Starting phenix.real_space_refine on Fri Jul 3 04:39:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l44_62805/07_2026/9l44_62805.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l44_62805/07_2026/9l44_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_62805/07_2026/9l44_62805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l44_62805/07_2026/9l44_62805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l44_62805/07_2026/9l44_62805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l44_62805/07_2026/9l44_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-dev-6108/lib/python3.11/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, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 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, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 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, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 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, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.00, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 515.1 milliseconds 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: 0.40 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: 1.99 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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 3.250 nonbonded pdb=" O TYR B 344 " pdb="CA CA B 504 " model vdw 1.872 3.250 nonbonded pdb=" O GLY B 298 " pdb="CA CA B 504 " model vdw 1.920 3.250 nonbonded pdb=" OD1 ASN B 378 " pdb="CA CA B 505 " model vdw 1.923 3.250 nonbonded pdb=" O GLY A 298 " pdb="CA CA A 504 " model vdw 1.937 3.250 ... (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: 0.03 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: 1.790 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: 0.030 Set scattering table: 0.040 Process input model: 12.130 Find NCS groups from input model: 0.350 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 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 are 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/Z covalent geometry : bond 0.01139 / 0.54 (12452) covalent geometry : angle 1.16400 / 0.71 (16924) SS BOND : bond 0.01386 / 0.89 ( 32) SS BOND : angle 3.40068 / 2.26 ( 64) hydrogen bonds : bond 0.26438 / 18.34 ( 386) hydrogen bonds : angle 8.91286 / 6.30 ( 1032) link_NAG-ASN : bond 0.01061 / 0.61 ( 12) link_NAG-ASN : angle 4.51905 / 2.89 ( 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 : 0.475 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: 0.1135 time to fit residues: 26.1188 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 : 0.512 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.088518 restraints weight = 16312.713| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.32 r_work: 0.2811 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12496 Z= 0.118 Angle : 0.634 8.572 17024 Z= 0.335 Chirality : 0.050 0.265 1796 Planarity : 0.004 0.036 2188 Dihedral : 6.312 58.945 1919 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.45 % Allowed : 4.37 % Favored : 95.18 % 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 are not related in a simple way. whole: -0.97 (0.20), residues: 1540 helix: -2.54 (0.54), residues: 24 sheet: 0.51 (0.22), residues: 548 loop : -1.36 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 220 TYR 0.008 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 A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (12452) covalent geometry : angle 0.61280 / 0.33 (16924) SS BOND : bond 0.00350 / 0.24 ( 32) SS BOND : angle 1.95442 / 1.30 ( 64) hydrogen bonds : bond 0.04609 / 3.07 ( 386) hydrogen bonds : angle 6.45403 / 4.62 ( 1032) link_NAG-ASN : bond 0.00625 / 0.34 ( 12) link_NAG-ASN : angle 2.63963 / 1.76 ( 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 92 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: C 220 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7110 (mtp180) outliers start: 6 outliers final: 2 residues processed: 90 average time/residue: 0.0910 time to fit residues: 13.1662 Evaluate side-chains 75 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 386 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.089589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.078028 restraints weight = 16627.975| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 1.39 r_work: 0.2639 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12496 Z= 0.236 Angle : 0.743 9.997 17024 Z= 0.385 Chirality : 0.054 0.212 1796 Planarity : 0.005 0.040 2188 Dihedral : 6.245 58.267 1916 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.83 % Allowed : 6.33 % Favored : 92.85 % 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 are not related in a simple way. whole: -0.78 (0.20), residues: 1540 helix: -3.59 (0.29), residues: 24 sheet: 0.96 (0.22), residues: 520 loop : -1.36 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 220 TYR 0.016 0.002 TYR D 344 PHE 0.015 0.002 PHE B 422 TRP 0.018 0.002 TRP A 179 HIS 0.006 0.002 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.24 (12452) covalent geometry : angle 0.72084 / 0.38 (16924) SS BOND : bond 0.00325 / 0.20 ( 32) SS BOND : angle 2.41979 / 1.64 ( 64) hydrogen bonds : bond 0.05065 / 3.38 ( 386) hydrogen bonds : angle 6.31433 / 4.52 ( 1032) link_NAG-ASN : bond 0.00384 / 0.23 ( 12) link_NAG-ASN : angle 2.54034 / 1.70 ( 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 86 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.7405 (mtp180) REVERT: D 220 ARG cc_start: 0.8189 (mmt90) cc_final: 0.7419 (mtp85) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.0844 time to fit residues: 11.2379 Evaluate side-chains 74 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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 392 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.088735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.077279 restraints weight = 16679.268| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 1.36 r_work: 0.2626 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12496 Z= 0.241 Angle : 0.731 10.158 17024 Z= 0.381 Chirality : 0.053 0.207 1796 Planarity : 0.006 0.040 2188 Dihedral : 6.278 58.956 1916 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.66 % Allowed : 7.53 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.84 (0.20), residues: 1540 helix: -4.25 (0.19), residues: 24 sheet: 1.00 (0.22), residues: 520 loop : -1.43 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 220 TYR 0.016 0.002 TYR D 344 PHE 0.017 0.002 PHE C 121 TRP 0.022 0.002 TRP A 179 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.24 (12452) covalent geometry : angle 0.71058 / 0.37 (16924) SS BOND : bond 0.00328 / 0.20 ( 32) SS BOND : angle 2.23193 / 1.50 ( 64) hydrogen bonds : bond 0.05000 / 3.34 ( 386) hydrogen bonds : angle 6.27603 / 4.49 ( 1032) link_NAG-ASN : bond 0.00364 / 0.22 ( 12) link_NAG-ASN : angle 2.49424 / 1.67 ( 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 94 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.433 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: C 220 ARG cc_start: 0.8411 (mtt-85) cc_final: 0.7523 (mtp85) outliers start: 22 outliers final: 8 residues processed: 90 average time/residue: 0.0863 time to fit residues: 12.1798 Evaluate side-chains 76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 147 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.090815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.078807 restraints weight = 16490.036| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.43 r_work: 0.2703 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12496 Z= 0.109 Angle : 0.584 9.807 17024 Z= 0.307 Chirality : 0.048 0.206 1796 Planarity : 0.004 0.041 2188 Dihedral : 5.820 56.450 1916 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.05 % Allowed : 8.58 % Favored : 90.36 % 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 are not related in a simple way. whole: -0.62 (0.20), residues: 1540 helix: -3.89 (0.21), residues: 24 sheet: 1.17 (0.23), residues: 500 loop : -1.25 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 220 TYR 0.008 0.001 TYR D 344 PHE 0.012 0.001 PHE A 121 TRP 0.017 0.001 TRP A 179 HIS 0.002 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (12452) covalent geometry : angle 0.56544 / 0.30 (16924) SS BOND : bond 0.00319 / 0.21 ( 32) SS BOND : angle 1.98221 / 1.29 ( 64) hydrogen bonds : bond 0.03561 / 2.37 ( 386) hydrogen bonds : angle 5.90717 / 4.22 ( 1032) link_NAG-ASN : bond 0.00240 / 0.14 ( 12) link_NAG-ASN : angle 2.04319 / 1.39 ( 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 82 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.498 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: C 220 ARG cc_start: 0.8320 (mtt-85) cc_final: 0.7403 (mtp85) outliers start: 14 outliers final: 8 residues processed: 79 average time/residue: 0.0711 time to fit residues: 9.3726 Evaluate side-chains 67 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.091130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.079384 restraints weight = 16409.623| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.39 r_work: 0.2709 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12496 Z= 0.131 Angle : 0.591 9.840 17024 Z= 0.309 Chirality : 0.049 0.209 1796 Planarity : 0.004 0.039 2188 Dihedral : 5.688 56.728 1916 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.51 % Allowed : 9.34 % Favored : 89.16 % 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 are not related in a simple way. whole: -0.48 (0.21), residues: 1540 helix: -3.58 (0.29), residues: 24 sheet: 1.15 (0.22), residues: 520 loop : -1.13 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 220 TYR 0.008 0.001 TYR D 344 PHE 0.014 0.002 PHE D 121 TRP 0.017 0.001 TRP D 179 HIS 0.004 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (12452) covalent geometry : angle 0.57405 / 0.30 (16924) SS BOND : bond 0.00213 / 0.13 ( 32) SS BOND : angle 1.88558 / 1.24 ( 64) hydrogen bonds : bond 0.03771 / 2.51 ( 386) hydrogen bonds : angle 5.89290 / 4.21 ( 1032) link_NAG-ASN : bond 0.00261 / 0.15 ( 12) link_NAG-ASN : angle 1.97732 / 1.34 ( 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 85 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.390 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 426 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8556 (mt) REVERT: B 426 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8536 (mt) REVERT: C 220 