Starting phenix.real_space_refine on Mon Apr 6 00:23:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y96_72690/04_2026/9y96_72690.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y96_72690/04_2026/9y96_72690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y96_72690/04_2026/9y96_72690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y96_72690/04_2026/9y96_72690.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y96_72690/04_2026/9y96_72690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y96_72690/04_2026/9y96_72690.map" } resolution = 3.36 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9190 2.51 5 N 2295 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14165 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2800 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "B" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2800 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "C" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2800 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "D" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2800 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "E" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2800 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.40, per 1000 atoms: 0.24 Number of scatterers: 14165 At special positions: 0 Unit cell: (93.24, 90.72, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2590 8.00 N 2295 7.00 C 9190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 243 " distance=2.04 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.04 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 243 " distance=2.04 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.04 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 243 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 72 " " NAG A 502 " - " ASN A 103 " " NAG B 501 " - " ASN B 72 " " NAG B 502 " - " ASN B 103 " " NAG C 501 " - " ASN C 72 " " NAG C 502 " - " ASN C 103 " " NAG D 501 " - " ASN D 72 " " NAG D 502 " - " ASN D 103 " " NAG E 502 " - " ASN E 72 " " NAG E 503 " - " ASN E 103 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 542.9 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 25 sheets defined 41.2% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.770A pdb=" N LEU A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.521A pdb=" N TRP A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 278 Processing helix chain 'A' and resid 282 through 306 removed outlier: 4.117A pdb=" N ALA A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 345 Processing helix chain 'A' and resid 411 through 442 removed outlier: 3.691A pdb=" N ALA A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.682A pdb=" N ASP A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 53 Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.771A pdb=" N LEU B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 261 through 274 removed outlier: 3.521A pdb=" N TRP B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 278 Processing helix chain 'B' and resid 282 through 306 removed outlier: 4.117A pdb=" N ALA B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 345 Processing helix chain 'B' and resid 411 through 442 removed outlier: 3.691A pdb=" N ALA B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.683A pdb=" N ASP B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 53 Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.770A pdb=" N LEU C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Processing helix chain 'C' and resid 261 through 274 removed outlier: 3.521A pdb=" N TRP C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 282 through 306 removed outlier: 4.117A pdb=" N ALA C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 345 Processing helix chain 'C' and resid 411 through 442 removed outlier: 3.691A pdb=" N ALA C 424 " --> pdb=" O THR C 420 " (cutoff:3.500A) Proline residue: C 427 - end of helix Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.682A pdb=" N ASP C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 53 Processing helix chain 'D' and resid 105 through 108 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.770A pdb=" N LEU D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 Processing helix chain 'D' and resid 261 through 274 removed outlier: 3.521A pdb=" N TRP D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 278 Processing helix chain 'D' and resid 282 through 306 removed outlier: 4.118A pdb=" N ALA D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 345 Processing helix chain 'D' and resid 411 through 442 removed outlier: 3.691A pdb=" N ALA D 424 " --> pdb=" O THR D 420 " (cutoff:3.500A) Proline residue: D 427 - end of helix Processing helix chain 'D' and resid 443 through 448 removed outlier: 3.682A pdb=" N ASP D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 105 through 108 Processing helix chain 'E' and resid 120 through 127 removed outlier: 3.770A pdb=" N LEU E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP E 125 " --> pdb=" O SER E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 