Starting phenix.real_space_refine on Sat Aug 23 12:49:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l44_62805/08_2025/9l44_62805.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l44_62805/08_2025/9l44_62805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l44_62805/08_2025/9l44_62805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l44_62805/08_2025/9l44_62805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l44_62805/08_2025/9l44_62805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l44_62805/08_2025/9l44_62805.map" } resolution = 3.02 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= -0.001 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 96 5.16 5 C 7596 2.51 5 N 2048 2.21 5 O 2376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12124 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2987 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "B" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2987 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "C" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2987 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "D" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2987 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.90, per 1000 atoms: 0.24 Number of scatterers: 12124 At special positions: 0 Unit cell: (121.26, 121.26, 75.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 96 16.00 O 2376 8.00 N 2048 7.00 C 7596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.09 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.05 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.07 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.04 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.04 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.02 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.02 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.04 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 88 " " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 235 " " NAG B 501 " - " ASN B 88 " " NAG B 502 " - " ASN B 146 " " NAG B 503 " - " ASN B 235 " " NAG C 501 " - " ASN C 88 " " NAG C 502 " - " ASN C 146 " " NAG C 503 " - " ASN C 235 " " NAG D 501 " - " ASN D 88 " " NAG D 502 " - " ASN D 146 " " NAG D 503 " - " ASN D 235 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 439.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 28 sheets defined 5.9% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.524A pdb=" N ILE A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.522A pdb=" N ILE B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.524A pdb=" N ILE C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.573A pdb=" N ASN C 146 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.523A pdb=" N ILE D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.502A pdb=" N ASN D 146 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'D' and resid 465 through 469 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.684A pdb=" N GLY A 96 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER A 444 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS A 102 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER A 442 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.907A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER A 160 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N PHE A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 185 removed outlier: 3.662A pdb=" N ASP A 214 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR A 208 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE A 212 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 6.730A pdb=" N TYR A 253 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A 268 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 255 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A 266 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS A 257 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 284 removed outlier: 5.633A pdb=" N GLU A 278 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG A 293 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 315 " --> pdb=" O TRP A 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 353 removed outlier: 6.660A pdb=" N SER A 369 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU A 395 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE A 371 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 389 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.684A pdb=" N GLY B 96 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER B 444 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS B 102 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER B 442 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 124 removed outlier: 5.024A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER B 160 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N PHE B 174 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 185 removed outlier: 3.662A pdb=" N ASP B 214 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR B 208 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE B 212 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 225 removed outlier: 6.729A pdb=" N TYR B 253 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU B 268 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 255 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 266 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS B 257 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 277 through 284 removed outlier: 5.633A pdb=" N GLU B 278 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG B 293 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 315 " --> pdb=" O TRP B 303 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 353 removed outlier: 6.660A pdb=" N SER B 369 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLU B 395 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE B 371 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 389 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.684A pdb=" N GLY C 96 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER C 444 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS C 102 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER C 442 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 124 removed outlier: 5.037A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER C 160 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N PHE C 174 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 181 through 185 removed outlier: 3.661A pdb=" N ASP C 214 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR C 208 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AC1, first strand: chain 'C' and resid 224 through 225 removed outlier: 6.730A pdb=" N TYR C 253 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 268 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE C 255 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER C 266 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 277 through 284 removed outlier: 5.633A pdb=" N GLU C 278 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG C 293 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 315 " --> pdb=" O TRP C 303 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 350 through 353 removed outlier: 6.659A pdb=" N SER C 369 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLU C 395 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE C 371 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 389 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.684A pdb=" N GLY D 96 " --> pdb=" O VAL D 448 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER D 444 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.968A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER D 160 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N PHE D 174 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 181 through 185 removed outlier: 3.661A pdb=" N ASP D 214 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR D 208 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AC8, first strand: chain 'D' and resid 224 through 225 removed outlier: 6.730A pdb=" N TYR D 253 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU D 268 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE D 255 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER D 266 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS D 257 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 277 through 284 removed outlier: 5.633A pdb=" N GLU D 278 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG D 293 " --> pdb=" O GLU D 278 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 315 " --> pdb=" O TRP D 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 350 through 353 removed outlier: 6.658A pdb=" N SER D 369 " --> pdb=" O GLU D 395 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU D 395 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE D 371 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 389 " --> pdb=" O TRP D 375 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1032 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: 1.87 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2443 1.32 - 1.47: 4751 1.47 - 1.61: 5134 1.61 - 1.75: 0 1.75 - 1.89: 124 Bond restraints: 12452 Sorted by residual: bond pdb=" N PRO C 337 " pdb=" CD PRO C 337 " ideal model delta sigma weight residual 1.473 1.328 0.145 1.40e-02 5.10e+03 1.07e+02 bond pdb=" CA SER D 336 " pdb=" CB SER D 336 " ideal model delta sigma weight residual 1.536 1.479 0.057 1.25e-02 6.40e+03 2.05e+01 bond pdb=" CA SER A 385 " pdb=" CB SER A 385 " ideal model delta sigma weight residual 1.527 1.468 0.059 1.36e-02 5.41e+03 1.88e+01 bond pdb=" CA SER B 385 " pdb=" CB SER B 385 " ideal model delta sigma weight residual 1.527 1.471 0.056 1.39e-02 5.18e+03 1.61e+01 bond pdb=" N SER B 336 " pdb=" CA SER B 336 " ideal model delta sigma weight residual 1.455 1.482 -0.027 7.00e-03 2.04e+04 1.48e+01 ... (remaining 12447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 16212 2.62 - 5.24: 611 5.24 - 7.86: 70 7.86 - 10.47: 24 10.47 - 13.09: 7 Bond angle restraints: 16924 Sorted by residual: angle pdb=" N THR D 148 " pdb=" CA THR D 