ARG cc_start: 0.8321 (mtt-85) cc_final: 0.7403 (mtp85) REVERT: C 426 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8574 (mt) REVERT: D 426 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8563 (mt) outliers start: 20 outliers final: 14 residues processed: 84 average time/residue: 0.0736 time to fit residues: 10.4323 Evaluate side-chains 81 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 426 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 231 CYS 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 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 416 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 450 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 21 optimal weight: 0.0370 chunk 87 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.090357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.078610 restraints weight = 16400.723| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.39 r_work: 0.2675 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12496 Z= 0.154 Angle : 0.613 9.827 17024 Z= 0.320 Chirality : 0.049 0.209 1796 Planarity : 0.005 0.040 2188 Dihedral : 5.712 57.197 1916 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.03 % Allowed : 9.19 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.51 (0.21), residues: 1540 helix: -3.61 (0.33), residues: 24 sheet: 1.10 (0.22), residues: 520 loop : -1.12 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 220 TYR 0.009 0.001 TYR D 344 PHE 0.013 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/Z covalent geometry : bond 0.00381 / 0.15 (12452) covalent geometry : angle 0.59701 / 0.31 (16924) SS BOND : bond 0.00237 / 0.15 ( 32) SS BOND : angle 1.83613 / 1.21 ( 64) hydrogen bonds : bond 0.03990 / 2.67 ( 386) hydrogen bonds : angle 5.92569 / 4.24 ( 1032) link_NAG-ASN : bond 0.00272 / 0.16 ( 12) link_NAG-ASN : angle 2.03671 / 1.37 ( 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 92 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.467 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 426 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8569 (mt) REVERT: B 426 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8564 (mt) REVERT: C 220 ARG cc_start: 0.8282 (mtt-85) cc_final: 0.7334 (mtp85) REVERT: C 426 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8584 (mt) REVERT: D 426 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8580 (mt) outliers start: 27 outliers final: 17 residues processed: 90 average time/residue: 0.0762 time to fit residues: 11.6201 Evaluate side-chains 86 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 384 ASP 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 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 416 ASP Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 450 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.092068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.079362 restraints weight = 16355.399| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 1.57 r_work: 0.2695 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 12496 Z= 0.120 Angle : 0.590 11.259 17024 Z= 0.307 Chirality : 0.048 0.211 1796 Planarity : 0.004 0.040 2188 Dihedral : 5.586 56.361 1916 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.43 % Allowed : 9.34 % Favored : 89.23 % 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 are not related in a simple way. whole: -0.41 (0.21), residues: 1540 helix: -3.27 (0.43), residues: 24 sheet: 1.13 (0.22), residues: 520 loop : -1.04 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.007 0.001 TYR D 344 PHE 0.011 0.001 PHE A 422 TRP 0.016 0.001 TRP A 179 HIS 0.002 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (12452) covalent geometry : angle 0.55699 / 0.29 (16924) SS BOND : bond 0.00686 / 0.47 ( 32) SS BOND : angle 2.91578 / 1.89 ( 64) hydrogen bonds : bond 0.03451 / 2.30 ( 386) hydrogen bonds : angle 5.76177 / 4.11 ( 1032) link_NAG-ASN : bond 0.00233 / 0.14 ( 12) link_NAG-ASN : angle 1.86000 / 1.26 ( 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 86 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.488 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: 0.8616 (OUTLIER) cc_final: 0.8299 (mt) REVERT: B 426 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8278 (mt) REVERT: C 220 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7017 (mtp85) REVERT: C 426 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8298 (mt) REVERT: D 426 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8320 (mt) outliers start: 19 outliers final: 14 residues processed: 84 average time/residue: 0.0800 time to fit residues: 10.6033 Evaluate side-chains 80 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 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 416 ASP Chi-restraints excluded: chain D residue 426 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 124 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.089543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.077586 restraints weight = 16410.153| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 1.42 r_work: 0.2676 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 12496 Z= 0.185 Angle : 0.657 9.994 17024 Z= 0.340 Chirality : 0.050 0.212 1796 Planarity : 