Starting phenix.real_space_refine on Wed Mar 4 14:37:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6plz_20381/03_2026/6plz_20381.cif Found real_map, /net/cci-nas-00/data/ceres_data/6plz_20381/03_2026/6plz_20381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6plz_20381/03_2026/6plz_20381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6plz_20381/03_2026/6plz_20381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6plz_20381/03_2026/6plz_20381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6plz_20381/03_2026/6plz_20381.map" } resolution = 3.0 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= 0.062 sd= 2.818 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 9250 2.51 5 N 2290 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 14210 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.01, per 1000 atoms: 0.21 Number of scatterers: 14210 At special positions: 0 Unit cell: (108.636, 104.521, 134.149, 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 2570 8.00 N 2290 7.00 C 9250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 580.0 milliseconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 19 sheets defined 40.3% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 removed outlier: 3.840A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.249A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.653A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 108 " --> pdb=" O MET A 105 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 removed outlier: 3.510A pdb=" N ILE A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.780A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 264 through 285 removed outlier: 3.622A pdb=" N VAL A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 312 removed outlier: 4.138A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.658A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 427 removed outlier: 3.803A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.834A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.878A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.203A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 87 through 90 removed outlier: 3.506A pdb=" N ALA B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.636A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 108 " --> pdb=" O MET B 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 3.512A pdb=" N ILE B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.773A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.714A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 312 removed outlier: 4.113A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 325 removed outlier: 3.646A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 427 removed outlier: 3.851A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.757A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 removed outlier: 3.895A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.205A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.615A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 108 " --> pdb=" O MET C 105 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 removed outlier: 3.506A pdb=" N ILE C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 254 removed outlier: 3.622A pdb=" N SER C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 264 through 285 removed outlier: 3.611A pdb=" N VAL C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 312 removed outlier: 4.139A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 324 removed outlier: 3.727A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 427 removed outlier: 3.836A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.825A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.864A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.192A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 109 removed outlier: 3.651A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER D 108 " --> pdb=" O MET D 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 removed outlier: 3.523A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 254 removed outlier: 3.622A pdb=" N SER D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.674A pdb=" N VAL D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 312 removed outlier: 4.092A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 325 removed outlier: 3.702A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 427 removed outlier: 3.816A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.734A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.867A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.233A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 40' Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 109 removed outlier: 3.670A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER E 108 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE E 109 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.516A pdb=" N ILE E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 254 removed outlier: 3.529A pdb=" N SER E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 264 through 285 removed outlier: 3.642A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 312 removed outlier: 4.032A pdb=" N LEU E 307 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 325 removed outlier: 3.640A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 427 removed outlier: 3.861A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.737A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.072A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.072A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 193 " --> pdb=" O ILE A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 123 removed outlier: 6.046A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.046A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 193 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AA8, first strand: chain 'B' and resid 165 through 168 Processing sheet with id=AA9, first strand: chain 'C' and resid 122 through 123 removed outlier: 6.100A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.100A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 193 " --> pdb=" O ILE C 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB3, first strand: chain 'C' and resid 165 through 168 Processing sheet with id=AB4, first strand: chain 'D' and resid 122 through 123 removed outlier: 