148 " pdb=" C THR D 148 " ideal model delta sigma weight residual 113.02 103.78 9.24 1.20e+00 6.94e-01 5.92e+01 angle pdb=" C THR B 148 " pdb=" CA THR B 148 " pdb=" CB THR B 148 " ideal model delta sigma weight residual 110.17 121.94 -11.77 1.69e+00 3.50e-01 4.85e+01 angle pdb=" C THR A 148 " pdb=" CA THR A 148 " pdb=" CB THR A 148 " ideal model delta sigma weight residual 109.55 119.68 -10.13 1.68e+00 3.54e-01 3.63e+01 angle pdb=" C ASN A 221 " pdb=" CA ASN A 221 " pdb=" CB ASN A 221 " ideal model delta sigma weight residual 111.51 120.97 -9.46 1.58e+00 4.01e-01 3.58e+01 angle pdb=" C THR C 148 " pdb=" CA THR C 148 " pdb=" CB THR C 148 " ideal model delta sigma weight residual 109.72 121.00 -11.28 1.92e+00 2.71e-01 3.45e+01 ... (remaining 16919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 6870 16.33 - 32.66: 502 32.66 - 48.99: 90 48.99 - 65.32: 16 65.32 - 81.65: 6 Dihedral angle restraints: 7484 sinusoidal: 3112 harmonic: 4372 Sorted by residual: dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 14.63 78.37 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS B 92 " pdb=" SG CYS B 92 " pdb=" SG CYS B 417 " pdb=" CB CYS B 417 " ideal model delta sinusoidal sigma weight residual 93.00 14.93 78.07 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" C ASN A 221 " pdb=" N ASN A 221 " pdb=" CA ASN A 221 " pdb=" CB ASN A 221 " ideal model delta harmonic sigma weight residual -122.60 -140.65 18.05 0 2.50e+00 1.60e-01 5.21e+01 ... (remaining 7481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 1700 0.135 - 0.269: 82 0.269 - 0.404: 9 0.404 - 0.538: 4 0.538 - 0.673: 1 Chirality restraints: 1796 Sorted by residual: chirality pdb=" CA ASN A 221 " pdb=" N ASN A 221 " pdb=" C ASN A 221 " pdb=" CB ASN A 221 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" CA ASN B 235 " pdb=" N ASN B 235 " pdb=" C ASN B 235 " pdb=" CB ASN B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 1793 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 501 " -0.301 2.00e-02 2.50e+03 2.65e-01 8.81e+02 pdb=" C7 NAG A 501 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A 501 " -0.088 2.00e-02 2.50e+03 pdb=" N2 NAG A 501 " 0.477 2.00e-02 2.50e+03 pdb=" O7 NAG A 501 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 503 " -0.286 2.00e-02 2.50e+03 2.44e-01 7.44e+02 pdb=" C7 NAG A 503 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A 503 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG A 503 " 0.424 2.00e-02 2.50e+03 pdb=" O7 NAG A 503 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " 0.179 2.00e-02 2.50e+03 1.50e-01 2.80e+02 pdb=" C7 NAG D 501 " -0.047 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " 0.130 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " -0.246 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " -0.016 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 44 2.40 - 3.03: 6902 3.03 - 3.65: 15751 3.65 - 4.28: 26032 4.28 - 4.90: 48061 Nonbonded interactions: 96790 Sorted by model distance: nonbonded pdb=" O GLY C 298 " pdb="CA CA C 504 " model vdw 1.777 2.510 nonbonded pdb=" O TYR B 344 " pdb="CA CA B 504 " model vdw 1.872 2.510 nonbonded pdb=" O GLY B 298 " pdb="CA CA B 504 " model vdw 1.920 2.510 nonbonded pdb=" OD1 ASN B 378 " pdb="CA CA B 505 " model vdw 1.923 2.510 nonbonded pdb=" O GLY A 298 " pdb="CA CA A 504 " model vdw 1.937 2.510 ... (remaining 96785 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.290 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.011 0.145 12496 Z= 0.544 Angle : 1.197 13.093 17024 Z= 0.718 Chirality : 0.075 0.673 1796 Planarity : 0.011 0.265 2188 Dihedral : 11.449 81.655 4612 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.15 % Allowed : 1.51 % Favored : 98.34 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -1.65 (0.20), residues: 1540 helix: -3.37 (0.36), residues: 24 sheet: 0.01 (0.23), residues: 504 loop : -1.73 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 430 TYR 0.025 0.003 TYR B 344 PHE 0.029 0.003 PHE B 387 TRP 0.029 0.003 TRP D 455 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.01139 (12452) covalent geometry : angle 1.16400 (16924) SS BOND : bond 0.01386 ( 32) SS BOND : angle 3.40068 ( 64) hydrogen bonds : bond 0.26438 ( 386) hydrogen bonds : angle 8.91286 ( 1032) link_NAG-ASN : bond 0.01061 ( 12) link_NAG-ASN : angle 4.51905 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 157 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 438 THR cc_start: 0.9016 (t) cc_final: 0.8786 (m) outliers start: 2 outliers final: 1 residues processed: 158 average time/residue: 0.1018 time to fit residues: 23.5665 Evaluate side-chains 74 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.088502 restraints weight = 16303.339| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.32 r_work: 0.2809 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12496 Z= 0.112 Angle : 0.621 9.741 17024 Z= 0.328 Chirality : 0.050 0.221 1796 Planarity : 0.004 0.035 2188 Dihedral : 6.349 59.768 1919 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.38 % Allowed : 4.37 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: -0.97 (0.20), residues: 1540 helix: -2.49 (0.55), residues: 24 sheet: 0.54 (0.22), residues: 548 loop : -1.38 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 220 TYR 0.014 0.001 TYR D 344 PHE 0.013 0.001 PHE D 121 TRP 0.013 0.001 TRP B 179 HIS 0.002 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00232 (12452) covalent geometry : angle 0.60652 (16924) SS BOND : bond 0.00307 ( 32) SS BOND : angle 1.27933 ( 64) hydrogen bonds : bond 0.04118 ( 386) hydrogen bonds : angle 6.35252 ( 1032) link_NAG-ASN : bond 0.00604 ( 12) link_NAG-ASN : angle 2.60587 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: C 136 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8736 (mm-40) REVERT: C 220 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7087 (mtp180) outliers start: 5 outliers final: 1 residues processed: 91 average time/residue: 0.0836 time to fit residues: 12.1887 Evaluate side-chains 72 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 14 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 137 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.092014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.080638 restraints weight = 16598.615| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.39 r_work: 0.2681 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12496 Z= 0.179 Angle : 0.669 10.054 17024 Z= 0.347 Chirality : 0.051 0.214 1796 Planarity : 0.005 0.036 2188 Dihedral : 5.973 58.014 1916 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.83 % Allowed : 5.87 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -0.67 (0.21), residues: 1540 helix: -2.84 (0.47), residues: 24 sheet: 1.00 (0.23), residues: 520 loop : -1.27 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 220 TYR 0.016 0.001 TYR D 344 PHE 0.012 0.002 PHE D 422 TRP 0.015 0.002 TRP D 179 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00440 (12452) covalent geometry : angle 0.64850 (16924) SS BOND : bond 0.00425 ( 32) SS BOND : angle 2.16218 ( 64) hydrogen bonds : bond 0.04568 ( 386) hydrogen bonds : angle 6.17610 ( 1032) link_NAG-ASN : bond 0.00335 ( 12) link_NAG-ASN : angle 2.31460 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.7310 (mtp180) outliers start: 11 outliers final: 10 residues processed: 83 average time/residue: 0.0841 time to fit residues: 11.0076 Evaluate side-chains 79 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 273 ASN Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 392 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 138 optimal weight: 0.1980 chunk 135 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.092274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.081161 restraints weight = 16685.941| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.33 r_work: 0.2687 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12496 Z= 0.130 Angle : 0.587 9.899 17024 Z= 0.307 Chirality : 0.049 0.207 1796 Planarity : 0.004 0.037 2188 Dihedral : 5.673 56.701 1916 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.05 % Allowed : 6.25 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.54 (0.21), residues: 1540 helix: -2.46 (0.59), residues: 24 sheet: 1.15 (0.23), residues: 500 loop : -1.18 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 220 TYR 0.013 0.001 TYR D 344 PHE 0.012 0.002 PHE C 422 TRP 0.015 0.001 TRP D 179 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00315 (12452) covalent geometry : angle 0.57090 (16924) SS BOND : bond 0.00198 ( 32) SS BOND : angle 1.76280 ( 64) hydrogen bonds : bond 0.03762 ( 386) hydrogen bonds : angle 5.91889 ( 1032) link_NAG-ASN : bond 0.00261 ( 12) link_NAG-ASN : angle 2.02726 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 ARG cc_start: 0.8367 (mtt-85) cc_final: 0.7474 (mtp85) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.0740 time to fit residues: 9.6822 Evaluate side-chains 76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 392 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 147 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.092147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.081009 restraints weight = 16541.685| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.34 r_work: 0.2710 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12496 Z= 0.152 Angle : 0.616 9.901 17024 Z= 0.321 Chirality : 0.049 0.207 1796 Planarity : 0.004 0.039 2188 Dihedral : 5.733 57.025 1916 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.05 % Allowed : 7.45 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -0.46 (0.21), residues: 1540 helix: -2.53 (0.57), residues: 24 sheet: 1.21 (0.23), residues: 500 loop : -1.12 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.011 0.001 TYR D 344 PHE 0.014 0.002 PHE A 121 TRP 0.016 0.001 TRP D 179 HIS 0.005 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00379 (12452) covalent geometry : angle 0.59481 (16924) SS BOND : bond 0.00388 ( 32) SS BOND : angle 2.21380 ( 64) hydrogen bonds : bond 0.03953 ( 386) hydrogen bonds : angle 5.92625 ( 1032) link_NAG-ASN : bond 0.00281 ( 12) link_NAG-ASN : angle 2.06023 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 ARG cc_start: 