0.005 0.040 2188 Dihedral : 5.834 57.582 1916 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.81 % Allowed : 9.26 % Favored : 88.93 % 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 are not related in a simple way. whole: -0.52 (0.21), residues: 1540 helix: -3.48 (0.38), residues: 24 sheet: 1.10 (0.23), residues: 520 loop : -1.14 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.009 0.001 TYR D 344 PHE 0.013 0.002 PHE D 121 TRP 0.017 0.002 TRP C 179 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 (12452) covalent geometry : angle 0.62850 / 0.33 (16924) SS BOND : bond 0.00519 / 0.34 ( 32) SS BOND : angle 2.80755 / 1.83 ( 64) hydrogen bonds : bond 0.04184 / 2.80 ( 386) hydrogen bonds : angle 5.94728 / 4.25 ( 1032) link_NAG-ASN : bond 0.00290 / 0.17 ( 12) link_NAG-ASN : angle 2.05048 / 1.37 ( 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 91 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.420 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 426 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8611 (mt) REVERT: B 426 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8612 (mt) REVERT: C 220 ARG cc_start: 0.8327 (mtt-85) cc_final: 0.7389 (mtp85) REVERT: C 426 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8619 (mt) REVERT: D 426 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8622 (mt) outliers start: 24 outliers final: 18 residues processed: 88 average time/residue: 0.0759 time to fit residues: 11.1511 Evaluate side-chains 89 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 384 ASP 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 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 416 ASP 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: 0.7980 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.090330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.077651 restraints weight = 16454.493| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 1.55 r_work: 0.2658 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 12496 Z= 0.163 Angle : 0.635 10.259 17024 Z= 0.330 Chirality : 0.050 0.212 1796 Planarity : 0.005 0.040 2188 Dihedral : 5.815 57.396 1916 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.73 % Allowed : 9.64 % Favored : 88.63 % 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 are not related in a simple way. whole: -0.50 (0.21), residues: 1540 helix: -3.41 (0.43), residues: 24 sheet: 1.10 (0.23), residues: 520 loop : -1.12 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.008 0.001 TYR D 344 PHE 0.013 0.002 PHE A 121 TRP 0.017 0.001 TRP A 179 HIS 0.004 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.16 (12452) covalent geometry : angle 0.60651 / 0.32 (16924) SS BOND : bond 0.00549 / 0.37 ( 32) SS BOND : angle 2.77844 / 1.81 ( 64) hydrogen bonds : bond 0.03972 / 2.66 ( 386) hydrogen bonds : angle 5.89552 / 4.22 ( 1032) link_NAG-ASN : bond 0.00256 / 0.15 ( 12) link_NAG-ASN : angle 2.01304 / 1.35 ( 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 89 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 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: symmetry clash REVERT: A 426 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8374 (mt) REVERT: B 426 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8382 (mt) REVERT: C 220 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7063 (mtp85) REVERT: C 426 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8394 (mt) REVERT: D 426 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8399 (mt) outliers start: 23 outliers final: 18 residues processed: 86 average time/residue: 0.0764 time to fit residues: 10.9374 Evaluate side-chains 87 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 92 CYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 384 ASP 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 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 92 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.093923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.082276 restraints weight = 16186.818| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 1.39 r_work: 0.2697 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12496 Z= 0.125 Angle : 0.590 10.007 17024 Z= 0.307 Chirality : 0.048 0.214 1796 Planarity : 0.004 0.040 2188 Dihedral : 5.625 56.371 1916 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.73 % Allowed : 9.64 % Favored : 88.63 % 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 are not related in a simple way. whole: -0.43 (0.21), residues: 1540 helix: -3.19 (0.49), residues: 24 sheet: 1.21 (0.23), residues: 500 loop : -1.06 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 220 TYR 0.007 0.001 TYR C 344 PHE 0.012 0.001 PHE D 121 TRP 0.016 0.001 TRP C 179 HIS 0.003 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.12 (12452) covalent geometry : angle 0.56148 / 0.30 (16924) SS BOND : bond 0.00533 / 0.36 ( 32) SS BOND : angle 2.68433 / 1.75 ( 64) hydrogen bonds : bond 0.03532 / 2.36 ( 386) hydrogen bonds : angle 5.75946 / 4.11 ( 1032) link_NAG-ASN : bond 0.00226 / 0.13 ( 12) link_NAG-ASN : angle 1.82395 / 1.23 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.85 seconds wall clock time: 37 minutes 51.73 seconds (2271.73 seconds total)