6.112A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.112A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN D 193 " --> pdb=" O ILE D 59 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AB7, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AB8, first strand: chain 'E' and resid 122 through 123 removed outlier: 6.122A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.122A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN E 193 " --> pdb=" O ILE E 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 114 through 116 removed outlier: 4.471A pdb=" N HIS E 231 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU E 208 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLU E 233 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS E 206 " --> pdb=" O GLU E 233 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1848 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: 2.21 Time building geometry restraints manager: 1.35 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: 4315 1.34 - 1.46: 3384 1.46 - 1.58: 6691 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 14560 Sorted by residual: bond pdb=" C1 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sigma weight residual 1.410 1.456 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.564 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.561 -0.042 2.00e-02 2.50e+03 4.44e+00 ... (remaining 14555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 18930 2.19 - 4.39: 660 4.39 - 6.58: 125 6.58 - 8.77: 20 8.77 - 10.96: 5 Bond angle restraints: 19740 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 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 132.47 -10.93 1.91e+00 2.74e-01 3.27e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 132.38 -10.84 1.91e+00 2.74e-01 3.22e+01 ... (remaining 19735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 8583 21.43 - 42.86: 157 42.86 - 64.28: 60 64.28 - 85.71: 70 85.71 - 107.14: 35 Dihedral angle restraints: 8905 sinusoidal: 3805 harmonic: 5100 Sorted by residual: dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual -86.00 -176.49 90.49 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -176.31 90.31 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 214 " pdb=" SG CYS B 214 " pdb=" SG CYS B 225 " pdb=" CB CYS B 225 " ideal model delta sinusoidal sigma weight residual -86.00 -176.23 90.23 1 1.00e+01 1.00e-02 9.64e+01 ... (remaining 8902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1822 0.066 - 0.132: 347 0.132 - 0.198: 61 0.198 - 0.264: 10 0.264 - 0.330: 15 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 54 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 54 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 54 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2252 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 151 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C VAL C 151 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL C 151 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU C 152 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " -0.040 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 411 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.56e+00 pdb=" N PRO D 411 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " 0.033 5.00e-02 4.00e+02 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4606 2.85 - 3.36: 12424 3.36 - 3.88: 22434 3.88 - 4.39: 26405 4.39 - 4.90: 46359 Nonbonded interactions: 112228 Sorted by model distance: nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.338 3.040 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.359 3.040 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.365 3.040 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.369 3.040 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.377 3.040 ... (remaining 112223 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.006 0.055 14585 Z= 0.249 Angle : 0.975 10.963 19805 Z= 0.510 Chirality : 0.061 0.330 2255 Planarity : 0.007 0.060 2445 Dihedral : 14.941 107.141 5565 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: -5.25 (0.15), residues: 1705 helix: -4.61 (0.08), residues: 580 sheet: -2.73 (0.20), residues: 425 loop : -2.66 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 401 TYR 0.015 0.002 TYR E 144 PHE 0.019 0.003 PHE D 115 TRP 0.023 0.003 TRP E 110 HIS 0.004 0.002 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00576 (14560) covalent geometry : angle 0.96826 (19740) SS BOND : bond 0.00749 ( 10) SS BOND : angle 1.87442 ( 20) hydrogen bonds : bond 0.27659 ( 554) hydrogen bonds : angle 10.33991 ( 1848) link_BETA1-4 : bond 0.01027 ( 10) link_BETA1-4 : angle 2.55257 ( 30) link_NAG-ASN : bond 0.00184 ( 5) link_NAG-ASN : angle 1.70443 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8824 (ptm) cc_final: 0.8384 (ptp) REVERT: A 28 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8157 (mt-10) REVERT: A 102 ASP cc_start: 0.8208 (t70) cc_final: 0.7604 (t70) REVERT: A 129 THR cc_start: 0.8518 (m) cc_final: 0.8247 (p) REVERT: A 130 ASP cc_start: 0.8180 (m-30) cc_final: 0.7959 (m-30) REVERT: A 210 ASP cc_start: 0.8104 (m-30) cc_final: 0.7715 (m-30) REVERT: A 261 ASN cc_start: 0.8383 (t0) cc_final: 0.8006 (t0) REVERT: A 391 MET cc_start: 0.8341 (tpt) cc_final: 0.7987 (tpp) REVERT: B 24 MET cc_start: 0.8875 (ptm) cc_final: 0.7957 (ptp) REVERT: B 28 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8233 (mt-10) REVERT: B 36 LYS cc_start: 0.9145 (mttt) cc_final: 0.8907 (mppt) REVERT: B 43 ARG cc_start: 0.9079 (mtm-85) cc_final: 0.8458 (mtm180) REVERT: B 102 ASP cc_start: 0.8241 (t70) cc_final: 0.7689 (t70) REVERT: B 129 THR cc_start: 0.8514 (m) cc_final: 0.8205 (p) REVERT: B 179 MET cc_start: 0.8665 (tpt) cc_final: 0.8391 (mmt) REVERT: B 181 ASP cc_start: 0.8407 (m-30) cc_final: 0.8161 (m-30) REVERT: B 210 ASP cc_start: 0.8000 (m-30) cc_final: 0.7644 (m-30) REVERT: B 391 MET cc_start: 0.8299 (tpt) cc_final: 0.7861 (tpp) REVERT: B 397 SER cc_start: 0.8717 (t) cc_final: 0.8404 (p) REVERT: C 24 MET cc_start: 0.8770 (ptm) cc_final: 0.7717 (ptp) REVERT: C 28 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8119 (mt-10) REVERT: C 36 LYS cc_start: 0.9206 (mttt) cc_final: 0.8930 (mppt) REVERT: C 43 ARG cc_start: 0.9013 (mtm-85) cc_final: 0.8362 (mtm180) REVERT: C 102 ASP cc_start: 0.8235 (t70) cc_final: 0.7762 (t70) REVERT: C 163 MET cc_start: 0.8149 (mpp) cc_final: 0.6897 (mpp) REVERT: C 164 