261 Processing helix chain 'E' and resid 261 through 274 removed outlier: 3.521A pdb=" N TRP E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 278 Processing helix chain 'E' and resid 282 through 306 removed outlier: 4.117A pdb=" N ALA E 306 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 345 Processing helix chain 'E' and resid 411 through 442 removed outlier: 3.690A pdb=" N ALA E 424 " --> pdb=" O THR E 420 " (cutoff:3.500A) Proline residue: E 427 - end of helix Processing helix chain 'E' and resid 443 through 448 removed outlier: 3.683A pdb=" N ASP E 448 " --> pdb=" O ILE E 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.552A pdb=" N LEU A 152 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 141 removed outlier: 6.506A pdb=" N THR A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 167 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA5, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 119 removed outlier: 4.553A pdb=" N LEU B 152 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 137 through 141 removed outlier: 6.505A pdb=" N THR B 169 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA B 140 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR B 167 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AA9, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB2, first strand: chain 'C' and resid 116 through 119 removed outlier: 4.552A pdb=" N LEU C 152 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 137 through 141 removed outlier: 6.506A pdb=" N THR C 169 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA C 140 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR C 167 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB5, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB6, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AB7, first strand: chain 'D' and resid 116 through 119 removed outlier: 4.551A pdb=" N LEU D 152 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 137 through 141 removed outlier: 6.506A pdb=" N THR D 169 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA D 140 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR D 167 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 132 through 134 Processing sheet with id=AC1, first strand: chain 'D' and resid 132 through 134 Processing sheet with id=AC2, first strand: chain 'D' and resid 234 through 235 Processing sheet with id=AC3, first strand: chain 'E' and resid 116 through 119 removed outlier: 4.552A pdb=" N LEU E 152 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 137 through 141 removed outlier: 6.505A pdb=" N THR E 169 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA E 140 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR E 167 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 132 through 134 Processing sheet with id=AC6, first strand: chain 'E' and resid 132 through 134 Processing sheet with id=AC7, first strand: chain 'E' and resid 234 through 235 885 hydrogen bonds defined for protein. 2550 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: 2.62 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4378 1.35 - 1.47: 3640 1.47 - 1.59: 6342 1.59 - 1.72: 0 1.72 - 1.84: 150 Bond restraints: 14510 Sorted by residual: bond pdb=" N TRP D 277 " pdb=" CA TRP D 277 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.86e+00 bond pdb=" N TRP E 277 " pdb=" CA TRP E 277 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.86e+00 bond pdb=" N TRP C 277 " pdb=" CA TRP C 277 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.18e-02 7.18e+03 7.68e+00 bond pdb=" N TRP A 277 " pdb=" CA TRP A 277 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.18e-02 7.18e+03 7.56e+00 bond pdb=" N TRP B 277 " pdb=" CA TRP B 277 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.18e-02 7.18e+03 7.47e+00 ... (remaining 14505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 18113 1.25 - 2.51: 1220 2.51 - 3.76: 269 3.76 - 5.02: 54 5.02 - 6.27: 29 Bond angle restraints: 19685 Sorted by residual: angle pdb=" N LYS B 442 " pdb=" CA LYS B 442 " pdb=" C LYS B 442 " ideal model delta sigma weight residual 109.95 104.89 5.06 1.44e+00 4.82e-01 1.23e+01 angle pdb=" N LYS A 442 " pdb=" CA LYS A 442 " pdb=" C LYS A 442 " ideal model delta sigma weight residual 109.95 104.91 5.04 1.44e+00 4.82e-01 1.22e+01 angle pdb=" N LYS C 442 " pdb=" CA LYS C 442 " pdb=" C LYS C 442 " ideal model delta sigma weight residual 109.95 104.92 5.03 1.44e+00 4.82e-01 1.22e+01 angle pdb=" N LYS E 442 " pdb=" CA LYS E 442 " pdb=" C LYS E 442 " ideal model delta sigma weight residual 109.95 104.93 5.02 1.44e+00 4.82e-01 1.22e+01 angle pdb=" N LYS D 442 " pdb=" CA LYS D 442 " pdb=" C LYS D 442 " ideal model delta sigma weight residual 109.95 104.95 5.00 1.44e+00 4.82e-01 1.21e+01 ... (remaining 19680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.77: 7672 13.77 - 27.53: 863 27.53 - 41.30: 185 41.30 - 55.06: 30 55.06 - 68.83: 25 Dihedral angle restraints: 8775 sinusoidal: 3660 harmonic: 5115 Sorted by residual: dihedral pdb=" CB MET C 297 " pdb=" CG MET C 297 " pdb=" SD MET C 297 " pdb=" CE