0.8357 (mtt-85) cc_final: 0.7451 (mtp85) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.1027 time to fit residues: 12.6923 Evaluate side-chains 76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 416 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 0.2980 chunk 69 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.092284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.080838 restraints weight = 16412.799| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 1.38 r_work: 0.2697 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12496 Z= 0.156 Angle : 0.618 9.865 17024 Z= 0.322 Chirality : 0.050 0.208 1796 Planarity : 0.005 0.040 2188 Dihedral : 5.743 57.273 1916 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.43 % Allowed : 8.13 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -0.46 (0.21), residues: 1540 helix: -2.60 (0.54), residues: 24 sheet: 1.24 (0.23), residues: 500 loop : -1.14 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 220 TYR 0.010 0.001 TYR D 344 PHE 0.015 0.002 PHE C 121 TRP 0.017 0.001 TRP B 179 HIS 0.005 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00389 (12452) covalent geometry : angle 0.59906 (16924) SS BOND : bond 0.00263 ( 32) SS BOND : angle 2.07148 ( 64) hydrogen bonds : bond 0.04038 ( 386) hydrogen bonds : angle 5.93513 ( 1032) link_NAG-ASN : bond 0.00272 ( 12) link_NAG-ASN : angle 2.07683 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8539 (mt) REVERT: B 426 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8509 (mt) REVERT: C 220 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.7388 (mtp85) REVERT: C 426 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8579 (mt) REVERT: D 426 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8531 (mt) outliers start: 19 outliers final: 10 residues processed: 80 average time/residue: 0.0838 time to fit residues: 11.1881 Evaluate side-chains 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 426 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.090901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.079459 restraints weight = 16392.086| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 1.37 r_work: 0.2631 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12496 Z= 0.200 Angle : 0.669 9.898 17024 Z= 0.348 Chirality : 0.051 0.206 1796 Planarity : 0.005 0.040 2188 Dihedral : 5.907 57.855 1916 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.81 % Allowed : 8.73 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -0.51 (0.21), residues: 1540 helix: -2.92 (0.44), residues: 24 sheet: 1.15 (0.23), residues: 520 loop : -1.18 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 220 TYR 0.010 0.001 TYR D 344 PHE 0.015 0.002 PHE B 121 TRP 0.019 0.002 TRP B 179 HIS 0.006 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00504 (12452) covalent geometry : angle 0.65071 (16924) SS BOND : bond 0.00296 ( 32) SS BOND : angle 2.04656 ( 64) hydrogen bonds : bond 0.04478 ( 386) hydrogen bonds : angle 6.05672 ( 1032) link_NAG-ASN : bond 0.00305 ( 12) link_NAG-ASN : angle 2.20757 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8620 (mt) REVERT: B 426 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8591 (mt) REVERT: C 220 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.7348 (mtp85) REVERT: C 426 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8606 (mt) REVERT: D 426 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8612 (mt) outliers start: 24 outliers final: 12 residues processed: 85 average time/residue: 0.0936 time to fit residues: 12.9081 Evaluate side-chains 81 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 426 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.090906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.079424 restraints weight = 16421.509| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 1.39 r_work: 0.2666 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 12496 Z= 0.200 Angle : 0.687 11.305 17024 Z= 0.356 Chirality : 0.051 0.208 1796 Planarity : 0.005 0.042 2188 Dihedral : 6.012 57.834 1916 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.81 % Allowed : 8.73 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -0.60 (0.21), residues: 1540 helix: -3.33 (0.34), residues: 24 sheet: 1.08 (0.22), residues: 520 loop : -1.22 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 220 TYR 0.010 0.001 TYR D 344 PHE 0.014 0.002 PHE C 422 TRP 0.020 0.002 TRP C 179 HIS 0.006 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00510 (12452) covalent geometry : angle 0.65537 (16924) SS BOND : bond 0.00630 ( 32) SS BOND : angle 3.04325 ( 64) hydrogen bonds : bond 0.04390 ( 386) hydrogen bonds : angle 6.03666 ( 1032) link_NAG-ASN : bond 0.00293 ( 12) link_NAG-ASN : angle 2.19516 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8591 (mt) REVERT: B 426 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8586 (mt) REVERT: C 220 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.7355 (mtp85) REVERT: C 426 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8630 (mt) REVERT: D 426 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8597 (mt) outliers start: 24 outliers final: 17 residues processed: 85 average time/residue: 0.0889 time to fit residues: 12.4451 Evaluate side-chains 85 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 450 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 124 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 79 optimal weight: 0.0770 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.092498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.081333 restraints weight = 16287.616| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 1.33 r_work: 0.2669 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12496 Z= 0.146 Angle : 0.624 10.700 17024 Z= 0.324 Chirality : 0.049 0.209 1796 Planarity : 0.005 0.042 2188 Dihedral : 5.801 56.971 1916 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.66 % Allowed : 9.04 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -0.55 (0.21), residues: 1540 helix: -2.73 (0.48), residues: 24 sheet: 1.14 (0.23), residues: 500 loop : -1.17 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 220 TYR 0.010 0.001 TYR D 344 PHE 0.013 0.002 PHE A 422 TRP 0.019 0.001 TRP D 179 HIS 0.005 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00367 (12452) covalent geometry : angle 0.59319 (16924) SS BOND : bond 0.00616 ( 32) SS BOND : angle 2.85604 ( 64) hydrogen bonds : bond 0.03795 ( 386) hydrogen bonds : angle 5.87297 ( 1032) link_NAG-ASN : bond 0.00240 ( 12) link_NAG-ASN : angle 2.00441 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8514 (mt) REVERT: B 426 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8505 (mt) REVERT: C 220 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7355 (mtp85) REVERT: C 426 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8552 (mt) REVERT: D 426 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8524 (mt) outliers start: 22 outliers final: 17 residues processed: 81 average time/residue: 0.0857 time to fit residues: 11.6043 Evaluate side-chains 82 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 450 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 80 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.0170 chunk 17 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.100250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.087479 restraints weight = 16089.843| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.59 r_work: 0.2808 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 12496 Z= 0.100 Angle : 0.554 10.267 17024 Z= 0.289 Chirality : 0.047 0.214 1796 Planarity : 0.004 0.041 2188 Dihedral : 5.450 55.559 1916 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.28 % Allowed : 9.71 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -0.41 (0.21), residues: 1540 helix: -2.06 (0.68), residues: 24 sheet: 0.94 (0.22), residues: 552 loop : -1.01 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 220 TYR 0.007 0.001 TYR C 282 PHE 0.011 0.001 PHE C 121 TRP 0.014 0.001 TRP C 179 HIS 0.002 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00240 (12452) covalent geometry : angle 0.52530 (16924) SS BOND : bond 0.00562 ( 32) SS BOND : angle 2.69178 ( 64) hydrogen bonds : bond 0.03129 ( 386) hydrogen bonds : angle 5.60644 ( 1032) link_NAG-ASN : bond 0.00214 ( 12) link_NAG-ASN : angle 1.63849 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8424 (mt) REVERT: B 426 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8386 (mt) REVERT: C 220 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.7216 (mtp85) REVERT: D 426 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8407 (mt) outliers start: 17 outliers final: 14 residues processed: 75 average time/residue: 0.0900 time to fit residues: 10.5486 Evaluate side-chains 74 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 426 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 92 optimal weight: 3.9990 chunk 147 optimal weight: 0.0010 chunk 82 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.098112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.085092 restraints weight = 16181.150| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.62 r_work: 0.2807 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 12496 Z= 0.101 Angle : 0.550 9.672 17024 Z= 0.287 Chirality : 0.047 0.218 1796 Planarity : 0.004 0.040 2188 Dihedral : 5.377 55.907 1916 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.51 % Allowed : 9.49 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -0.33 (0.21), residues: 1540 helix: -2.04 (0.68), residues: 24 sheet: 0.99 (0.22), residues: 552 loop : -0.94 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 220 TYR 0.007 0.001 TYR D 344 PHE 0.011 0.001 PHE A 422 TRP 0.015 0.001 TRP C 179 HIS 0.002 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00242 (12452) covalent geometry : angle 0.52458 (16924) SS BOND : bond 0.00507 ( 32) SS BOND : angle 2.51668 ( 64) hydrogen bonds : bond 0.03139 ( 386) hydrogen bonds : angle 5.56104 ( 1032) link_NAG-ASN : bond 0.00234 ( 12) link_NAG-ASN : angle 1.60486 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2386.03 seconds wall clock time: 41 minutes 47.60 seconds (2507.60 seconds total)