ASP cc_start: 0.8082 (p0) cc_final: 0.7799 (p0) REVERT: C 208 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7868 (mt-10) REVERT: C 210 ASP cc_start: 0.8129 (m-30) cc_final: 0.7780 (m-30) REVERT: C 233 GLU cc_start: 0.7512 (tt0) cc_final: 0.7296 (tt0) REVERT: C 261 ASN cc_start: 0.8425 (t0) cc_final: 0.7975 (t0) REVERT: C 391 MET cc_start: 0.8264 (tpt) cc_final: 0.8011 (tpp) REVERT: C 397 SER cc_start: 0.8683 (t) cc_final: 0.8391 (p) REVERT: C 403 ASP cc_start: 0.8397 (t0) cc_final: 0.8027 (t0) REVERT: D 24 MET cc_start: 0.8763 (ptm) cc_final: 0.8321 (ptp) REVERT: D 28 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8121 (mt-10) REVERT: D 36 LYS cc_start: 0.9184 (mttt) cc_final: 0.8872 (mppt) REVERT: D 43 ARG cc_start: 0.9068 (mtm-85) cc_final: 0.8360 (mtm180) REVERT: D 130 ASP cc_start: 0.8194 (m-30) cc_final: 0.7988 (m-30) REVERT: D 210 ASP cc_start: 0.8128 (m-30) cc_final: 0.7785 (m-30) REVERT: D 212 ARG cc_start: 0.7591 (ptp-170) cc_final: 0.7327 (ptp-110) REVERT: D 227 GLU cc_start: 0.8072 (pt0) cc_final: 0.7846 (pt0) REVERT: D 261 ASN cc_start: 0.8332 (t0) cc_final: 0.7936 (t0) REVERT: D 391 MET cc_start: 0.8231 (tpt) cc_final: 0.7745 (tpp) REVERT: E 24 MET cc_start: 0.8900 (ptm) cc_final: 0.8318 (ptp) REVERT: E 28 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8165 (mt-10) REVERT: E 31 ASP cc_start: 0.8747 (m-30) cc_final: 0.8541 (m-30) REVERT: E 36 LYS cc_start: 0.9130 (mttt) cc_final: 0.8860 (mppt) REVERT: E 43 ARG cc_start: 0.9017 (mtm-85) cc_final: 0.8326 (mtm180) REVERT: E 129 THR cc_start: 0.8479 (m) cc_final: 0.8174 (p) REVERT: E 164 ASP cc_start: 0.8302 (p0) cc_final: 0.7993 (p0) REVERT: E 210 ASP cc_start: 0.8143 (m-30) cc_final: 0.7845 (m-30) REVERT: E 227 GLU cc_start: 0.8139 (pt0) cc_final: 0.7853 (pt0) REVERT: E 261 ASN cc_start: 0.8389 (t0) cc_final: 0.7952 (t0) REVERT: E 391 MET cc_start: 0.8250 (tpt) cc_final: 0.7830 (tpp) outliers start: 0 outliers final: 4 residues processed: 451 average time/residue: 0.6172 time to fit residues: 302.3070 Evaluate side-chains 286 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 282 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 141 ASN B 131 ASN B 171 GLN C 131 ASN C 171 GLN D 131 ASN E 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096708 restraints weight = 18816.479| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.19 r_work: 0.2931 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14585 Z= 0.156 Angle : 0.768 11.924 19805 Z= 0.383 Chirality : 0.050 0.282 2255 Planarity : 0.005 0.049 2445 Dihedral : 15.350 72.336 2203 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.56 % Allowed : 12.56 % Favored : 83.88 % 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: -3.50 (0.17), residues: 1705 helix: -2.91 (0.15), residues: 600 sheet: -1.71 (0.24), residues: 395 loop : -1.90 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 229 TYR 0.015 0.001 TYR E 425 PHE 0.016 0.001 PHE E 48 TRP 0.013 0.002 TRP E 110 HIS 0.003 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00358 (14560) covalent geometry : angle 0.74937 (19740) SS BOND : bond 0.01352 ( 10) SS BOND : angle 4.24304 ( 20) hydrogen bonds : bond 0.04453 ( 554) hydrogen bonds : angle 5.92801 ( 1848) link_BETA1-4 : bond 0.01052 ( 10) link_BETA1-4 : angle 2.66173 ( 30) link_NAG-ASN : bond 0.00091 ( 5) link_NAG-ASN : angle 0.79918 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 288 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8151 (ptm) cc_final: 0.7733 (ptp) REVERT: A 94 TYR cc_start: 0.7908 (t80) cc_final: 0.7519 (t80) REVERT: A 102 ASP cc_start: 0.8209 (t70) cc_final: 0.7625 (t70) REVERT: A 208 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: A 391 MET cc_start: 0.8293 (tpt) cc_final: 0.7679 (tpp) REVERT: A 393 LYS cc_start: 0.6689 (mmtt) cc_final: 0.6016 (mptt) REVERT: B 24 MET cc_start: 0.8291 (ptm) cc_final: 0.8045 (ptp) REVERT: B 36 LYS cc_start: 0.9428 (mttt) cc_final: 0.9008 (mppt) REVERT: B 43 ARG cc_start: 0.9190 (mtm-85) cc_final: 0.8583 (mtm180) REVERT: B 102 ASP cc_start: 0.8200 (t70) cc_final: 0.7642 (t70) REVERT: B 179 MET cc_start: 0.8722 (tpt) cc_final: 0.8474 (mmt) REVERT: B 391 MET cc_start: 0.8318 (tpt) cc_final: 0.7695 (tpp) REVERT: B 397 SER cc_start: 0.8318 (t) cc_final: 0.8076 (p) REVERT: C 24 MET cc_start: 0.8203 (ptm) cc_final: 0.7871 (ptp) REVERT: C 36 LYS cc_start: 0.9393 (mttt) cc_final: 0.8982 (mppt) REVERT: C 102 ASP cc_start: 0.8205 (t70) cc_final: 0.7728 (t70) REVERT: C 261 ASN cc_start: 0.8368 (t0) cc_final: 0.7724 (t0) REVERT: C 325 ARG cc_start: 0.7237 (ttp-110) cc_final: 0.6865 (mtp-110) REVERT: C 391 MET cc_start: 0.8217 (tpt) cc_final: 0.7804 (tpp) REVERT: C 393 LYS cc_start: 0.6564 (mmtt) cc_final: 0.5766 (mptp) REVERT: C 397 SER cc_start: 0.8402 (t) cc_final: 0.8174 (p) REVERT: C 403 ASP cc_start: 0.8324 (t0) cc_final: 0.8009 (t0) REVERT: D 36 LYS cc_start: 0.9403 (mttt) cc_final: 0.8897 (mppt) REVERT: D 102 ASP cc_start: 0.8264 (t70) cc_final: 0.7815 (t0) REVERT: D 208 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7654 (tp30) REVERT: D 212 ARG cc_start: 0.7541 (ptp-170) cc_final: 0.7190 (ptp-110) REVERT: D 391 MET cc_start: 0.8164 (tpt) cc_final: 0.7603 (tpp) REVERT: D 393 LYS cc_start: 0.6314 (mmtt) cc_final: 0.5747 (ptpt) REVERT: D 397 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7984 (p) REVERT: E 36 LYS cc_start: 0.9411 (mttt) cc_final: 0.8956 (mppt) REVERT: E 43 ARG cc_start: 0.9075 (mtm-85) cc_final: 0.8643 (mtm180) REVERT: E 179 MET cc_start: 0.8510 (tpt) cc_final: 0.8239 (tpt) REVERT: E 208 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7716 (pt0) REVERT: E 261 ASN cc_start: 0.8386 (t0) cc_final: 0.7835 (t0) REVERT: E 391 MET cc_start: 0.8171 (tpt) cc_final: 0.7549 (tpp) outliers start: 55 outliers final: 19 residues processed: 323 average time/residue: 0.5340 time to fit residues: 189.9623 Evaluate side-chains 249 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 325 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 101 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN B 141 ASN C 141 ASN D 62 ASN D 141 ASN E 141 ASN E 231 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.092336 restraints weight = 19156.078| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.28 r_work: 0.2870 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14585 Z= 0.188 Angle : 0.744 9.934 19805 Z= 0.368 Chirality : 0.050 0.250 2255 Planarity : 0.004 0.032 2445 Dihedral : 12.325 58.313 2201 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.60 % Allowed : 15.21 % Favored : 80.19 % 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: -2.69 (0.19), residues: 1705 helix: -1.79 (0.18), residues: 615 sheet: -1.34 (0.23), residues: 445 loop : -1.85 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 229 TYR 0.018 0.002 TYR E 425 PHE 0.012 0.001 PHE B 116 TRP 0.011 0.001 TRP B 84 HIS 0.003 0.001 HIS D 327 Details of bonding type rmsd covalent geometry : bond 0.00459 (14560) covalent geometry : angle 0.71991 (19740) SS BOND : bond 0.00758 ( 10) SS BOND : angle 4.96453 ( 20) hydrogen bonds : bond 0.03632 ( 554) hydrogen bonds : angle 5.25208 ( 1848) link_BETA1-4 : bond 0.01125 ( 10) link_BETA1-4 : angle 2.75870 ( 30) link_NAG-ASN : bond 0.00023 ( 5) link_NAG-ASN : angle 0.65275 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 277 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8043 (ptm) cc_final: 0.7394 (ptp) REVERT: A 43 ARG cc_start: 0.9132 (mtm-85) cc_final: 0.8462 (mtm180) REVERT: A 94 TYR cc_start: 0.7938 (t80) cc_final: 0.7473 (t80) REVERT: A 102 ASP cc_start: 0.8212 (t70) cc_final: 0.7871 (t70) REVERT: A 208 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7589 (tp30) REVERT: A 391 MET cc_start: 0.8269 (tpt) cc_final: 0.7631 (tpp) REVERT: A 397 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.8078 (p) REVERT: B 24 MET cc_start: 0.8374 (ptm) cc_final: 0.8079 (ptp) REVERT: B 36 LYS cc_start: 0.9488 (mttt) cc_final: 0.9064 (mppt) REVERT: B 43 ARG cc_start: 0.9215 (mtm-85) cc_final: 0.8550 (mtm180) REVERT: B 102 ASP cc_start: 0.8223 (t70) cc_final: 0.7762 (t70) REVERT: B 216 LYS cc_start: 0.8120 (mttp) cc_final: 0.7912 (ptpp) REVERT: B 391 MET cc_start: 0.8270 (tpt) cc_final: 0.7755 (tpp) REVERT: B 397 SER cc_start: 0.8152 (t) cc_final: 0.7932 (p) REVERT: C 24 MET cc_start: 0.8327 (ptm) cc_final: 0.8016 (ptp) REVERT: C 28 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8607 (mt-10) REVERT: C 36 LYS cc_start: 0.9472 (mttt) cc_final: 0.9040 (mppt) REVERT: C 43 ARG cc_start: 0.9196 (mtm-85) cc_final: 0.8627 (mtm180) REVERT: C 102 ASP cc_start: 0.8212 (t70) cc_final: 0.7691 (t0) REVERT: C 170 MET cc_start: 0.8694 (ttm) cc_final: 0.8457 (ttm) REVERT: C 208 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8088 (mt-10) REVERT: C 261 ASN cc_start: 0.8337 (t0) cc_final: 0.7679 (t0) REVERT: C 325 ARG cc_start: 0.7195 (ttp-110) cc_final: 0.6860 (mtp-110) REVERT: C 391 MET cc_start: 0.8126 (tpt) cc_final: 0.7619 (tpp) REVERT: C 393 LYS cc_start: 0.6398 (mmtt) cc_final: 0.5588 (mptp) REVERT: C 397 SER cc_start: 0.8224 (t) cc_final: 0.8008 (p) REVERT: D 36 LYS cc_start: 0.9474 (mttt) cc_final: 0.8961 (mppt) REVERT: D 43 ARG cc_start: 0.9198 (mtm-85) cc_final: 0.8834 (mtm-85) REVERT: D 156 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8817 (mtt) REVERT: D 391 MET cc_start: 0.8129 (tpt) cc_final: 0.7558 (tpp) REVERT: D 393 LYS cc_start: 0.6316 (mmtt) cc_final: 0.5551 (mptp) REVERT: D 397 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7824 (p) REVERT: E 36 LYS cc_start: 0.9462 (mttt) cc_final: 0.8969 (mppt) REVERT: E 43 ARG cc_start: 0.9134 (mtm-85) cc_final: 0.8631 (mtm180) REVERT: E 58 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7946 (p0) REVERT: E 181 ASP cc_start: 0.8353 (m-30) cc_final: 0.8108 (t0) REVERT: E 229 ARG cc_start: 0.8537 (mtp85) cc_final: 0.8320 (mtp85) REVERT: E 391 MET cc_start: 0.8110 (tpt) cc_final: 0.7427 (tpp) outliers start: 71 outliers final: 30 residues processed: 314 average time/residue: 0.5940 time to fit residues: 203.9802 Evaluate side-chains 279 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 397 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 59 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093856 restraints weight = 18981.036| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.27 r_work: 0.2883 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14585 Z= 0.138 Angle : 0.700 9.741 19805 Z= 0.345 Chirality : 0.048 0.228 2255 Planarity : 0.003 0.025 2445 Dihedral : 10.147 56.562 2201 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.82 % Allowed : 17.28 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.07 (0.19), residues: 1705 helix: -1.02 (0.20), residues: 610 sheet: -0.98 (0.24), residues: 425 loop : -1.80 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 229 TYR 0.014 0.001 TYR C 425 PHE 0.009 0.001 PHE E 116 TRP 0.011 0.001 TRP D 84 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00328 (14560) covalent geometry : angle 0.67528 (19740) SS BOND : bond 0.00520 ( 10) SS BOND : angle 4.87745 ( 20) hydrogen bonds : bond 0.03057 ( 554) hydrogen bonds : angle 4.91052 ( 1848) link_BETA1-4 : bond 0.01086 ( 10) link_BETA1-4 : angle 2.78015 ( 30) link_NAG-ASN : bond 0.00121 ( 5) link_NAG-ASN : angle 0.53128 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8055 (ptm) cc_final: 0.7344 (ptp) REVERT: A 94 TYR cc_start: 0.7973 (t80) cc_final: 0.7369 (t80) REVERT: A 102 ASP cc_start: 0.8172 (t70) cc_final: 0.7677 (t0) REVERT: A 391 MET cc_start: 0.8249 (tpt) cc_final: 0.7557 (tpp) REVERT: A 393 LYS cc_start: 0.6605 (mmtt) cc_final: 0.5862 (mptp) REVERT: B 36 LYS cc_start: 0.9494 (mttt) cc_final: 0.9064 (mppt) REVERT: B 43 ARG cc_start: 0.9223 (mtm-85) cc_final: 0.8627 (mtm180) REVERT: B 102 ASP cc_start: 0.8272 (t70) cc_final: 0.7743 (t70) REVERT: B 202 GLN cc_start: 0.8466 (mt0) cc_final: 0.8174 (mt0) REVERT: B 391 MET cc_start: 0.8296 (tpt) cc_final: 0.7691 (tpp) REVERT: B 393 LYS cc_start: 0.6332 (mmtt) cc_final: 0.5541 (mptp) REVERT: C 24 MET cc_start: 0.8345 (ptm) cc_final: 0.8083 (ptp) REVERT: C 36 LYS cc_start: 0.9486 (mttt) cc_final: 0.9064 (mppt) REVERT: C 102 ASP cc_start: 0.8215 (t70) cc_final: 0.7631 (t0) REVERT: C 170 MET cc_start: 0.8626 (ttm) cc_final: 0.8376 (ttm) REVERT: C 261 ASN cc_start: 0.8342 (t0) cc_final: 0.7680 (t0) REVERT: C 325 ARG cc_start: 0.7173 (ttp-110) cc_final: 0.6870 (ttp-110) REVERT: C 391 MET cc_start: 0.8100 (tpt) cc_final: 0.7552 (tpp) REVERT: C 393 LYS cc_start: 0.6336 (mmtt) cc_final: 0.5572 (mptp) REVERT: D 36 LYS cc_start: 0.9469 (mttt) cc_final: 0.8967 (mppt) REVERT: D 212 ARG cc_start: 0.7457 (ptp-170) cc_final: 0.7140 (ptp-110) REVERT: D 216 LYS cc_start: 0.7832 (mtpp) cc_final: 0.7619 (mtpp) REVERT: D 391 MET cc_start: 0.8128 (tpt) cc_final: 0.7539 (tpp) REVERT: D 397 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7783 (p) REVERT: E 36 LYS cc_start: 0.9458 (mttt) cc_final: 0.8952 (mppt) REVERT: E 43 ARG cc_start: 0.9145 (mtm-85) cc_final: 0.8720 (mtm180) REVERT: E 102 ASP cc_start: 0.7900 (t70) cc_final: 0.7685 (t0) REVERT: E 156 MET cc_start: 0.9046 (mtt) cc_final: 0.8781 (mtt) REVERT: E 229 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8358 (mtp85) REVERT: E 391 MET cc_start: 0.8093 (tpt) cc_final: 0.7382 (tpp) REVERT: E 393 LYS cc_start: 0.6445 (mmtt) cc_final: 0.5800 (mptp) outliers start: 59 outliers final: 26 residues processed: 283 average time/residue: 0.6335 time to fit residues: 195.0191 Evaluate side-chains 254 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 325 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093633 restraints weight = 19093.043| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.20 r_work: 0.2884 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14585 Z= 0.137 Angle : 0.666 8.378 19805 Z= 0.330 Chirality : 0.047 0.192 2255 Planarity : 0.003 0.032 2445 Dihedral : 9.255 56.766 2197 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.60 % Allowed : 17.48 % Favored : 77.93 % 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: -1.69 (0.20), residues: 1705 helix: -0.61 (0.21), residues: 615 sheet: -0.74 (0.25), residues: 425 loop : -1.72 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 75 TYR 0.013 0.001 TYR A 317 PHE 0.009 0.001 PHE B 116 TRP 0.013 0.001 TRP E 259 HIS 0.002 0.001 HIS D 327 Details of bonding type rmsd covalent geometry : bond 0.00326 (14560) covalent geometry : angle 0.64407 (19740) SS BOND : bond 0.00512 ( 10) SS BOND : angle 4.07086 ( 20) hydrogen bonds : bond 0.02971 ( 554) hydrogen bonds : angle 4.71838 ( 1848) link_BETA1-4 : bond 0.01001 ( 10) link_BETA1-4 : angle 2.90163 ( 30) link_NAG-ASN : bond 0.00066 ( 5) link_NAG-ASN : angle 0.52513 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 246 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8052 (ptm) cc_final: 0.7523 (ptm) REVERT: A 43 ARG cc_start: 0.9112 (mtm-85) cc_final: 0.8357 (mtm180) REVERT: A 71 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.8785 (t) REVERT: A 94 TYR cc_start: 0.7951 (t80) cc_final: 0.7416 (t80) REVERT: A 102 ASP cc_start: 0.8177 (t70) cc_final: 0.7750 (t70) REVERT: A 156 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8610 (mtt) REVERT: A 163 MET cc_start: 0.8946 (mtm) cc_final: 0.8737 (mpp) REVERT: A 208 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7608 (tp30) REVERT: A 391 MET cc_start: 0.8236 (tpt) cc_final: 0.7510 (tpp) REVERT: A 393 LYS cc_start: 0.6503 (mmtt) cc_final: 0.5846 (mptt) REVERT: B 36 LYS cc_start: 0.9485 (mttt) cc_final: 0.9036 (mppt) REVERT: B 43 ARG cc_start: 0.9233 (mtm-85) cc_final: 0.8663 (mtm180) REVERT: B 71 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.8679 (t) REVERT: B 102 ASP cc_start: 0.8290 (t70) cc_final: 0.7824 (t70) REVERT: B 202 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: B 391 MET cc_start: 0.8280 (tpt) cc_final: 0.7627 (tpp) REVERT: B 393 LYS cc_start: 0.6334 (mmtt) cc_final: 0.5534 (mptp) REVERT: C 24 MET cc_start: 0.8376 (ptm) cc_final: 0.8126 (ptp) REVERT: C 36 LYS cc_start: 0.9490 (mttt) cc_final: 0.9068 (mppt) REVERT: C 43 ARG cc_start: 0.9211 (mtm-85) cc_final: 0.8676 (mtm180) REVERT: C 71 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.8737 (t) REVERT: C 102 ASP cc_start: 0.8195 (t70) cc_final: 0.7633 (t0) REVERT: C 170 MET cc_start: 0.8709 (ttm) cc_final: 0.8418 (ttm) REVERT: C 171 GLN cc_start: 0.8305 (pt0) cc_final: 0.8067 (mt0) REVERT: C 261 ASN cc_start: 0.8369 (t0) cc_final: 0.7703 (t0) REVERT: C 391 MET cc_start: 0.8091 (tpt) cc_final: 0.7635 (tpp) REVERT: C 393 LYS cc_start: 0.6332 (mmtt) cc_final: 0.5574 (mptp) REVERT: D 36 LYS cc_start: 0.9478 (mttt) cc_final: 0.8979 (mppt) REVERT: D 156 MET cc_start: 0.8984 (mtt) cc_final: 0.8731 (mtt) REVERT: D 202 GLN cc_start: 0.8380 (mt0) cc_final: 0.8104 (mt0) REVERT: D 391 MET cc_start: 0.8088 (tpt) cc_final: 0.7453 (tpp) REVERT: D 393 LYS cc_start: 0.6332 (mmtt) cc_final: 0.5964 (ptpt) REVERT: D 397 SER cc_start: 0.7900 (OUTLIER) cc_final: 0.7698 (p) REVERT: E 36 LYS cc_start: 0.9443 (mttt) cc_final: 0.8949 (mppt) REVERT: E 43 ARG cc_start: 0.9125 (mtm-85) cc_final: 0.8668 (mtm180) REVERT: E 229 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8293 (mtp85) REVERT: E 391 MET cc_start: 0.8100 (tpt) cc_final: 0.7355 (tpp) REVERT: E 393 LYS cc_start: 0.6436 (mmtt) cc_final: 0.5802 (mptp) outliers start: 71 outliers final: 34 residues processed: 288 average time/residue: 0.6088 time to fit residues: 191.2661 Evaluate side-chains 266 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 397 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.091715 restraints weight = 19020.461| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.10 r_work: 0.2850 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 0.037 14585 Z= 0.191 Angle : 0.684 8.973 19805 Z= 0.342 Chirality : 0.047 0.183 2255 Planarity : 0.004 0.031 2445 Dihedral : 8.675 56.575 2197 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.72 % Allowed : 18.19 % Favored : 77.09 % 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: -1.51 (0.20), residues: 1705 helix: -0.37 (0.21), residues: 615 sheet: -0.66 (0.25), residues: 425 loop : -1.71 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 229 TYR 0.016 0.002 TYR C 425 PHE 0.011 0.001 PHE A 124 TRP 0.020 0.002 TRP E 259 HIS 0.003 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00472 (14560) covalent geometry : angle 0.66278 (19740) SS BOND : bond 0.00341 ( 10) SS BOND : angle 4.00256 ( 20) hydrogen bonds : bond 0.03123 ( 554) hydrogen bonds : angle 4.68128 ( 1848) link_BETA1-4 : bond 0.01015 ( 10) link_BETA1-4 : angle 2.98536 ( 30) link_NAG-ASN : bond 0.00075 ( 5) link_NAG-ASN : angle 0.68386 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 243 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8062 (ptm) cc_final: 0.7610 (ptm) REVERT: A 71 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.8674 (t) REVERT: A 94 TYR cc_start: 0.7968 (t80) cc_final: 0.7406 (t80) REVERT: A 102 ASP cc_start: 0.8198 (t70) cc_final: 0.7753 (t70) REVERT: A 208 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: A 261 ASN cc_start: 0.8391 (t0) cc_final: 0.7728 (t0) REVERT: A 292 LYS cc_start: 0.8403 (mttt) cc_final: 0.7885 (mmpt) REVERT: A 391 MET cc_start: 0.8258 (tpt) cc_final: 0.7495 (tpp) REVERT: A 393 LYS cc_start: 