MET C 297 " ideal model delta sinusoidal sigma weight residual -180.00 -122.47 -57.53 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CB MET B 297 " pdb=" CG MET B 297 " pdb=" SD MET B 297 " pdb=" CE MET B 297 " ideal model delta sinusoidal sigma weight residual 180.00 -122.50 -57.50 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CB MET A 297 " pdb=" CG MET A 297 " pdb=" SD MET A 297 " pdb=" CE MET A 297 " ideal model delta sinusoidal sigma weight residual -180.00 -122.51 -57.49 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 8772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1432 0.035 - 0.070: 507 0.070 - 0.104: 187 0.104 - 0.139: 89 0.139 - 0.174: 35 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CA VAL E 274 " pdb=" N VAL E 274 " pdb=" C VAL E 274 " pdb=" CB VAL E 274 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA VAL D 274 " pdb=" N VAL D 274 " pdb=" C VAL D 274 " pdb=" CB VAL D 274 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA VAL A 274 " pdb=" N VAL A 274 " pdb=" C VAL A 274 " pdb=" CB VAL A 274 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 ... (remaining 2247 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 208 " 0.058 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO D 209 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 209 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 209 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 208 " 0.058 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO C 209 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 208 " 0.058 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO A 209 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " 0.050 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 534 2.72 - 3.26: 13635 3.26 - 3.81: 23287 3.81 - 4.35: 28751 4.35 - 4.90: 49621 Nonbonded interactions: 115828 Sorted by model distance: nonbonded pdb=" NE2 GLN B 253 " pdb=" OG SER C 312 " model vdw 2.170 3.120 nonbonded pdb=" OG1 THR D 196 " pdb=" OD1 ASN D 198 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR E 196 " pdb=" OD1 ASN E 198 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR A 196 " pdb=" OD1 ASN A 198 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR B 196 " pdb=" OD1 ASN B 198 " model vdw 2.273 3.040 ... (remaining 115823 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' and (resid 41 through 449 or resid 502)) selection = (chain 'B' and (resid 41 through 449 or resid 502)) selection = (chain 'C' and (resid 41 through 449 or resid 502)) selection = (chain 'D' and (resid 41 through 449 or resid 502)) selection = (chain 'E' and (resid 41 through 449 or resid 502)) } 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.260 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 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 : 0.004 0.043 14530 Z= 0.253 Angle : 0.759 7.448 19735 Z= 0.459 Chirality : 0.049 0.174 2250 Planarity : 0.009 0.089 2445 Dihedral : 12.350 68.828 5425 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.47 (0.19), residues: 1710 helix: -0.10 (0.18), residues: 605 sheet: -0.24 (0.27), residues: 375 loop : -0.34 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG C 61 TYR 0.021 0.002 TYR D 112 PHE 0.017 0.001 PHE B 433 TRP 0.009 0.001 TRP C 273 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00408 (14510) covalent geometry : angle 0.73949 (19685) SS BOND : bond 0.00648 ( 10) SS BOND : angle 2.67736 ( 20) hydrogen bonds : bond 0.16903 ( 740) hydrogen bonds : angle 7.24279 ( 2550) link_NAG-ASN : bond 0.00244 ( 10) link_NAG-ASN : angle 3.91999 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 0.527 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: symmetry clash REVERT: A 52 MET cc_start: 0.8158 (ppp) cc_final: 0.7717 (ppp) REVERT: A 144 ASP cc_start: 0.8223 (p0) cc_final: 0.7984 (p0) REVERT: A 256 TYR cc_start: 0.9021 (t80) cc_final: 0.8671 (t80) REVERT: A 279 ASN cc_start: 0.8109 (t0) cc_final: 0.7904 (t0) REVERT: A 304 SER cc_start: 0.8805 (p) cc_final: 0.8492 (p) REVERT: B 45 SER cc_start: 0.7914 (m) cc_final: 0.7232 (p) REVERT: B 84 SER cc_start: 0.9311 (m) cc_final: 0.9086 (t) REVERT: B 256 TYR cc_start: 0.8974 (t80) cc_final: 0.8724 (t80) REVERT: C 52 MET cc_start: 0.8209 (ppp) cc_final: 0.7831 (ppp) REVERT: C 144 ASP cc_start: 0.7987 (p0) cc_final: 0.7701 (p0) REVERT: C 188 MET cc_start: 0.8941 (ttm) cc_final: 0.8721 (ttm) REVERT: C 256 TYR cc_start: 0.9017 (t80) cc_final: 0.8737 (t80) REVERT: D 52 MET cc_start: 0.8237 (ppp) cc_final: 0.7887 (ppp) REVERT: D 90 MET cc_start: 0.9137 (mmt) cc_final: 0.8777 (mmm) REVERT: D 310 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8660 (mmtt) REVERT: D 435 ILE cc_start: 0.9164 (mm) cc_final: 0.8903 (mt) REVERT: E 52 MET cc_start: 0.8226 (ppp) cc_final: 0.7813 (ppp) REVERT: E 144 ASP cc_start: 0.8174 (p0) cc_final: 0.7852 (p0) REVERT: E 197 MET cc_start: 0.8923 (mmm) cc_final: 0.8679 (mmm) REVERT: E 279 ASN cc_start: 0.8081 (t0) cc_final: 0.7737 (t0) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.1358 time to fit residues: 82.0723 Evaluate side-chains 248 