28 GLU cc_start: 0.8703 (tp30) cc_final: 0.8279 (tt0) REVERT: D 72 MET cc_start: 0.8843 (mtm) cc_final: 0.8602 (mtt) REVERT: D 75 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7208 (mtp-110) REVERT: D 97 ASP cc_start: 0.8217 (m-30) cc_final: 0.7434 (t0) REVERT: D 126 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7539 (mt-10) REVERT: D 130 ASP cc_start: 0.8088 (m-30) cc_final: 0.7682 (m-30) REVERT: D 138 LYS cc_start: 0.8497 (mtpt) cc_final: 0.8281 (mtpp) REVERT: D 210 ASP cc_start: 0.8331 (m-30) cc_final: 0.7932 (m-30) REVERT: D 243 MET cc_start: 0.8003 (tpp) cc_final: 0.7480 (mtt) REVERT: D 420 PHE cc_start: 0.8086 (t80) cc_final: 0.7759 (t80) REVERT: E 28 GLU cc_start: 0.8534 (tp30) cc_final: 0.8154 (tt0) REVERT: E 97 ASP cc_start: 0.8213 (m-30) cc_final: 0.7394 (t0) REVERT: E 126 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7272 (pm20) REVERT: E 210 ASP cc_start: 0.8313 (m-30) cc_final: 0.7885 (m-30) REVERT: E 322 PHE cc_start: 0.7795 (t80) cc_final: 0.7444 (t80) outliers start: 54 outliers final: 20 residues processed: 333 average time/residue: 0.5448 time to fit residues: 200.4272 Evaluate side-chains 327 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 304 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 424 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 141 ASN B 62 ASN B 141 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN E 58 ASN E 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.108983 restraints weight = 16716.630| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.35 r_work: 0.3086 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14535 Z= 0.150 Angle : 0.680 8.663 19745 Z= 0.340 Chirality : 0.047 0.202 2260 Planarity : 0.004 0.042 2435 Dihedral : 7.314 34.450 2195 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.66 % Allowed : 18.43 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.18), residues: 1710 helix: -2.06 (0.20), residues: 565 sheet: -0.31 (0.29), residues: 320 loop : -2.24 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 75 TYR 0.015 0.002 TYR A 317 PHE 0.022 0.002 PHE A 322 TRP 0.010 0.001 TRP A 259 HIS 0.001 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00359 (14510) covalent geometry : angle 0.67062 (19680) SS BOND : bond 0.00567 ( 10) SS BOND : angle 1.69756 ( 20) hydrogen bonds : bond 0.03926 ( 520) hydrogen bonds : angle 4.73902 ( 1914) link_BETA1-4 : bond 0.00373 ( 10) link_BETA1-4 : angle 2.61266 ( 30) link_NAG-ASN : bond 0.00100 ( 5) link_NAG-ASN : angle 0.57141 ( 15) *********************** 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 374 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 318 time to evaluate : 0.568 Fit side-chains REVERT: A 28 GLU cc_start: 0.8464 (tp30) cc_final: 0.8205 (tt0) REVERT: A 43 ARG cc_start: 0.8976 (mtm-85) cc_final: 0.8696 (mtm180) REVERT: A 72 MET cc_start: 0.8787 (mtm) cc_final: 0.8404 (mtt) REVERT: A 97 ASP cc_start: 0.8278 (m-30) cc_final: 0.7568 (t0) REVERT: A 126 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7601 (mt-10) REVERT: A 130 ASP cc_start: 0.8178 (m-30) cc_final: 0.7789 (m-30) REVERT: A 138 LYS cc_start: 0.8539 (mtpt) cc_final: 0.8286 (mttm) REVERT: A 163 MET cc_start: 0.8430 (mpp) cc_final: 0.8012 (mtp) REVERT: A 206 LYS cc_start: 0.8476 (mtpt) cc_final: 0.7909 (mttm) REVERT: A 210 ASP cc_start: 0.8319 (m-30) cc_final: 0.7913 (m-30) REVERT: A 227 GLU cc_start: 0.8651 (pt0) cc_final: 0.8343 (pt0) REVERT: A 420 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: B 28 GLU cc_start: 0.8560 (tp30) cc_final: 0.8218 (tt0) REVERT: B 43 ARG cc_start: 0.9112 (mtm-85) cc_final: 0.8701 (mtm180) REVERT: B 97 ASP cc_start: 0.8284 (m-30) cc_final: 0.7584 (t0) REVERT: B 113 ASP cc_start: 0.8609 (p0) cc_final: 0.8280 (p0) REVERT: B 126 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7774 (mt-10) REVERT: B 207 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8405 (tt0) REVERT: B 235 GLN cc_start: 0.8416 (mm110) cc_final: 0.8087 (mt0) REVERT: B 243 MET cc_start: 0.8063 (tpp) cc_final: 0.7797 (mtt) REVERT: B 420 PHE cc_start: 0.8571 (t80) cc_final: 0.8224 (m-80) REVERT: C 28 GLU cc_start: 0.8557 (tp30) cc_final: 0.8220 (tt0) REVERT: C 31 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8448 (m-30) REVERT: C 97 ASP cc_start: 0.8274 (m-30) cc_final: 0.7623 (t0) REVERT: C 113 ASP cc_start: 0.8629 (p0) cc_final: 0.8308 (p0) REVERT: C 126 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7494 (mt-10) REVERT: C 130 ASP cc_start: 0.8029 (m-30) cc_final: 0.7794 (m-30) REVERT: C 206 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7961 (mttm) REVERT: C 207 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8617 (tt0) REVERT: C 210 ASP cc_start: 0.8248 (m-30) cc_final: 0.7978 (m-30) REVERT: C 243 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7598 (mtt) REVERT: C 420 PHE cc_start: 0.8433 (t80) cc_final: 0.8210 (m-80) REVERT: D 28 GLU cc_start: 0.8681 (tp30) cc_final: 0.8241 (tt0) REVERT: D 72 MET cc_start: 0.8886 (mtm) cc_final: 0.8660 (mtt) REVERT: D 75 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7316 (mtp-110) REVERT: D 97 ASP cc_start: 0.8264 (m-30) cc_final: 0.7559 (t0) REVERT: D 126 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7627 (mt-10) REVERT: D 210 ASP cc_start: 0.8315 (m-30) cc_final: 0.8069 (m-30) REVERT: D 322 PHE cc_start: 0.7797 (t80) cc_final: 0.7503 (t80) REVERT: D 391 MET cc_start: 0.6098 (tpt) cc_final: 0.5188 (ttp) REVERT: D 420 PHE cc_start: 0.8066 (t80) cc_final: 0.7732 (t80) REVERT: E 28 GLU cc_start: 0.8533 (tp30) cc_final: 0.8131 (tt0) REVERT: E 97 ASP cc_start: 0.8238 (m-30) cc_final: 0.7464 (t0) REVERT: E 126 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7700 (mt-10) REVERT: E 156 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8320 (mmp) REVERT: E 210 ASP cc_start: 0.8312 (m-30) cc_final: 0.7911 (m-30) REVERT: E 243 MET cc_start: 0.7968 (tpp) cc_final: 0.7665 (mtt) REVERT: E 322 PHE cc_start: 0.7851 (t80) cc_final: 0.7516 (t80) outliers start: 56 outliers final: 23 residues processed: 345 average time/residue: 0.4680 time to fit residues: 180.8208 Evaluate side-chains 323 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 296 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 77 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 282 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 180 ASN E 141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.110887 restraints weight = 16617.622| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.36 r_work: 0.3061 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14535 Z= 0.126 Angle : 0.661 8.863 19745 Z= 0.330 Chirality : 0.046 0.196 2260 Planarity : 0.003 0.039 2435 Dihedral : 6.080 23.128 2195 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.46 % Allowed : 20.39 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.19), residues: 1710 helix: -1.74 (0.21), residues: 565 sheet: -0.19 (0.29), residues: 320 loop : -2.13 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 229 TYR 0.014 0.001 TYR A 317 PHE 0.023 0.001 PHE B 322 TRP 0.011 0.001 TRP A 422 HIS 0.001 0.000 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00300 (14510) covalent geometry : angle 0.65375 (19680) SS BOND : bond 0.00498 ( 10) SS BOND : angle 1.53445 ( 20) hydrogen bonds : bond 0.03674 ( 520) hydrogen bonds : angle 4.50920 ( 1914) link_BETA1-4 : bond 0.00383 ( 10) link_BETA1-4 : angle 2.25495 ( 30) link_NAG-ASN : bond 0.00123 ( 5) link_NAG-ASN : angle 0.50171 ( 15) *********************** 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 366 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 313 time to evaluate : 0.485 Fit side-chains REVERT: A 28 GLU cc_start: 0.8485 (tp30) cc_final: 0.8207 (tt0) REVERT: A 43 ARG cc_start: 0.8971 (mtm-85) cc_final: 0.8726 (mtm180) REVERT: A 72 MET cc_start: 0.8777 (mtm) cc_final: 0.8428 (mtt) REVERT: A 97 ASP cc_start: 0.8239 (m-30) cc_final: 0.7558 (t0) REVERT: A 126 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7667 (mt-10) REVERT: A 138 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8285 (mttm) REVERT: A 163 MET cc_start: 0.8344 (mpp) cc_final: 0.7893 (mtp) REVERT: A 206 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8199 (mttt) REVERT: A 210 ASP cc_start: 0.8291 (m-30) cc_final: 0.7822 (m-30) REVERT: A 419 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7435 (mp) REVERT: A 420 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: B 28 GLU cc_start: 0.8544 (tp30) cc_final: 0.8127 (tt0) REVERT: B 43 ARG cc_start: 0.9115 (mtm-85) cc_final: 0.8899 (mtm180) REVERT: B 97 ASP cc_start: 0.8273 (m-30) cc_final: 0.7583 (t0) REVERT: B 113 ASP cc_start: 0.8654 (p0) cc_final: 0.8325 (p0) REVERT: B 126 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7776 (mt-10) REVERT: B 235 GLN cc_start: 0.8423 (mm110) cc_final: 0.8095 (mt0) REVERT: B 243 MET cc_start: 0.8030 (tpp) cc_final: 0.7768 (mtt) REVERT: B 316 GLU cc_start: 0.6415 (tm-30) cc_final: 0.6167 (tm-30) REVERT: B 420 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: C 28 GLU cc_start: 0.8553 (tp30) cc_final: 0.8220 (tt0) REVERT: C 31 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8449 (m-30) REVERT: C 97 ASP cc_start: 0.8254 (m-30) cc_final: 0.7664 (t0) REVERT: C 113 ASP cc_start: 0.8554 (p0) cc_final: 0.8255 (p0) REVERT: C 126 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7503 (mt-10) REVERT: C 130 ASP cc_start: 0.7935 (m-30) cc_final: 0.7717 (m-30) REVERT: C 206 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7936 (mttm) REVERT: C 210 ASP cc_start: 0.8241 (m-30) cc_final: 0.7948 (m-30) REVERT: C 243 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7546 (mtt) REVERT: C 418 ASN cc_start: 0.8087 (t0) cc_final: 0.7766 (m110) REVERT: C 420 PHE cc_start: 0.8466 (t80) cc_final: 0.8247 (m-80) REVERT: D 28 GLU cc_start: 0.8676 (tp30) cc_final: 0.8248 (tt0) REVERT: D 72 MET cc_start: 0.8884 (mtm) cc_final: 0.8659 (mtt) REVERT: D 75 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7359 (mtp-110) REVERT: D 97 ASP cc_start: 0.8232 (m-30) cc_final: 0.7500 (t0) REVERT: D 126 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7599 (mt-10) REVERT: D 130 ASP cc_start: 0.8036 (m-30) cc_final: 0.7750 (m-30) REVERT: D 210 ASP cc_start: 0.8224 (m-30) cc_final: 0.7969 (m-30) REVERT: D 227 GLU cc_start: 0.8696 (pt0) cc_final: 0.8437 (pt0) REVERT: D 391 MET cc_start: 0.6184 (tpt) cc_final: 0.5198 (ptm) REVERT: E 28 GLU cc_start: 0.8501 (tp30) cc_final: 0.8115 (tt0) REVERT: E 97 ASP cc_start: 0.8198 (m-30) cc_final: 0.7469 (t0) REVERT: E 126 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7292 (pm20) REVERT: E 156 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8238 (mmp) REVERT: E 210 ASP cc_start: 0.8308 (m-30) cc_final: 0.7864 (m-30) REVERT: E 243 MET cc_start: 0.7975 (tpp) cc_final: 0.7662 (mtt) outliers start: 53 outliers final: 20 residues processed: 336 average time/residue: 0.4752 time to fit residues: 178.0130 Evaluate side-chains 329 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 303 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 44 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 100 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 0.0270 chunk 2 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.148795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110612 restraints weight = 16635.792| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.37 r_work: 0.3114 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14535 Z= 0.140 Angle : 0.684 12.281 19745 Z= 0.342 Chirality : 0.046 0.168 2260 Planarity : 0.003 0.037 2435 Dihedral : 5.631 40.490 2195 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.73 % Allowed : 21.44 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.19), residues: 1710 helix: -1.56 (0.21), residues: 565 sheet: -0.06 (0.29), residues: 320 loop : -2.04 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 229 TYR 0.014 0.001 TYR A 317 PHE 0.025 0.001 PHE C 322 TRP 0.010 0.001 TRP A 422 HIS 0.001 0.000 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00341 (14510) covalent geometry : angle 0.67444 (19680) SS BOND : bond 0.00748 ( 10) SS BOND : angle 2.83913 ( 20) hydrogen bonds : bond 0.03605 ( 520) hydrogen bonds : angle 4.48283 ( 1914) link_BETA1-4 : bond 0.00455 ( 10) link_BETA1-4 : angle 2.02342 ( 30) link_NAG-ASN : bond 0.00142 ( 5) link_NAG-ASN : angle 0.53336 ( 15) *********************** 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 372 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 time to evaluate : 0.567 Fit side-chains REVERT: A 28 GLU cc_start: 0.8524 (tp30) cc_final: 0.8223 (tt0) REVERT: A 43 ARG cc_start: 0.9000 (mtm-85) cc_final: 0.8747 (mtm180) REVERT: A 97 ASP cc_start: 0.8313 (m-30) cc_final: 0.7657 (t0) REVERT: A 126 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7602 (mt-10) REVERT: A 130 ASP cc_start: 0.8046 (m-30) cc_final: 0.7669 (m-30) REVERT: A 138 LYS cc_start: 0.8543 (mtpt) cc_final: 0.8285 (mttm) REVERT: A 163 MET cc_start: 0.8356 (mpp) cc_final: 0.7900 (mtp) REVERT: A 206 LYS cc_start: 0.8412 (mtpt) cc_final: 0.7947 (mttm) REVERT: A 210 ASP cc_start: 0.8253 (m-30) cc_final: 0.7787 (m-30) REVERT: B 28 GLU cc_start: 0.8545 (tp30) cc_final: 0.8188 (tt0) REVERT: B 43 ARG cc_start: 0.9090 (mtm-85) cc_final: 0.8837 (mtm180) REVERT: B 96 ASP cc_start: 0.8644 (m-30) cc_final: 0.8196 (m-30) REVERT: B 97 ASP cc_start: 0.8260 (m-30) cc_final: 0.7595 (t0) REVERT: B 113 ASP cc_start: 0.8666 (p0) cc_final: 0.8343 (p0) REVERT: B 126 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7738 (mt-10) REVERT: B 235 GLN cc_start: 0.8455 (mm110) cc_final: 0.8124 (mt0) REVERT: B 303 MET cc_start: 0.9284 (mmt) cc_final: 0.8909 (mmt) REVERT: B 419 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7490 (mp) REVERT: B 420 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: C 28 GLU cc_start: 0.8565 (tp30) cc_final: 0.8190 (tt0) REVERT: C 31 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8478 (m-30) REVERT: C 97 ASP cc_start: 0.8252 (m-30) cc_final: 0.7671 (t0) REVERT: C 113 ASP cc_start: 0.8581 (p0) cc_final: 0.8299 (p0) REVERT: C 126 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7541 (mt-10) REVERT: C 206 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7930 (mttm) REVERT: C 210 ASP cc_start: 0.8236 (m-30) cc_final: 0.7924 (m-30) REVERT: C 243 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7564 (mtt) REVERT: C 418 ASN cc_start: 0.7988 (t0) cc_final: 0.7637 (m110) REVERT: C 420 PHE cc_start: 0.8412 (t80) cc_final: 0.8150 (m-80) REVERT: D 28 GLU cc_start: 0.8669 (tp30) cc_final: 0.8285 (tt0) REVERT: D 72 MET cc_start: 0.8913 (mtm) cc_final: 0.8690 (mtt) REVERT: D 75 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7323 (mtp-110) REVERT: D 97 ASP cc_start: 0.8281 (m-30) cc_final: 0.7606 (t0) REVERT: D 126 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7579 (mt-10) REVERT: D 130 ASP cc_start: 0.8038 (m-30) cc_final: 0.7751 (m-30) REVERT: D 208 GLU cc_start: 0.8214 (tp30) cc_final: 0.7714 (tm-30) REVERT: D 210 ASP cc_start: 0.8184 (m-30) cc_final: 0.7846 (m-30) REVERT: D 243 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7783 (mtt) REVERT: D 391 MET cc_start: 0.6214 (tpt) cc_final: 0.5329 (ttp) REVERT: D 420 PHE cc_start: 0.8023 (t80) cc_final: 0.7732 (t80) REVERT: E 28 GLU cc_start: 0.8499 (tp30) cc_final: 0.8127 (tt0) REVERT: E 93 GLU cc_start: 0.9033 (pp20) cc_final: 0.8711 (pp20) REVERT: E 97 ASP cc_start: 0.8212 (m-30) cc_final: 0.7495 (t0) REVERT: E 210 ASP cc_start: 0.8279 (m-30) cc_final: 0.7897 (m-30) REVERT: E 243 MET cc_start: 0.8046 (tpp) cc_final: 0.7745 (mtt) outliers start: 57 outliers final: 28 residues processed: 340 average time/residue: 0.4840 time to fit residues: 183.7692 Evaluate side-chains 335 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 302 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 138 optimal weight: 0.0010 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN B 261 ASN ** B 282 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 = 0.3745 r_free = 0.3745 target = 0.148456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110671 restraints weight = 16563.642| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.35 r_work: 0.3055 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14535 Z= 0.144 Angle : 0.706 13.089 19745 Z= 0.353 Chirality : 0.047 0.170 2260 Planarity : 0.003 0.037 2435 Dihedral : 5.621 44.933 2195 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.73 % Allowed : 22.16 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.19), residues: 1710 helix: -1.43 (0.21), residues: 565 sheet: 0.07 (0.29), residues: 320 loop : -1.98 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 229 TYR 0.014 0.002 TYR A 317 PHE 0.026 0.001 PHE B 322 TRP 0.009 0.001 TRP A 422 HIS 0.001 0.000 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00354 (14510) covalent geometry : angle 0.69124 (19680) SS BOND : bond 0.00552 ( 10) SS BOND : angle 4.01678 ( 20) hydrogen bonds : bond 0.03605 ( 520) hydrogen bonds : angle 4.46891 ( 1914) link_BETA1-4 : bond 0.00435 ( 10) link_BETA1-4 : angle 1.84875 ( 30) link_NAG-ASN : bond 0.00129 ( 5) link_NAG-ASN : angle 0.52778 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 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 361 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 304 time to evaluate : 0.567 Fit side-chains REVERT: A 28 GLU cc_start: 0.8515 (tp30) cc_final: 0.8232 (mt-10) REVERT: A 43 ARG cc_start: 0.9000 (mtm-85) cc_final: 0.8721 (mtm180) REVERT: A 97 ASP cc_start: 0.8299 (m-30) cc_final: 0.7664 (t0) REVERT: A 126 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 130 ASP cc_start: 0.8042 (m-30) cc_final: 0.7666 (m-30) REVERT: A 138 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8235 (mttm) REVERT: A 163 MET cc_start: 0.8322 (mpp) cc_final: 0.7886 (mtp) REVERT: A 206 LYS cc_start: 0.8369 (mtpt) cc_final: 0.7914 (mttm) REVERT: A 210 ASP cc_start: 0.8250 (m-30) cc_final: 0.7783 (m-30) REVERT: A 279 MET cc_start: 0.7162 (tpp) cc_final: 0.6778 (mpp) REVERT: B 28 GLU cc_start: 0.8560 (tp30) cc_final: 0.8144 (tt0) REVERT: B 43 ARG cc_start: 0.9085 (mtm-85) cc_final: 0.8847 (mtm180) REVERT: B 96 ASP cc_start: 0.8637 (m-30) cc_final: 0.8180 (m-30) REVERT: B 97 ASP cc_start: 0.8265 (m-30) cc_final: 0.7633 (t0) REVERT: B 113 ASP cc_start: 0.8646 (p0) cc_final: 0.8350 (p0) REVERT: B 126 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7721 (mt-10) REVERT: B 235 GLN cc_start: 0.8450 (mm110) cc_final: 0.8095 (mt0) REVERT: B 303 MET cc_start: 0.9240 (mmt) cc_final: 0.8831 (mmt) REVERT: B 316 GLU cc_start: 0.6411 (tm-30) cc_final: 0.6142 (tm-30) REVERT: B 420 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: C 28 GLU cc_start: 0.8553 (tp30) cc_final: 0.8198 (tt0) REVERT: C 31 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8461 (m-30) REVERT: C 93 GLU cc_start: 0.9028 (pp20) cc_final: 0.8822 (pp20) REVERT: C 97 ASP cc_start: 0.8224 (m-30) cc_final: 0.7661 (t0) REVERT: C 102 ASP cc_start: 0.8201 (p0) cc_final: 0.7949 (p0) REVERT: C 113 ASP cc_start: 0.8550 (p0) cc_final: 0.8264 (p0) REVERT: C 126 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7647 (mt-10) REVERT: C 206 LYS cc_start: 0.8337 (mtpt) cc_final: 0.7905 (mttm) REVERT: C 210 ASP cc_start: 0.8214 (m-30) cc_final: 0.7898 (m-30) REVERT: C 236 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7053 (tmm) REVERT: C 243 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7518 (mtt) REVERT: C 420 PHE cc_start: 0.8366 (t80) cc_final: 0.8089 (m-80) REVERT: D 28 GLU cc_start: 0.8666 (tp30) cc_final: 0.8341 (mt-10) REVERT: D 72 MET cc_start: 0.8906 (mtm) cc_final: 0.8681 (mtt) REVERT: D 75 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7322 (mtp-110) REVERT: D 97 ASP cc_start: 0.8256 (m-30) cc_final: 0.7576 (t0) REVERT: D 126 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7569 (mt-10) REVERT: D 130 ASP cc_start: 0.8023 (m-30) cc_final: 0.7733 (m-30) REVERT: D 163 MET cc_start: 0.8108 (mpp) cc_final: 0.7848 (mtp) REVERT: D 210 ASP cc_start: 0.8187 (m-30) cc_final: 0.7834 (m-30) REVERT: D 243 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7788 (mtt) REVERT: D 420 PHE cc_start: 0.7988 (t80) cc_final: 0.7690 (t80) REVERT: E 28 GLU cc_start: 0.8485 (tp30) cc_final: 0.8174 (mt-10) REVERT: E 97 ASP cc_start: 0.8178 (m-30) cc_final: 0.7440 (t0) REVERT: E 210 ASP cc_start: 0.8249 (m-30) cc_final: 0.7824 (m-30) REVERT: E 243 MET cc_start: 0.8022 (tpp) cc_final: 0.7703 (mtt) outliers start: 57 outliers final: 31 residues processed: 327 average time/residue: 0.5010 time to fit residues: 182.0359 Evaluate side-chains 329 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 108 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 81 optimal weight: 0.0970 chunk 122 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN E 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111041 restraints weight = 16637.246| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.36 r_work: 0.3055 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14535 Z= 0.137 Angle : 0.686 9.266 19745 Z= 0.343 Chirality : 0.046 0.189 2260 Planarity : 0.003 0.048 2435 Dihedral : 5.480 48.404 2195 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.66 % Allowed : 22.61 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.19), residues: 1710 helix: -1.33 (0.22), residues: 565 sheet: -0.10 (0.28), residues: 365 loop : -1.76 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.014 0.001 TYR A 317 PHE 0.027 0.001 PHE B 322 TRP 0.008 0.001 TRP E 186 HIS 0.001 0.000 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00342 (14510) covalent geometry : angle 0.67464 (19680) SS BOND : bond 0.00439 ( 10) SS BOND : angle 3.56193 ( 20) hydrogen bonds : bond 0.03587 ( 520) hydrogen bonds : angle 4.40346 ( 1914) link_BETA1-4 : bond 0.00436 ( 10) link_BETA1-4 : angle 1.65329 ( 30) link_NAG-ASN : bond 0.00118 ( 5) link_NAG-ASN : angle 0.52614 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 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 353 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 0.473 Fit side-chains REVERT: A 28 GLU cc_start: 0.8518 (tp30) cc_final: 0.8217 (mt-10) REVERT: A 43 ARG cc_start: 0.9001 (mtm-85) cc_final: 0.8645 (mtm180) REVERT: A 97 ASP cc_start: 0.8289 (m-30) cc_final: 0.7646 (t0) REVERT: A 126 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 130 ASP cc_start: 0.8003 (m-30) cc_final: 0.7633 (m-30) REVERT: A 138 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8151 (mttm) REVERT: A 163 MET cc_start: 0.8211 (mpp) cc_final: 0.7814 (mtp) REVERT: A 210 ASP cc_start: 0.8203 (m-30) cc_final: 0.7721 (m-30) REVERT: B 28 GLU cc_start: 0.8526 (tp30) cc_final: 0.8154 (mt-10) REVERT: B 97 ASP cc_start: 0.8255 (m-30) cc_final: 0.7615 (t0) REVERT: B 113 ASP cc_start: 0.8635 (p0) cc_final: 0.8331 (p0) REVERT: B 126 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7708 (mt-10) REVERT: B 206 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7921 (mttm) REVERT: B 235 GLN cc_start: 0.8441 (mm110) cc_final: 0.8086 (mt0) REVERT: B 279 MET cc_start: 0.7175 (tpp) cc_final: 0.6460 (mpp) REVERT: B 303 MET cc_start: 0.9175 (mmt) cc_final: 0.8846 (mmt) REVERT: B 316 GLU cc_start: 0.6391 (tm-30) cc_final: 0.6098 (tm-30) REVERT: B 420 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: C 28 GLU cc_start: 0.8519 (tp30) cc_final: 0.8157 (tt0) REVERT: C 31 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8457 (m-30) REVERT: C 93 GLU cc_start: 0.9040 (pp20) cc_final: 0.8826 (pp20) REVERT: C 97 ASP cc_start: 0.8174 (m-30) cc_final: 0.7634 (t0) REVERT: C 102 ASP cc_start: 0.8155 (p0) cc_final: 0.7848 (p0) REVERT: C 113 ASP cc_start: 0.8504 (p0) cc_final: 0.8222 (p0) REVERT: C 126 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7669 (mt-10) REVERT: C 206 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7816 (mttm) REVERT: C 210 ASP cc_start: 0.8145 (m-30) cc_final: 0.7821 (m-30) REVERT: C 243 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7378 (mtt) REVERT: C 418 ASN cc_start: 0.7805 (m-40) cc_final: 0.7417 (m110) REVERT: D 28 GLU cc_start: 0.8638 (tp30) cc_final: 0.8221 (tt0) REVERT: D 72 MET cc_start: 0.8862 (mtm) cc_final: 0.8612 (mtt) REVERT: D 75 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7264 (mtp-110) REVERT: D 97 ASP cc_start: 0.8227 (m-30) cc_final: 0.7562 (t0) REVERT: D 126 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7539 (mt-10) REVERT: D 130 ASP cc_start: 0.7974 (m-30) cc_final: 0.7710 (m-30) REVERT: D 210 ASP cc_start: 0.8096 (m-30) cc_final: 0.7732 (m-30) REVERT: D 243 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7758 (mtt) REVERT: D 391 MET cc_start: 0.6080 (tpt) cc_final: 0.5272 (ttp) REVERT: D 420 PHE cc_start: 0.7926 (t80) cc_final: 0.7616 (t80) REVERT: E 28 GLU cc_start: 0.8427 (tp30) cc_final: 0.8127 (mt-10) REVERT: E 97 ASP cc_start: 0.8136 (m-30) cc_final: 0.7457 (t0) REVERT: E 210 ASP cc_start: 0.8207 (m-30) cc_final: 0.7817 (m-30) REVERT: E 243 MET cc_start: 0.7927 (tpp) cc_final: 0.7619 (mtt) REVERT: E 420 PHE cc_start: 0.7824 (t80) cc_final: 0.7528 (t80) outliers start: 56 outliers final: 31 residues processed: 325 average time/residue: 0.5317 time to fit residues: 191.4891 Evaluate side-chains 320 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 25 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 261 ASN B 62 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN C 261 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111023 restraints weight = 16573.997| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.34 r_work: 0.3058 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14535 Z= 0.141 Angle : 0.689 10.664 19745 Z= 0.344 Chirality : 0.047 0.195 2260 Planarity : 0.003 0.040 2435 Dihedral : 5.401 47.525 2195 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.40 % Allowed : 23.46 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.19), residues: 1710 helix: -1.27 (0.22), residues: 565 sheet: -0.05 (0.28), residues: 365 loop : -1.69 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 407 TYR 0.014 0.001 TYR A 317 PHE 0.028 0.001 PHE B 322 TRP 0.009 0.001 TRP D 186 HIS 0.001 0.000 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00351 (14510) covalent geometry : angle 0.67896 (19680) SS BOND : bond 0.00451 ( 10) SS BOND : angle 3.39426 ( 20) hydrogen bonds : bond 0.03597 ( 520) hydrogen bonds : angle 4.41539 ( 1914) link_BETA1-4 : bond 0.00436 ( 10) link_BETA1-4 : angle 1.54760 ( 30) link_NAG-ASN : bond 0.00118 ( 5) link_NAG-ASN : angle 0.53053 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 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 349 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.601 Fit side-chains REVERT: A 28 GLU cc_start: 0.8527 (tp30) cc_final: 0.8232 (mt-10) REVERT: A 43 ARG cc_start: 0.9023 (mtm-85) cc_final: 0.8779 (mtm180) REVERT: A 97 ASP cc_start: 0.8321 (m-30) cc_final: 0.7697 (t0) REVERT: A 126 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7648 (mt-10) REVERT: A 130 ASP cc_start: 0.8023 (m-30) cc_final: 0.7688 (m-30) REVERT: A 138 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8164 (mttm) REVERT: A 156 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7995 (mmt) REVERT: A 163 MET cc_start: 0.8224 (mpp) cc_final: 0.7879 (mtp) REVERT: A 206 LYS cc_start: 0.8352 (mtpt) cc_final: 0.7926 (mmtp) REVERT: A 210 ASP cc_start: 0.8230 (m-30) cc_final: 0.7766 (m-30) REVERT: B 28 GLU cc_start: 0.8555 (tp30) cc_final: 0.8187 (mt-10) REVERT: B 96 ASP cc_start: 0.8596 (m-30) cc_final: 0.8334 (m-30) REVERT: B 97 ASP cc_start: 0.8261 (m-30) cc_final: 0.7662 (t0) REVERT: B 113 ASP cc_start: 0.8633 (p0) cc_final: 0.8336 (p0) REVERT: B 126 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7740 (mt-10) REVERT: B 206 LYS cc_start: 0.8384 (mtpt) cc_final: 0.8026 (mttm) REVERT: B 235 GLN cc_start: 0.8436 (mm110) cc_final: 0.8086 (mt0) REVERT: B 316 GLU cc_start: 0.6471 (tm-30) cc_final: 0.6162 (tm-30) REVERT: B 420 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: C 28 GLU cc_start: 0.8546 (tp30) cc_final: 0.8188 (tt0) REVERT: C 31 ASP cc_start: 0.8771 (m-30) cc_final: 0.8435 (m-30) REVERT: C 93 GLU cc_start: 0.9039 (pp20) cc_final: 0.8830 (pp20) REVERT: C 97 ASP cc_start: 0.8148 (m-30) cc_final: 0.7670 (t0) REVERT: C 102 ASP cc_start: 0.8163 (p0) cc_final: 0.7872 (p0) REVERT: C 113 ASP cc_start: 0.8532 (p0) cc_final: 0.8263 (p0) REVERT: C 126 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7713 (mt-10) REVERT: C 206 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7826 (mttm) REVERT: C 210 ASP cc_start: 0.8182 (m-30) cc_final: 0.7834 (m-30) REVERT: C 227 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: C 243 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7436 (mtt) REVERT: C 418 ASN cc_start: 0.7867 (m-40) cc_final: 0.7483 (m110) REVERT: D 28 GLU cc_start: 0.8655 (tp30) cc_final: 0.8348 (mt-10) REVERT: D 72 MET cc_start: 0.8902 (mtm) cc_final: 0.8657 (mtt) REVERT: D 75 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7307 (mtp-110) REVERT: D 97 ASP cc_start: 0.8219 (m-30) cc_final: 0.7586 (t0) REVERT: D 126 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7571 (mt-10) REVERT: D 130 ASP cc_start: 0.8003 (m-30) cc_final: 0.7754 (m-30) REVERT: D 210 ASP cc_start: 0.8131 (m-30) cc_final: 0.7776 (m-30) REVERT: D 391 MET cc_start: 0.6247 (tpt) cc_final: 0.5403 (ttp) REVERT: D 420 PHE cc_start: 0.7901 (t80) cc_final: 0.7588 (t80) REVERT: E 28 GLU cc_start: 0.8476 (tp30) cc_final: 0.8166 (mt-10) REVERT: E 91 TYR cc_start: 0.8607 (p90) cc_final: 0.8357 (p90) REVERT: E 97 ASP cc_start: 0.8151 (m-30) cc_final: 0.7486 (t0) REVERT: E 105 MET cc_start: 0.8339 (mmt) cc_final: 0.7910 (mpp) REVERT: E 210 ASP cc_start: 0.8240 (m-30) cc_final: 0.7792 (m-30) REVERT: E 243 MET cc_start: 0.7953 (tpp) cc_final: 0.7637 (mtt) outliers start: 52 outliers final: 29 residues processed: 321 average time/residue: 0.5314 time to fit residues: 188.7789 Evaluate side-chains 329 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 296 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108886 restraints weight = 16664.907| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.37 r_work: 0.3089 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14535 Z= 0.172 Angle : 0.713 10.848 19745 Z= 0.356 Chirality : 0.048 0.237 2260 Planarity : 0.004 0.039 2435 Dihedral : 5.456 48.016 2195 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.61 % Allowed : 24.64 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.20), residues: 1710 helix: -1.23 (0.22), residues: 565 sheet: -0.08 (0.28), residues: 370 loop : -1.64 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 229 TYR 0.015 0.002 TYR A 317 PHE 0.027 0.002 PHE B 322 TRP 0.009 0.001 TRP A 186 HIS 0.001 0.000 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00433 (14510) covalent geometry : angle 0.70318 (19680) SS BOND : bond 0.00500 ( 10) SS BOND : angle 3.38658 ( 20) hydrogen bonds : bond 0.03684 ( 520) hydrogen bonds : angle 4.48804 ( 1914) link_BETA1-4 : bond 0.00458 ( 10) link_BETA1-4 : angle 1.52223 ( 30) link_NAG-ASN : bond 0.00070 ( 5) link_NAG-ASN : angle 0.61359 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 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 343 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 0.541 Fit side-chains REVERT: A 28 GLU cc_start: 0.8526 (tp30) cc_final: 0.8232 (mt-10) REVERT: A 43 ARG cc_start: 0.9040 (mtm-85) cc_final: 0.8738 (mtm180) REVERT: A 72 MET cc_start: 0.8850 (mtm) cc_final: 0.8405 (mtt) REVERT: A 97 ASP cc_start: 0.8373 (m-30) cc_final: 