0.6495 (mmtt) cc_final: 0.5862 (mptt) REVERT: B 24 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8125 (ptp) REVERT: B 36 LYS cc_start: 0.9490 (mttt) cc_final: 0.9044 (mppt) REVERT: B 43 ARG cc_start: 0.9203 (mtm-85) cc_final: 0.8560 (mtm180) REVERT: B 102 ASP cc_start: 0.8304 (t70) cc_final: 0.7858 (t70) REVERT: B 202 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8075 (mt0) REVERT: B 391 MET cc_start: 0.8271 (tpt) cc_final: 0.7603 (tpp) REVERT: B 393 LYS cc_start: 0.6333 (mmtt) cc_final: 0.5538 (mptp) REVERT: C 24 MET cc_start: 0.8329 (ptm) cc_final: 0.8070 (ptp) REVERT: C 36 LYS cc_start: 0.9525 (mttt) cc_final: 0.9114 (mppt) REVERT: C 43 ARG cc_start: 0.9203 (mtm-85) cc_final: 0.8614 (mtm180) REVERT: C 71 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8634 (t) REVERT: C 102 ASP cc_start: 0.8241 (t70) cc_final: 0.7672 (t0) REVERT: C 170 MET cc_start: 0.8893 (ttm) cc_final: 0.8594 (ttm) REVERT: C 189 LYS cc_start: 0.7427 (ptpp) cc_final: 0.7212 (ptpt) REVERT: C 261 ASN cc_start: 0.8382 (t0) cc_final: 0.7738 (t0) REVERT: C 391 MET cc_start: 0.8071 (tpt) cc_final: 0.7582 (tpp) REVERT: C 393 LYS cc_start: 0.6277 (mmtt) cc_final: 0.5533 (mptp) REVERT: D 36 LYS cc_start: 0.9495 (mttt) cc_final: 0.9003 (mppt) REVERT: D 156 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8665 (mtt) REVERT: D 292 LYS cc_start: 0.8308 (mttt) cc_final: 0.7961 (mmtm) REVERT: D 303 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7645 (mmm) REVERT: D 391 MET cc_start: 0.8076 (tpt) cc_final: 0.7486 (tpp) REVERT: D 393 LYS cc_start: 0.6328 (mmtt) cc_final: 0.5960 (ptpt) REVERT: D 397 SER cc_start: 0.7828 (OUTLIER) cc_final: 0.7624 (p) REVERT: E 36 LYS cc_start: 0.9444 (mttt) cc_final: 0.8946 (mppt) REVERT: E 43 ARG cc_start: 0.9126 (mtm-85) cc_final: 0.8665 (mtm180) REVERT: E 229 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8219 (mtp85) REVERT: E 261 ASN cc_start: 0.8264 (t0) cc_final: 0.7689 (t0) REVERT: E 391 MET cc_start: 0.8118 (tpt) cc_final: 0.7383 (tpp) REVERT: E 393 LYS cc_start: 0.6432 (mmtt) cc_final: 0.5796 (mptp) outliers start: 73 outliers final: 42 residues processed: 287 average time/residue: 0.6304 time to fit residues: 197.3525 Evaluate side-chains 270 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 397 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 134 optimal weight: 0.0170 chunk 81 optimal weight: 0.0770 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.095140 restraints weight = 18743.206| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.19 r_work: 0.2909 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14585 Z= 0.107 Angle : 0.615 8.693 19805 Z= 0.305 Chirality : 0.045 0.166 2255 Planarity : 0.003 0.024 2445 Dihedral : 8.068 56.428 2197 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.37 % Allowed : 19.74 % Favored : 76.89 % 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: -1.20 (0.20), residues: 1705 helix: 0.02 (0.22), residues: 610 sheet: -0.49 (0.25), residues: 425 loop : -1.68 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 229 TYR 0.012 0.001 TYR A 317 PHE 0.010 0.001 PHE C 115 TRP 0.019 0.002 TRP C 259 HIS 0.002 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00242 (14560) covalent geometry : angle 0.59976 (19740) SS BOND : bond 0.00264 ( 10) SS BOND : angle 2.84778 ( 20) hydrogen bonds : bond 0.02797 ( 554) hydrogen bonds : angle 4.49420 ( 1848) link_BETA1-4 : bond 0.00888 ( 10) link_BETA1-4 : angle 2.67787 ( 30) link_NAG-ASN : bond 0.00171 ( 5) link_NAG-ASN : angle 0.47596 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.9094 (mtm-85) cc_final: 0.8400 (mtm180) REVERT: A 71 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.8705 (t) REVERT: A 102 ASP cc_start: 0.8188 (t70) cc_final: 0.7695 (t70) REVERT: A 261 ASN cc_start: 0.8388 (t0) cc_final: 0.7689 (t0) REVERT: A 292 LYS cc_start: 0.8381 (mttt) cc_final: 0.7887 (mmpt) REVERT: A 391 MET cc_start: 0.8251 (tpt) cc_final: 0.7431 (tpp) REVERT: A 393 LYS cc_start: 0.6449 (mmtt) cc_final: 0.5819 (mptp) REVERT: B 24 MET cc_start: 0.8354 (ptm) cc_final: 0.8111 (ptp) REVERT: B 31 ASP cc_start: 0.8631 (m-30) cc_final: 0.8328 (m-30) REVERT: B 36 LYS cc_start: 0.9482 (mttt) cc_final: 0.9057 (mppt) REVERT: B 43 ARG cc_start: 0.9191 (mtm-85) cc_final: 0.8625 (mtm180) REVERT: B 63 SER cc_start: 0.8992 (t) cc_final: 0.8471 (m) REVERT: B 102 ASP cc_start: 0.8352 (t70) cc_final: 0.7870 (t0) REVERT: B 202 GLN cc_start: 0.8423 (mt0) cc_final: 0.8135 (mt0) REVERT: B 391 MET cc_start: 0.8236 (tpt) cc_final: 0.7556 (tpp) REVERT: B 393 LYS cc_start: 0.6324 (mmtt) cc_final: 0.5568 (mptp) REVERT: C 36 LYS cc_start: 0.9534 (mttt) cc_final: 0.9119 (mppt) REVERT: C 43 ARG cc_start: 0.9198 (mtm-85) cc_final: 0.8681 (mtm180) REVERT: C 71 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8658 (t) REVERT: C 102 ASP cc_start: 0.8238 (t70) cc_final: 0.7648 (t0) REVERT: C 170 MET cc_start: 0.8782 (ttm) cc_final: 0.8475 (ttm) REVERT: C 261 ASN cc_start: 0.8351 (t0) cc_final: 0.7684 (t0) REVERT: C 391 MET cc_start: 0.8088 (tpt) cc_final: 0.7572 (tpp) REVERT: C 393 LYS cc_start: 0.6337 (mmtt) cc_final: 0.6004 (tppt) REVERT: D 36 LYS cc_start: 0.9484 (mttt) cc_final: 0.8987 (mppt) REVERT: D 63 SER cc_start: 0.8942 (t) cc_final: 0.8732 (t) REVERT: D 69 GLU cc_start: 0.8181 (mp0) cc_final: 0.7974 (mp0) REVERT: D 156 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8688 (mtt) REVERT: D 391 MET cc_start: 0.8064 (tpt) cc_final: 0.7402 (tpp) REVERT: D 393 LYS cc_start: 0.6278 (mmtt) cc_final: 0.5930 (ptpt) REVERT: E 36 LYS cc_start: 0.9440 (mttt) cc_final: 0.8940 (mppt) REVERT: E 43 ARG cc_start: 0.9088 (mtm-85) cc_final: 0.8628 (mtm180) REVERT: E 163 MET cc_start: 0.8921 (mtm) cc_final: 0.8492 (mpp) REVERT: E 229 ARG cc_start: 0.8462 (mtp85) cc_final: 0.8175 (mtp85) REVERT: E 391 MET cc_start: 0.8097 (tpt) cc_final: 0.7223 (tpp) REVERT: E 393 LYS cc_start: 0.6426 (mmtt) cc_final: 0.5798 (mptp) outliers start: 52 outliers final: 33 residues processed: 279 average time/residue: 0.5859 time to fit residues: 179.1480 Evaluate side-chains 262 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 397 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 0.0170 chunk 125 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 140 optimal weight: 0.0770 chunk 78 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.094674 restraints weight = 19008.234| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.15 