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 184 GLN B 65 ASN B 76 ASN C 65 ASN D 65 ASN D 76 ASN D 184 GLN E 65 ASN E 184 GLN E 189 GLN E 260 GLN E 344 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.087966 restraints weight = 23277.721| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.07 r_work: 0.2838 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14530 Z= 0.184 Angle : 0.611 7.082 19735 Z= 0.323 Chirality : 0.043 0.217 2250 Planarity : 0.004 0.047 2445 Dihedral : 4.725 30.513 2090 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.73 % Allowed : 10.32 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.06 (0.20), residues: 1710 helix: 1.71 (0.20), residues: 610 sheet: 0.09 (0.25), residues: 420 loop : 0.34 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 61 TYR 0.023 0.002 TYR D 335 PHE 0.016 0.002 PHE B 433 TRP 0.008 0.001 TRP B 102 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00431 (14510) covalent geometry : angle 0.59507 (19685) SS BOND : bond 0.00270 ( 10) SS BOND : angle 2.51053 ( 20) hydrogen bonds : bond 0.05070 ( 740) hydrogen bonds : angle 4.88373 ( 2550) link_NAG-ASN : bond 0.00235 ( 10) link_NAG-ASN : angle 2.94335 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.8227 (ppp) cc_final: 0.7844 (ppp) REVERT: A 279 ASN cc_start: 0.8091 (t0) cc_final: 0.7856 (t0) REVERT: B 84 SER cc_start: 0.9362 (m) cc_final: 0.9057 (t) REVERT: C 52 MET cc_start: 0.8098 (ppp) cc_final: 0.7609 (ppp) REVERT: C 186 CYS cc_start: 0.7630 (m) cc_final: 0.7407 (m) REVERT: C 211 GLN cc_start: 0.8013 (mp10) cc_final: 0.7597 (mp10) REVERT: C 224 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8304 (mtpt) REVERT: C 226 GLU cc_start: 0.8152 (mp0) cc_final: 0.7234 (mp0) REVERT: D 52 MET cc_start: 0.8201 (ppp) cc_final: 0.7945 (ppp) REVERT: D 61 ARG cc_start: 0.8345 (mtm-85) cc_final: 0.8135 (mtm-85) REVERT: D 192 SER cc_start: 0.9403 (t) cc_final: 0.9099 (p) REVERT: D 195 TYR cc_start: 0.8993 (m-80) cc_final: 0.8650 (m-80) REVERT: D 224 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8210 (mtpt) REVERT: D 435 ILE cc_start: 0.9199 (mm) cc_final: 0.8930 (mt) REVERT: E 52 MET cc_start: 0.8224 (ppp) cc_final: 0.8004 (ppp) REVERT: E 144 ASP cc_start: 0.8472 (p0) cc_final: 0.8094 (p0) REVERT: E 186 CYS cc_start: 0.7617 (m) cc_final: 0.7361 (m) REVERT: E 279 ASN cc_start: 0.8054 (t0) cc_final: 0.7824 (t0) outliers start: 27 outliers final: 20 residues processed: 276 average time/residue: 0.1217 time to fit residues: 49.4450 Evaluate side-chains 240 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 120 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 101 GLN B 260 GLN C 260 GLN E 101 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.087131 restraints weight = 23594.717| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.10 r_work: 0.2816 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14530 Z= 0.151 Angle : 0.547 6.407 19735 Z= 0.288 Chirality : 0.042 0.169 2250 Planarity : 0.004 0.030 2445 Dihedral : 4.465 23.619 2090 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.37 % Allowed : 12.18 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.39 (0.20), residues: 1710 helix: 2.18 (0.21), residues: 610 sheet: 0.86 (0.28), residues: 350 loop : -0.04 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 61 TYR 0.024 0.001 TYR A 335 PHE 0.015 0.002 PHE B 329 TRP 0.007 0.001 TRP C 204 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00349 (14510) covalent geometry : angle 0.53316 (19685) SS BOND : bond 0.00352 ( 10) SS BOND : angle 2.02591 ( 20) hydrogen bonds : bond 0.04674 ( 740) hydrogen bonds : angle 4.43925 ( 2550) link_NAG-ASN : bond 0.00239 ( 10) link_NAG-ASN : angle 2.71323 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.8208 (ppp) cc_final: 0.7747 (ppp) REVERT: A 279 ASN cc_start: 0.8292 (t0) cc_final: 0.7935 (t0) REVERT: B 61 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.7992 (mtm-85) REVERT: B 192 SER cc_start: 0.9468 (t) cc_final: 0.9104 (p) REVERT: B 245 GLU cc_start: 0.8496 (pt0) cc_final: 0.8276 (pt0) REVERT: B 334 GLU cc_start: 0.9219 (tm-30) cc_final: 0.9004 (tm-30) REVERT: C 52 MET cc_start: 0.8116 (ppp) cc_final: 0.7896 (ppp) REVERT: C 61 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.8024 (mtm-85) REVERT: C 192 SER cc_start: 0.9467 (t) cc_final: 0.9220 (p) REVERT: C 211 GLN cc_start: 0.7947 (mp10) cc_final: 0.7628 (mp10) REVERT: D 52 MET cc_start: 0.8194 (ppp) cc_final: 0.7876 (ppp) REVERT: D 61 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: D 192 SER cc_start: 0.9503 (t) cc_final: 0.9240 (p) REVERT: D 224 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8358 (mtmt) REVERT: D 228 GLU cc_start: 0.8196 (mp0) cc_final: 0.7692 (mt-10) REVERT: D 260 GLN cc_start: 0.8734 (tt0) cc_final: 0.8422 (tp40) REVERT: D 279 ASN cc_start: 0.8309 (t0) cc_final: 0.7927 (t0) REVERT: D 280 MET cc_start: 0.7532 (mpp) cc_final: 0.7150 (mtt) REVERT: D 435 ILE cc_start: 0.9179 (mm) cc_final: 0.8909 (mt) REVERT: E 52 MET cc_start: 0.8244 (ppp) cc_final: 0.7956 (ppp) REVERT: E 61 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.8026 (mtm-85) REVERT: E 144 ASP cc_start: 0.8467 (p0) cc_final: 0.8099 (p0) REVERT: E 186 CYS cc_start: 0.7641 (m) cc_final: 0.7414 (m) REVERT: E 192 SER cc_start: 0.9434 (t) cc_final: 0.9069 (p) REVERT: E 279 ASN cc_start: 0.8243 (t0) cc_final: 0.7788 (t0) outliers start: 37 outliers final: 22 residues processed: 307 average time/residue: 0.1120 time to fit residues: 51.4960 Evaluate side-chains 252 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 128 optimal weight: 0.0070 chunk 151 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 101 GLN B 260 GLN C 260 GLN E 101 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.086502 restraints weight = 23593.155| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.02 r_work: 0.2836 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14530 Z= 0.126 Angle : 0.518 5.940 19735 Z= 0.274 Chirality : 0.041 0.142 2250 Planarity : 0.003 0.031 2445 Dihedral : 4.388 21.972 2090 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.69 % Allowed : 14.04 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.58 (0.20), residues: 1710 helix: 2.46 (0.21), residues: 610 sheet: 1.00 (0.28), residues: 350 loop : -0.09 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 61 TYR 0.022 0.001 TYR A 335 PHE 0.016 0.001 PHE D 47 TRP 0.008 0.001 TRP B 102 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00286 (14510) covalent geometry : angle 0.50724 (19685) SS BOND : bond 0.00204 ( 10) SS BOND : angle 1.39575 ( 20) hydrogen bonds : bond 0.04243 ( 740) hydrogen bonds : angle 4.23233 ( 2550) link_NAG-ASN : bond 0.00297 ( 10) link_NAG-ASN : angle 2.53405 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8209 (ppp) cc_final: 0.7699 (ppp) REVERT: A 61 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7993 (mtm-85) REVERT: A 279 ASN cc_start: 0.8301 (t0) cc_final: 0.7933 (t0) REVERT: B 192 SER cc_start: 0.9486 (t) cc_final: 0.9252 (p) REVERT: B 245 GLU cc_start: 0.8396 (pt0) cc_final: 0.8176 (pt0) REVERT: C 52 MET cc_start: 0.8160 (ppp) cc_final: 0.7912 (ppp) REVERT: C 61 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8011 (mtm-85) REVERT: C 87 GLU cc_start: 0.8827 (pm20) cc_final: 0.8521 (pm20) REVERT: C 211 GLN cc_start: 0.7938 (mp10) cc_final: 0.7600 (mp10) REVERT: C 343 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7536 (ttm170) REVERT: D 52 MET cc_start: 0.8134 (ppp) cc_final: 0.7893 (ppp) REVERT: D 61 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7953 (mtm-85) REVERT: D 192 SER cc_start: 0.9485 (t) cc_final: 0.9275 (p) REVERT: D 224 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8196 (mtmt) REVERT: D 228 GLU cc_start: 0.8157 (mp0) cc_final: 0.7666 (mt-10) REVERT: D 279 ASN cc_start: 0.8432 (t0) cc_final: 0.7988 (t0) REVERT: D 280 MET cc_start: 0.7542 (mpp) cc_final: 0.7200 (mtt) REVERT: D 435 ILE cc_start: 0.9158 (mm) cc_final: 0.8895 (mt) REVERT: E 52 MET cc_start: 0.8281 (ppp) cc_final: 0.7949 (ppp) REVERT: E 192 SER cc_start: 0.9442 (t) cc_final: 0.9118 (p) REVERT: E 279 ASN cc_start: 0.8223 (t0) cc_final: 0.7741 (t0) outliers start: 42 outliers final: 27 residues processed: 289 average time/residue: 0.1142 time to fit residues: 49.2163 Evaluate side-chains 262 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 77 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN D 345 HIS E 101 GLN E 260 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.087224 restraints weight = 23659.497| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.01 r_work: 0.2787 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14530 Z= 0.125 Angle : 0.512 5.386 19735 Z= 0.270 Chirality : 0.041 0.141 2250 Planarity : 0.003 0.032 2445 Dihedral : 4.315 22.444 2090 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.69 % Allowed : 15.06 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.66 (0.20), residues: 1710 helix: 2.55 (0.21), residues: 610 sheet: 1.06 (0.28), residues: 350 loop : -0.06 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.022 0.001 TYR A 335 PHE 0.014 0.001 PHE B 329 TRP 0.008 0.001 TRP D 102 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00286 (14510) covalent geometry : angle 0.50093 (19685) SS BOND : bond 0.00349 ( 10) SS BOND : angle 1.44529 ( 20) hydrogen bonds : bond 0.04186 ( 740) hydrogen bonds : angle 4.15287 ( 2550) link_NAG-ASN : bond 0.00297 ( 10) link_NAG-ASN : angle 2.50092 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8233 (ppp) cc_final: 0.7710 (ppp) REVERT: A 61 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.8068 (mtm-85) REVERT: A 279 ASN cc_start: 0.8351 (t0) cc_final: 0.7768 (t0) REVERT: A 280 MET cc_start: 0.7714 (mpp) cc_final: 0.7481 (mtt) REVERT: B 192 SER cc_start: 0.9426 (t) cc_final: 0.9079 (p) REVERT: C 52 MET cc_start: 0.8148 (ppp) cc_final: 0.7878 (ppp) REVERT: C 61 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.7996 (mtm-85) REVERT: C 87 GLU cc_start: 0.8836 (pm20) cc_final: 0.8541 (pm20) REVERT: C 131 ASP cc_start: 0.9147 (p0) cc_final: 0.8947 (p0) REVERT: C 211 GLN cc_start: 0.7931 (mp10) cc_final: 0.7570 (mp10) REVERT: C 279 ASN cc_start: 0.8328 (t0) cc_final: 0.8034 (t0) REVERT: D 52 MET