0.7760 (t0) REVERT: A 126 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 130 ASP cc_start: 0.8063 (m-30) cc_final: 0.7708 (m-30) REVERT: A 138 LYS cc_start: 0.8491 (mtpt) cc_final: 0.8185 (mttm) REVERT: A 163 MET cc_start: 0.8315 (mpp) cc_final: 0.7935 (mtp) REVERT: A 206 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7931 (mttm) REVERT: A 210 ASP cc_start: 0.8280 (m-30) cc_final: 0.7831 (m-30) REVERT: A 262 MET cc_start: 0.6162 (ptp) cc_final: 0.5552 (pmm) REVERT: B 28 GLU cc_start: 0.8559 (tp30) cc_final: 0.8190 (mt-10) REVERT: B 97 ASP cc_start: 0.8280 (m-30) cc_final: 0.7690 (t0) REVERT: B 113 ASP cc_start: 0.8645 (p0) cc_final: 0.8349 (p0) REVERT: B 126 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7750 (mt-10) REVERT: B 206 LYS cc_start: 0.8376 (mtpt) cc_final: 0.8016 (mttm) REVERT: B 235 GLN cc_start: 0.8453 (mm110) cc_final: 0.8058 (mt0) REVERT: B 316 GLU cc_start: 0.6423 (tm-30) cc_final: 0.6167 (tm-30) REVERT: B 420 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: C 28 GLU cc_start: 0.8557 (tp30) cc_final: 0.8197 (tt0) REVERT: C 31 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: C 93 GLU cc_start: 0.9044 (pp20) cc_final: 0.8834 (pp20) REVERT: C 97 ASP cc_start: 0.8179 (m-30) cc_final: 0.7734 (t0) REVERT: C 102 ASP cc_start: 0.8142 (p0) cc_final: 0.7883 (p0) REVERT: C 113 ASP cc_start: 0.8584 (p0) cc_final: 0.8314 (p0) REVERT: C 126 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7734 (mt-10) REVERT: C 206 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7846 (mttm) REVERT: C 210 ASP cc_start: 0.8176 (m-30) cc_final: 0.7804 (m-30) REVERT: C 227 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: C 243 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7566 (mtt) REVERT: C 418 ASN cc_start: 0.7810 (m-40) cc_final: 0.7482 (m110) REVERT: C 420 PHE cc_start: 0.8392 (t80) cc_final: 0.8136 (m-80) REVERT: D 28 GLU cc_start: 0.8649 (tp30) cc_final: 0.8282 (tt0) REVERT: D 72 MET cc_start: 0.8915 (mtm) cc_final: 0.8677 (mtt) REVERT: D 75 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7318 (mtp-110) REVERT: D 97 ASP cc_start: 0.8243 (m-30) cc_final: 0.7599 (t0) REVERT: D 126 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7572 (mt-10) REVERT: D 130 ASP cc_start: 0.8046 (m-30) cc_final: 0.7779 (m-30) REVERT: D 210 ASP cc_start: 0.8111 (m-30) cc_final: 0.7769 (m-30) REVERT: D 391 MET cc_start: 0.6233 (tpt) cc_final: 0.5467 (ttp) REVERT: D 420 PHE cc_start: 0.7882 (t80) cc_final: 0.7575 (t80) REVERT: E 28 GLU cc_start: 0.8510 (tp30) cc_final: 0.8194 (mt-10) REVERT: E 91 TYR cc_start: 0.8660 (p90) cc_final: 0.8422 (p90) REVERT: E 97 ASP cc_start: 0.8176 (m-30) cc_final: 0.7533 (t0) REVERT: E 210 ASP cc_start: 0.8251 (m-30) cc_final: 0.7879 (m-30) REVERT: E 243 MET cc_start: 0.7982 (tpp) cc_final: 0.7719 (mtt) REVERT: E 322 PHE cc_start: 0.7872 (t80) cc_final: 0.7525 (t80) REVERT: E 420 PHE cc_start: 0.7778 (t80) cc_final: 0.7518 (m-80) outliers start: 40 outliers final: 23 residues processed: 322 average time/residue: 0.5116 time to fit residues: 182.8420 Evaluate side-chains 317 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 301 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 145 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN B 62 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.108082 restraints weight = 16730.498| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.37 r_work: 0.3079 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 14535 Z= 0.181 Angle : 0.715 10.311 19745 Z= 0.358 Chirality : 0.048 0.204 2260 Planarity : 0.004 0.039 2435 Dihedral : 5.497 48.174 2195 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.42 % Allowed : 24.90 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.20), residues: 1710 helix: -1.19 (0.22), residues: 565 sheet: -0.05 (0.28), residues: 370 loop : -1.61 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 229 TYR 0.014 0.002 TYR C 317 PHE 0.028 0.002 PHE A 322 TRP 0.010 0.001 TRP A 186 HIS 0.001 0.000 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00452 (14510) covalent geometry : angle 0.70606 (19680) SS BOND : bond 0.00518 ( 10) SS BOND : angle 3.34911 ( 20) hydrogen bonds : bond 0.03731 ( 520) hydrogen bonds : angle 4.53814 ( 1914) link_BETA1-4 : bond 0.00452 ( 10) link_BETA1-4 : angle 1.48992 ( 30) link_NAG-ASN : bond 0.00063 ( 5) link_NAG-ASN : angle 0.58228 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4889.78 seconds wall clock time: 83 minutes 55.76 seconds (5035.76 seconds total)