r_work: 0.2891 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14585 Z= 0.113 Angle : 0.603 8.306 19805 Z= 0.300 Chirality : 0.045 0.161 2255 Planarity : 0.003 0.025 2445 Dihedral : 7.693 58.758 2195 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.04 % Allowed : 20.97 % Favored : 75.99 % 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: -1.01 (0.20), residues: 1705 helix: 0.22 (0.22), residues: 610 sheet: -0.35 (0.25), residues: 425 loop : -1.65 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 229 TYR 0.013 0.001 TYR A 317 PHE 0.012 0.001 PHE C 115 TRP 0.023 0.002 TRP C 259 HIS 0.002 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00262 (14560) covalent geometry : angle 0.58761 (19740) SS BOND : bond 0.00080 ( 10) SS BOND : angle 2.79921 ( 20) hydrogen bonds : bond 0.02766 ( 554) hydrogen bonds : angle 4.37227 ( 1848) link_BETA1-4 : bond 0.00947 ( 10) link_BETA1-4 : angle 2.68621 ( 30) link_NAG-ASN : bond 0.00191 ( 5) link_NAG-ASN : angle 1.00024 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.9096 (mtm-85) cc_final: 0.8351 (mtm180) REVERT: A 71 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8663 (t) REVERT: A 94 TYR cc_start: 0.7754 (t80) cc_final: 0.7524 (t80) REVERT: A 102 ASP cc_start: 0.8106 (t70) cc_final: 0.7587 (t70) REVERT: A 208 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: A 261 ASN cc_start: 0.8348 (t0) cc_final: 0.7641 (t0) REVERT: A 292 LYS cc_start: 0.8363 (mttt) cc_final: 0.7839 (mmpt) REVERT: A 391 MET cc_start: 0.8253 (tpt) cc_final: 0.7527 (tpp) REVERT: A 393 LYS cc_start: 0.6463 (mmtt) cc_final: 0.5832 (mptt) REVERT: B 36 LYS cc_start: 0.9461 (mttt) cc_final: 0.8997 (mppt) REVERT: B 43 ARG cc_start: 0.9166 (mtm-85) cc_final: 0.8591 (mtm180) REVERT: B 63 SER cc_start: 0.8921 (t) cc_final: 0.8394 (m) REVERT: B 102 ASP cc_start: 0.8310 (t70) cc_final: 0.7813 (t70) REVERT: B 202 GLN cc_start: 0.8424 (mt0) cc_final: 0.8120 (mt0) REVERT: B 391 MET cc_start: 0.8239 (tpt) cc_final: 0.7580 (tpp) REVERT: B 393 LYS cc_start: 0.6327 (mmtt) cc_final: 0.5587 (mptp) REVERT: C 36 LYS cc_start: 0.9538 (mttt) cc_final: 0.9112 (mppt) REVERT: C 43 ARG cc_start: 0.9193 (mtm-85) cc_final: 0.8748 (mtm180) REVERT: C 71 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8640 (t) REVERT: C 102 ASP cc_start: 0.8212 (t70) cc_final: 0.7626 (t0) REVERT: C 170 MET cc_start: 0.8792 (ttm) cc_final: 0.8442 (ttm) REVERT: C 261 ASN cc_start: 0.8331 (t0) cc_final: 0.7655 (t0) REVERT: C 391 MET cc_start: 0.8080 (tpt) cc_final: 0.7547 (tpp) REVERT: C 393 LYS cc_start: 0.6336 (mmtt) cc_final: 0.6004 (tppt) REVERT: D 36 LYS cc_start: 0.9494 (mttt) cc_final: 0.8997 (mppt) REVERT: D 63 SER cc_start: 0.8948 (t) cc_final: 0.8737 (t) REVERT: D 156 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8656 (mtt) REVERT: D 303 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7458 (mmm) REVERT: D 325 ARG cc_start: 0.7147 (ttp80) cc_final: 0.6842 (ttp80) REVERT: D 391 MET cc_start: 0.8054 (tpt) cc_final: 0.7436 (tpp) REVERT: D 393 LYS cc_start: 0.6250 (mmtt) cc_final: 0.5944 (ptpt) REVERT: E 36 LYS cc_start: 0.9441 (mttt) cc_final: 0.8936 (mppt) REVERT: E 43 ARG cc_start: 0.9101 (mtm-85) cc_final: 0.8695 (mtm180) REVERT: E 229 ARG cc_start: 0.8415 (mtp85) cc_final: 0.7953 (mtp85) REVERT: E 259 TRP cc_start: 0.8581 (m100) cc_final: 0.8350 (m100) REVERT: E 391 MET cc_start: 0.8077 (tpt) cc_final: 0.7200 (tpp) REVERT: E 393 LYS cc_start: 0.6428 (mmtt) cc_final: 0.5782 (mptp) outliers start: 47 outliers final: 30 residues processed: 264 average time/residue: 0.6049 time to fit residues: 174.4764 Evaluate side-chains 252 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 397 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 70 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.094588 restraints weight = 18933.632| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.22 r_work: 0.2892 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14585 Z= 0.118 Angle : 0.601 8.147 19805 Z= 0.301 Chirality : 0.045 0.162 2255 Planarity : 0.003 0.024 2445 Dihedral : 7.493 59.114 2195 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.65 % Allowed : 21.55 % Favored : 75.79 % 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: -0.85 (0.20), residues: 1705 helix: 0.39 (0.22), residues: 610 sheet: -0.24 (0.25), residues: 425 loop : -1.60 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 229 TYR 0.013 0.001 TYR A 317 PHE 0.011 0.001 PHE C 115 TRP 0.027 0.002 TRP C 259 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00278 (14560) covalent geometry : angle 0.58535 (19740) SS BOND : bond 0.00197 ( 10) SS BOND : angle 2.75891 ( 20) hydrogen bonds : bond 0.02727 ( 554) hydrogen bonds : angle 4.33603 ( 1848) link_BETA1-4 : bond 0.00965 ( 10) link_BETA1-4 : angle 2.52595 ( 30) link_NAG-ASN : bond 0.00375 ( 5) link_NAG-ASN : angle 1.83039 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.9074 (mtm-85) cc_final: 0.8333 (mtm180) REVERT: A 71 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8653 (t) REVERT: A 102 ASP cc_start: 0.8123 (t70) cc_final: 0.7616 (t70) REVERT: A 208 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7638 (tp30) REVERT: A 261 ASN cc_start: 0.8315 (t0) cc_final: 0.7627 (t0) REVERT: A 292 LYS cc_start: 0.8379 (mttt) cc_final: 0.7897 (mmpt) REVERT: A 391 MET cc_start: 0.8250 (tpt) cc_final: 0.7494 (tpp) REVERT: A 393 LYS cc_start: 0.6462 (mmtt) cc_final: 0.5841 (mptt) REVERT: B 36 LYS cc_start: 0.9486 (mttt) cc_final: 0.9016 (mppt) REVERT: B 43 ARG cc_start: 0.9159 (mtm-85) cc_final: 0.8591 (mtm180) REVERT: B 63 SER cc_start: 0.8920 (t) cc_final: 0.8399 (m) REVERT: B 102 ASP cc_start: 0.8323 (t70) cc_final: 0.7851 (t0) REVERT: B 202 GLN cc_start: 0.8383 (mt0) cc_final: 0.8071 (mt0) REVERT: B 229 ARG cc_start: 0.8350 (mtp85) cc_final: 0.8144 (mtp85) REVERT: B 303 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7340 (mmt) REVERT: B 391 MET cc_start: 0.8228 (tpt) cc_final: 0.7551 (tpp) REVERT: B 393 LYS cc_start: 0.6295 (mmtt) cc_final: 0.5561 (mptp) REVERT: C 36 LYS cc_start: 0.9530 (mttt) cc_final: 0.9097 (mppt) REVERT: C 43 ARG cc_start: 0.9198 (mtm-85) cc_final: 0.8748 (mtm180) REVERT: C 71 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8595 (t) REVERT: C 102 ASP cc_start: 0.8266 (t70) cc_final: 0.7697 (t0) REVERT: C 170 MET cc_start: 0.8784 (ttm) cc_final: 0.8445 (ttm) REVERT: C 261 ASN cc_start: 0.8322 (t0) cc_final: 0.7648 (t0) REVERT: C 391 MET