cc_start: 0.8130 (ppp) cc_final: 0.7853 (ppp) REVERT: D 61 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.7949 (mtm-85) REVERT: D 279 ASN cc_start: 0.8454 (t0) cc_final: 0.8236 (t0) REVERT: D 435 ILE cc_start: 0.9156 (mm) cc_final: 0.8899 (mt) REVERT: E 52 MET cc_start: 0.8268 (ppp) cc_final: 0.7902 (ppp) REVERT: E 192 SER cc_start: 0.9478 (t) cc_final: 0.9136 (p) REVERT: E 279 ASN cc_start: 0.8238 (t0) cc_final: 0.7661 (t0) outliers start: 42 outliers final: 33 residues processed: 288 average time/residue: 0.1140 time to fit residues: 49.2208 Evaluate side-chains 267 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 44 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 0.0170 chunk 2 optimal weight: 0.0370 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN D 101 GLN D 260 GLN D 345 HIS E 101 GLN E 260 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.088155 restraints weight = 23533.985| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.04 r_work: 0.2851 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14530 Z= 0.102 Angle : 0.498 6.872 19735 Z= 0.262 Chirality : 0.041 0.131 2250 Planarity : 0.003 0.032 2445 Dihedral : 4.169 21.798 2090 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.69 % Allowed : 15.71 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.76 (0.20), residues: 1710 helix: 2.65 (0.21), residues: 610 sheet: 1.10 (0.28), residues: 350 loop : -0.02 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 61 TYR 0.021 0.001 TYR A 335 PHE 0.015 0.001 PHE C 433 TRP 0.008 0.001 TRP D 102 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00220 (14510) covalent geometry : angle 0.48803 (19685) SS BOND : bond 0.00334 ( 10) SS BOND : angle 1.31388 ( 20) hydrogen bonds : bond 0.03958 ( 740) hydrogen bonds : angle 4.06391 ( 2550) link_NAG-ASN : bond 0.00334 ( 10) link_NAG-ASN : angle 2.38413 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8241 (ppp) cc_final: 0.7742 (ppp) REVERT: A 61 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8111 (mtm-85) REVERT: A 245 GLU cc_start: 0.8435 (pt0) cc_final: 0.8151 (pt0) REVERT: A 279 ASN cc_start: 0.8324 (t0) cc_final: 0.7744 (t0) REVERT: A 280 MET cc_start: 0.7679 (mpp) cc_final: 0.7392 (mtt) REVERT: B 192 SER cc_start: 0.9407 (t) cc_final: 0.9073 (p) REVERT: C 52 MET cc_start: 0.8163 (ppp) cc_final: 0.7889 (ppp) REVERT: C 61 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8017 (mtm-85) REVERT: C 87 GLU cc_start: 0.8838 (pm20) cc_final: 0.8542 (pm20) REVERT: C 131 ASP cc_start: 0.9150 (p0) cc_final: 0.8931 (p0) REVERT: C 245 GLU cc_start: 0.8349 (pt0) cc_final: 0.8102 (pt0) REVERT: C 279 ASN cc_start: 0.8337 (t0) cc_final: 0.8014 (t0) REVERT: D 52 MET cc_start: 0.8114 (ppp) cc_final: 0.7816 (ppp) REVERT: D 61 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7958 (mtm-85) REVERT: D 279 ASN cc_start: 0.8462 (t0) cc_final: 0.8260 (t0) REVERT: D 435 ILE cc_start: 0.9138 (mm) cc_final: 0.8887 (mt) REVERT: E 52 MET cc_start: 0.8260 (ppp) cc_final: 0.7897 (ppp) REVERT: E 192 SER cc_start: 0.9488 (t) cc_final: 0.9186 (p) REVERT: E 245 GLU cc_start: 0.8275 (pt0) cc_final: 0.8073 (pt0) REVERT: E 279 ASN cc_start: 0.8187 (t0) cc_final: 0.7720 (t0) outliers start: 42 outliers final: 36 residues processed: 287 average time/residue: 0.1148 time to fit residues: 49.4434 Evaluate side-chains 281 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 138 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 101 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN D 260 GLN D 345 HIS E 76 ASN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.084505 restraints weight = 23480.801| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.09 r_work: 0.2777 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14530 Z= 0.158 Angle : 0.532 6.558 19735 Z= 0.280 Chirality : 0.042 0.152 2250 Planarity : 0.003 0.036 2445 Dihedral : 4.360 22.923 2090 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.56 % Allowed : 16.03 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.71 (0.20), residues: 1710 helix: 2.63 (0.21), residues: 610 sheet: 1.05 (0.29), residues: 350 loop : -0.06 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 343 TYR 0.025 0.001 TYR A 335 PHE 0.014 0.002 PHE B 329 TRP 0.009 0.001 TRP B 102 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00367 (14510) covalent geometry : angle 0.51963 (19685) SS BOND : bond 0.00196 ( 10) SS BOND : angle 1.62657 ( 20) hydrogen bonds : bond 0.04353 ( 740) hydrogen bonds : angle 4.15866 ( 2550) link_NAG-ASN : bond 0.00225 ( 10) link_NAG-ASN : angle 2.65088 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8228 (ppp) cc_final: 0.7702 (ppp) REVERT: A 61 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.8047 (mtm-85) REVERT: A 279 ASN cc_start: 0.8350 (t0) cc_final: 0.7987 (t0) REVERT: C 52 MET cc_start: 0.8178 (ppp) cc_final: 0.7872 (ppp) REVERT: C 61 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.8066 (mtm-85) REVERT: C 87 GLU cc_start: 0.8904 (pm20) cc_final: 0.8600 (pm20) REVERT: C 131 ASP cc_start: 0.9163 (p0) cc_final: 0.8945 (p0) REVERT: C 279 ASN cc_start: 0.8346 (t0) cc_final: 0.7821 (t0) REVERT: D 52 MET cc_start: 0.8155 (ppp) cc_final: 0.7821 (ppp) REVERT: D 61 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.7962 (mtm-85) REVERT: D 279 ASN cc_start: 0.8500 (t0) cc_final: 0.8274 (t0) REVERT: D 343 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7770 (ttp80) REVERT: D 435 ILE cc_start: 0.9098 (mm) cc_final: 0.8863 (mt) REVERT: E 52 MET cc_start: 0.8260 (ppp) cc_final: 0.7839 (ppp) REVERT: E 144 ASP cc_start: 0.8530 (p0) cc_final: 0.8186 (p0) REVERT: E 192 SER cc_start: 0.9500 (t) cc_final: 0.9188 (p) REVERT: E 279 ASN cc_start: 0.8220 (t0) cc_final: 0.7721 (t0) outliers start: 40 outliers final: 36 residues processed: 271 average time/residue: 0.1160 time to fit residues: 47.1507 Evaluate side-chains 263 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN B 260 GLN C 260 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.088933 restraints weight = 23388.996| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.03 r_work: 0.2868 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14530 Z= 0.098 Angle : 0.493 7.056 19735 Z= 0.258 Chirality : 0.041 0.132 2250 Planarity : 0.003 0.033 2445 Dihedral : 4.108 21.026 2090 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.31 % Allowed : 16.41 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.82 (0.20), residues: 1710 helix: 2.73 (0.21), residues: 610 sheet: 1.09 (0.29), residues: 350 loop : -0.00 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 343 TYR 0.019 0.001 TYR A 335 PHE 0.014 0.001 PHE C 433 TRP 0.009 0.001 TRP C 102 HIS 0.002 0.000 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00208 (14510) covalent geometry : angle 0.48323 (19685) SS BOND : bond 0.00230 ( 10) SS BOND : angle 1.21556 ( 20) hydrogen bonds : bond 0.03868 ( 740) hydrogen bonds : angle 3.99727 ( 2550) link_NAG-ASN : bond 0.00377 ( 10) link_NAG-ASN : angle 2.40261 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8220 (ppp) cc_final: 0.7733 (ppp) REVERT: A 61 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.8167 (mtm-85) REVERT: A 245 GLU cc_start: 0.8404 (pt0) cc_final: 0.8163 (pt0) REVERT: A 279 ASN cc_start: 0.8286 (t0) cc_final: 0.7799 (t0) REVERT: A 280 MET cc_start: 0.7698 (mpp) cc_final: 0.7463 (mtt) REVERT: A 343 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7627 (ttm170) REVERT: B 280 MET cc_start: 0.7292 (mpp) cc_final: 0.7055 (mtt) REVERT: C 52 MET cc_start: 0.8174 (ppp) cc_final: 0.7884 (ppp) REVERT: C 61 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8192 (mtm-85) REVERT: C 87 GLU cc_start: 0.8831 (pm20) cc_final: 0.8528 (pm20) REVERT: C 131 ASP cc_start: 0.9146 (p0) cc_final: 0.8931 (p0) REVERT: C 279 ASN cc_start: 0.8346 (t0) cc_final: 0.7874 (t0) REVERT: C 297 MET cc_start: 0.9483 (mmm) cc_final: 0.9178 (mmm) REVERT: C 343 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7359 (ttp-170) REVERT: D 52 MET cc_start: 0.8131 (ppp) cc_final: 0.7805 (ppp) REVERT: D 61 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.7942 (mtm-85) REVERT: D 279 ASN cc_start: 0.8509 (t0) cc_final: 0.8282 (t0) REVERT: D 343 ARG cc_start: 0.7983 (ttm170) cc_final: 0.7671 (ttp80) REVERT: D 435 ILE cc_start: 0.9119 (mm) cc_final: 0.8874 (mt) REVERT: E 52 MET cc_start: 0.8241 (ppp) cc_final: 0.7853 (ppp) REVERT: E 61 ARG cc_start: 0.8491 (mtm-85) cc_final: 0.8106 (mtm-85) outliers start: 36 outliers final: 34 residues processed: 281 average time/residue: 0.1142 time to fit residues: 48.2460 Evaluate side-chains 268 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 25 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 101 GLN B 260 GLN C 260 GLN C 345 HIS E 260 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.085375 restraints weight = 23436.212| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.09 r_work: 0.2730 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14530 Z= 0.147 Angle : 0.530 7.151 19735 Z= 0.277 Chirality : 0.042 0.141 2250 Planarity : 0.003 0.031 2445 Dihedral : 4.257 21.535 2090 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.82 % Allowed : 16.41 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.77 (0.20), residues: 1710 helix: 2.71 (0.21), residues: 610 sheet: 1.07 (0.29), residues: 350 loop : -0.04 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 343 TYR 0.024 0.001 TYR C 335 PHE 0.017 0.001 PHE B 436 TRP 0.009 0.001 TRP D 102 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00343 (14510) covalent geometry : angle 0.51843 (19685) SS BOND : bond 0.00255 ( 10) SS BOND : angle 1.51736 ( 20) hydrogen bonds : bond 0.04189 ( 740) hydrogen bonds : angle 4.08506 ( 2550) link_NAG-ASN : bond 0.00238 ( 10) link_NAG-ASN : angle 2.59132 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8248 (ppp) cc_final: 0.7717 (ppp) REVERT: A 61 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8073 (mtm-85) REVERT: A 279 ASN cc_start: 0.8346 (t0) cc_final: 0.7933 (t0) REVERT: A 280 MET cc_start: 0.7808 (mpp) cc_final: 0.7603 (mtt) REVERT: B 280 MET cc_start: 0.7286 (mpp) cc_final: 0.7070 (mtt) REVERT: C 52 MET cc_start: 0.8180 (ppp) cc_final: 0.7846 (ppp) REVERT: C 61 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8085 (mtm-85) REVERT: C 87 GLU cc_start: 0.8873 (pm20) cc_final: 0.8567 (pm20) REVERT: C 131 ASP cc_start: 0.9159 (p0) cc_final: 0.8940 (p0) REVERT: C 279 ASN cc_start: 0.8369 (t0) cc_final: 0.7903 (t0) REVERT: C 343 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7363 (ttp-170) REVERT: D 52 MET cc_start: 0.8149 (ppp) cc_final: 0.7791 (ppp) REVERT: D 61 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.7964 (mtm-85) REVERT: D 279 ASN cc_start: 0.8549 (t0) cc_final: 0.8296 (t0) REVERT: D 343 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7753 (ttp80) REVERT: D 345 HIS cc_start: 0.5764 (t-170) cc_final: 0.5259 (t70) REVERT: D 435 ILE cc_start: 0.9130 (mm) cc_final: 0.8894 (mt) REVERT: E 52 MET cc_start: 0.8216 (ppp) cc_final: 0.7755 (ppp) REVERT: E 144 ASP cc_start: 0.8472 (p0) cc_final: 0.8145 (p0) outliers start: 44 outliers final: 37 residues processed: 266 average time/residue: 0.1181 time to fit residues: 47.0151 Evaluate side-chains 272 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 70 optimal weight: 0.0050 chunk 22 optimal weight: 4.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN C 260 GLN D 260 GLN E 260 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.088099 restraints weight = 23493.831| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.04 r_work: 0.2864 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14530 Z= 0.107 Angle : 0.511 7.269 19735 Z= 0.267 Chirality : 0.041 0.131 2250 Planarity : 0.003 0.032 2445 Dihedral : 4.179 20.879 2090 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.63 % Allowed : 16.41 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.82 (0.20), residues: 1710 helix: 2.77 (0.21), residues: 610 sheet: 1.08 (0.29), residues: 350 loop : -0.03 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.020 0.001 TYR A 335 PHE 0.018 0.001 PHE B 436 TRP 0.009 0.001 TRP C 102 HIS 0.005 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00235 (14510) covalent geometry : angle 0.50030 (19685) SS BOND : bond 0.00265 ( 10) SS BOND : angle 1.30437 ( 20) hydrogen bonds : bond 0.04004 ( 740) hydrogen bonds : angle 4.01128 ( 2550) link_NAG-ASN : bond 0.00342 ( 10) link_NAG-ASN : angle 2.48815 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8244 (ppp) cc_final: 0.7734 (ppp) REVERT: A 61 ARG cc_start: 0.8453 (mtm-85) cc_final: 0.8065 (mtm-85) REVERT: A 279 ASN cc_start: 0.8296 (t0) cc_final: 0.7882 (t0) REVERT: A 343 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7527 (ttm170) REVERT: C 52 MET cc_start: 0.8134 (ppp) cc_final: 0.7806 (ppp) REVERT: C 61 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.7682 (mtm-85) REVERT: C 87 GLU cc_start: 0.8845 (pm20) cc_final: 0.8547 (pm20) REVERT: C 131 ASP cc_start: 0.9134 (p0) cc_final: 0.8912 (p0) REVERT: C 260 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8546 (tp40) REVERT: C 279 ASN cc_start: 0.8401 (t0) cc_final: 0.7969 (t0) REVERT: C 297 MET cc_start: 0.9472 (mmm) cc_final: 0.9177 (mmm) REVERT: C 343 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7563 (ttp-170) REVERT: D 52 MET cc_start: 0.8109 (ppp) cc_final: 0.7746 (ppp) REVERT: D 61 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.7915 (mtm-85) REVERT: D 279 ASN cc_start: 0.8538 (t0) cc_final: 0.8288 (t0) REVERT: D 343 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7673 (ttp80) REVERT: D 435 ILE cc_start: 0.9129 (mm) cc_final: 0.8882 (mt) REVERT: E 52 MET cc_start: 0.8240 (ppp) cc_final: 0.7822 (ppp) REVERT: E 61 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8087 (mtm-85) outliers start: 41 outliers final: 35 residues processed: 274 average time/residue: 0.1110 time to fit residues: 45.6434 Evaluate side-chains 274 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 145 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 155 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN C 260 GLN D 260 GLN D 345 HIS E 260 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.088679 restraints weight = 23381.694| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.03 r_work: 0.2862 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14530 Z= 0.101 Angle : 0.512 6.938 19735 Z= 0.266 Chirality : 0.041 0.132 2250 Planarity : 0.003 0.032 2445 Dihedral : 4.128 20.457 2090 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.50 % Allowed : 16.54 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.82 (0.20), residues: 1710 helix: 2.79 (0.21), residues: 610 sheet: 1.07 (0.29), residues: 350 loop : -0.05 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 61 TYR 0.020 0.001 TYR A 335 PHE 0.017 0.001 PHE B 436 TRP 0.009 0.001 TRP D 102 HIS 0.004 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00216 (14510) covalent geometry : angle 0.50233 (19685) SS BOND : bond 0.00245 ( 10) SS BOND : angle 1.25882 ( 20) hydrogen bonds : bond 0.03894 ( 740) hydrogen bonds : angle 3.97120 ( 2550) link_NAG-ASN : bond 0.00347 ( 10) link_NAG-ASN : angle 2.41299 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2793.28 seconds wall clock time: 48 minutes 54.80 seconds (2934.80 seconds total)