cc_start: 0.8108 (tpt) cc_final: 0.7626 (tpp) REVERT: C 393 LYS cc_start: 0.6354 (mmtt) cc_final: 0.6008 (tppt) REVERT: D 36 LYS cc_start: 0.9499 (mttt) cc_final: 0.8991 (mppt) REVERT: D 63 SER cc_start: 0.8981 (t) cc_final: 0.8774 (t) REVERT: D 303 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7417 (mmm) REVERT: D 325 ARG cc_start: 0.7138 (ttp80) cc_final: 0.6838 (ttp80) REVERT: D 391 MET cc_start: 0.8040 (tpt) cc_final: 0.7388 (tpp) REVERT: D 393 LYS cc_start: 0.6271 (mmtt) cc_final: 0.5951 (ptpt) REVERT: E 36 LYS cc_start: 0.9441 (mttt) cc_final: 0.8941 (mppt) REVERT: E 43 ARG cc_start: 0.9111 (mtm-85) cc_final: 0.8707 (mtm180) REVERT: E 71 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8732 (p) REVERT: E 163 MET cc_start: 0.8939 (mtm) cc_final: 0.8337 (mpp) REVERT: E 229 ARG cc_start: 0.8422 (mtp85) cc_final: 0.7968 (mtp85) REVERT: E 259 TRP cc_start: 0.8558 (m100) cc_final: 0.8323 (m100) REVERT: E 261 ASN cc_start: 0.8348 (t0) cc_final: 0.7848 (t0) REVERT: E 391 MET cc_start: 0.8058 (tpt) cc_final: 0.7178 (tpp) REVERT: E 393 LYS cc_start: 0.6411 (mmtt) cc_final: 0.5774 (mptp) outliers start: 41 outliers final: 27 residues processed: 264 average time/residue: 0.6312 time to fit residues: 181.3776 Evaluate side-chains 258 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 397 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN E 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.092569 restraints weight = 18951.003| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.21 r_work: 0.2869 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14585 Z= 0.152 Angle : 0.619 7.901 19805 Z= 0.312 Chirality : 0.045 0.165 2255 Planarity : 0.003 0.024 2445 Dihedral : 7.403 59.514 2195 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.78 % Allowed : 21.49 % Favored : 75.73 % 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: -0.76 (0.20), residues: 1705 helix: 0.47 (0.22), residues: 610 sheet: -0.25 (0.25), residues: 425 loop : -1.54 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 229 TYR 0.015 0.001 TYR A 317 PHE 0.011 0.001 PHE C 115 TRP 0.037 0.002 TRP D 259 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00367 (14560) covalent geometry : angle 0.60319 (19740) SS BOND : bond 0.00216 ( 10) SS BOND : angle 3.00044 ( 20) hydrogen bonds : bond 0.02841 ( 554) hydrogen bonds : angle 4.37628 ( 1848) link_BETA1-4 : bond 0.00982 ( 10) link_BETA1-4 : angle 2.45060 ( 30) link_NAG-ASN : bond 0.00413 ( 5) link_NAG-ASN : angle 1.81610 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.9108 (mtm-85) cc_final: 0.8385 (mtm180) REVERT: A 102 ASP cc_start: 0.8161 (t70) cc_final: 0.7661 (t70) REVERT: A 208 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: A 261 ASN cc_start: 0.8362 (t0) cc_final: 0.7678 (t0) REVERT: A 292 LYS cc_start: 0.8451 (mttt) cc_final: 0.7959 (mmpt) REVERT: A 391 MET cc_start: 0.8297 (tpt) cc_final: 0.7532 (tpp) REVERT: A 393 LYS cc_start: 0.6508 (mmtt) cc_final: 0.5879 (mptt) REVERT: B 36 LYS cc_start: 0.9473 (mttt) cc_final: 0.9024 (mppt) REVERT: B 43 ARG cc_start: 0.9196 (mtm-85) cc_final: 0.8601 (mtm180) REVERT: B 102 ASP cc_start: 0.8367 (t70) cc_final: 0.7920 (t0) REVERT: B 303 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7440 (mmt) REVERT: B 391 MET cc_start: 0.8237 (tpt) cc_final: 0.7599 (tpp) REVERT: B 393 LYS cc_start: 0.6337 (mmtt) cc_final: 0.5597 (mptp) REVERT: C 36 LYS cc_start: 0.9516 (mttt) cc_final: 0.9079 (mppt) REVERT: C 43 ARG cc_start: 0.9229 (mtm-85) cc_final: 0.8670 (mtm180) REVERT: C 71 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8569 (t) REVERT: C 102 ASP cc_start: 0.8307 (t70) cc_final: 0.7757 (t0) REVERT: C 170 MET cc_start: 0.8874 (ttm) cc_final: 0.8540 (ttm) REVERT: C 261 ASN cc_start: 0.8376 (t0) cc_final: 0.7722 (t0) REVERT: C 391 MET cc_start: 0.8143 (tpt) cc_final: 0.7670 (tpp) REVERT: C 393 LYS cc_start: 0.6374 (mmtt) cc_final: 0.6029 (tppt) REVERT: D 36 LYS cc_start: 0.9490 (mttt) cc_final: 0.8999 (mppt) REVERT: D 63 SER cc_start: 0.8929 (t) cc_final: 0.8358 (m) REVERT: D 303 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7464 (mmm) REVERT: D 325 ARG cc_start: 0.7202 (ttp80) cc_final: 0.6894 (ttp80) REVERT: D 391 MET cc_start: 0.8022 (tpt) cc_final: 0.7355 (tpp) REVERT: D 393 LYS cc_start: 0.6273 (mmtt) cc_final: 0.5951 (ptpt) REVERT: E 36 LYS cc_start: 0.9446 (mttt) cc_final: 0.8961 (mppt) REVERT: E 43 ARG cc_start: 0.9134 (mtm-85) cc_final: 0.8640 (mtm180) REVERT: E 229 ARG cc_start: 0.8474 (mtp85) cc_final: 0.8198 (mtp85) REVERT: E 261 ASN cc_start: 0.8371 (t0) cc_final: 0.7915 (t0) REVERT: E 391 MET cc_start: 0.8087 (tpt) cc_final: 0.7208 (tpp) REVERT: E 393 LYS cc_start: 0.6463 (mmtt) cc_final: 0.5821 (mptp) outliers start: 43 outliers final: 29 residues processed: 259 average time/residue: 0.6095 time to fit residues: 172.1620 Evaluate side-chains 253 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 397 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 77 optimal weight: 0.4980 chunk 85 optimal weight: 0.0170 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 36 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 82 GLN E 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.095178 restraints weight = 18713.116| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.18 r_work: 0.2908 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14585 Z= 0.106 Angle : 0.587 8.146 19805 Z= 0.296 Chirality : 0.044 0.164 2255 Planarity : 0.003 0.024 2445 Dihedral : 7.245 59.907 2195 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.33 % Allowed : 22.20 % Favored : 75.47 % 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: -0.59 (0.21), residues: 1705 helix: 0.69 (0.22), residues: 610 sheet: -0.14 (0.25), residues: 425 loop : -1.54 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 229 TYR 0.012 0.001 TYR A 317 PHE 0.010 0.001 PHE C 115 TRP 0.057 0.002 TRP B 259 HIS 0.002 0.001 HIS D 327 Details of bonding type rmsd covalent geometry : bond 0.00242 (14560) covalent geometry : angle 0.57435 (19740) SS BOND : bond 0.00114 ( 10) SS BOND : angle 2.56879 ( 20) hydrogen bonds : bond 0.02688 ( 554) hydrogen bonds : angle 4.29048 ( 1848) link_BETA1-4 : bond 0.00919 ( 10) link_BETA1-4 : angle 2.20109 ( 30) link_NAG-ASN : bond 0.00368 ( 5) link_NAG-ASN : angle 1.75768 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4342.52 seconds wall clock time: 74 minutes 42.02 seconds (4482.02 seconds total)