Starting phenix.real_space_refine on Wed Jul 30 08:18:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l44_62805/07_2025/9l44_62805.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l44_62805/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9l44_62805/07_2025/9l44_62805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l44_62805/07_2025/9l44_62805.map" model { file = "/net/cci-nas-00/data/ceres_data/9l44_62805/07_2025/9l44_62805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l44_62805/07_2025/9l44_62805.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.68, per 1000 atoms: 0.72 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: 3.02 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.75 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: 5.49 Time building geometry restraints manager: 3.65 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: 0.03 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: 2.450 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.120 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:3.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.840 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.029 0.003 TRP D 455 HIS 0.004 0.001 HIS A 185 PHE 0.029 0.003 PHE B 387 TYR 0.025 0.003 TYR B 344 ARG 0.004 0.000 ARG C 430 Details of bonding type rmsd link_NAG-ASN : bond 0.01061 ( 12) link_NAG-ASN : angle 4.51905 ( 36) hydrogen bonds : bond 0.26438 ( 386) hydrogen bonds : angle 8.91286 ( 1032) SS BOND : bond 0.01386 ( 32) SS BOND : angle 3.40068 ( 64) covalent geometry : bond 0.01139 (12452) covalent geometry : angle 1.16400 (16924) *********************** 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 : 1.581 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: 0.2731 time to fit residues: 62.2426 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 : 1.515 ------------------------------------------------------------------------------- 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 128 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3018 r_free = 0.3018 target = 0.096559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.086217 restraints weight = 16252.197| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.26 r_work: 0.2722 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12496 Z= 0.154 Angle : 0.654 8.317 17024 Z= 0.345 Chirality : 0.051 0.203 1796 Planarity : 0.005 0.038 2188 Dihedral : 6.435 59.678 1919 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.38 % Allowed : 4.52 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1540 helix: -2.72 (0.49), residues: 24 sheet: 0.50 (0.22), residues: 548 loop : -1.38 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 179 HIS 0.002 0.001 HIS C 297 PHE 0.015 0.002 PHE A 406 TYR 0.018 0.001 TYR D 344 ARG 0.005 0.001 ARG C 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 12) link_NAG-ASN : angle 2.52908 ( 36) hydrogen bonds : bond 0.04342 ( 386) hydrogen bonds : angle 6.37320 ( 1032) SS BOND : bond 0.00391 ( 32) SS BOND : angle 1.85764 ( 64) covalent geometry : bond 0.00348 (12452) covalent geometry : angle 0.63504 (16924) *********************** 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 87 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: C 220 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7121 (mtp180) outliers start: 5 outliers final: 1 residues processed: 87 average time/residue: 0.2141 time to fit residues: 30.0723 Evaluate side-chains 66 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 72 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.2927 r_free = 0.2927 target = 0.090097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.078906 restraints weight = 16529.136| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 1.35 r_work: 0.2623 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12496 Z= 0.236 Angle : 0.752 10.287 17024 Z= 0.388 Chirality : 0.053 0.216 1796 Planarity : 0.005 0.040 2188 Dihedral : 6.284 59.250 1916 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.98 % Allowed : 6.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1540 helix: -3.62 (0.30), residues: 24 sheet: 0.97 (0.23), residues: 520 loop : -1.39 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 179 HIS 0.008 0.002 HIS C 297 PHE 0.015 0.002 PHE D 422 TYR 0.021 0.002 TYR D 344 ARG 0.003 0.001 ARG C 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 12) link_NAG-ASN : angle 2.60495 ( 36) hydrogen bonds : bond 0.05389 ( 386) hydrogen bonds : angle 6.33819 ( 1032) SS BOND : bond 0.00365 ( 32) SS BOND : angle 2.67922 ( 64) covalent geometry : bond 0.00591 (12452) covalent geometry : angle 0.72649 (16924) *********************** 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 89 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.327 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: 0.8436 (mtt-85) cc_final: 0.7546 (mtp180) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.2376 time to fit residues: 31.5620 Evaluate side-chains 80 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 28 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 107 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.2943 r_free = 0.2943 target = 0.091225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.079770 restraints weight = 16453.626| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 1.38 r_work: 0.2651 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12496 Z= 0.124 Angle : 0.595 9.905 17024 Z= 0.313 Chirality : 0.049 0.207 1796 Planarity : 0.004 0.039 2188 Dihedral : 5.875 57.013 1916 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.51 % Allowed : 7.38 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1540 helix: -3.26 (0.35), residues: 24 sheet: 0.87 (0.22), residues: 568 loop : -1.19 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 179 HIS 0.003 0.001 HIS D 297 PHE 0.013 0.002 PHE C 121 TYR 0.011 0.001 TYR D 344 ARG 0.004 0.000 ARG A 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 12) link_NAG-ASN : angle 2.15274 ( 36) hydrogen bonds : bond 0.03829 ( 386) hydrogen bonds : angle 6.00477 ( 1032) SS BOND : bond 0.00205 ( 32) SS BOND : angle 1.59099 ( 64) covalent geometry : bond 0.00298 (12452) covalent geometry : angle 0.58045 (16924) *********************** 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 85 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 1.627 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: 0.8353 (mtt-85) cc_final: 0.7469 (mtp85) outliers start: 20 outliers final: 10 residues processed: 81 average time/residue: 0.2362 time to fit residues: 30.4897 Evaluate side-chains 74 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 273 ASN 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 392 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 147 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.0000 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.0980 overall best weight: 0.7988 ------------------------------------------------------------------------------- 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 = 0.2987 r_free = 0.2987 target = 0.093979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.082842 restraints weight = 16224.272| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.34 r_work: 0.2705 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12496 Z= 0.103 Angle : 0.555 9.820 17024 Z= 0.291 Chirality : 0.048 0.210 1796 Planarity : 0.004 0.040 2188 Dihedral : 5.579 55.907 1916 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.20 % Allowed : 8.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.21), residues: 1540 helix: -2.27 (0.62), residues: 24 sheet: 1.01 (0.22), residues: 548 loop : -1.09 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 179 HIS 0.003 0.001 HIS D 297 PHE 0.013 0.001 PHE C 121 TYR 0.008 0.001 TYR D 344 ARG 0.006 0.000 ARG D 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 12) link_NAG-ASN : angle 1.84561 ( 36) hydrogen bonds : bond 0.03352 ( 386) hydrogen bonds : angle 5.77472 ( 1032) SS BOND : bond 0.00256 ( 32) SS BOND : angle 1.99205 ( 64) covalent geometry : bond 0.00241 (12452) covalent geometry : angle 0.53649 (16924) *********************** 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: 16 poor density : 66 time to evaluate : 1.432 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: 0.8297 (mtt-85) cc_final: 0.7439 (mtp85) outliers start: 16 outliers final: 12 residues processed: 78 average time/residue: 0.1905 time to fit residues: 24.9591 Evaluate side-chains 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 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 273 ASN 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 87 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 21 optimal weight: 0.0010 chunk 78 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 0.8166 ------------------------------------------------------------------------------- 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 = 0.3002 r_free = 0.3002 target = 0.095002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.083804 restraints weight = 16501.656| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.35 r_work: 0.2727 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 12496 Z= 0.103 Angle : 0.539 9.765 17024 Z= 0.282 Chirality : 0.047 0.213 1796 Planarity : 0.004 0.039 2188 Dihedral : 5.372 55.981 1916 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.36 % Allowed : 8.96 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1540 helix: -2.22 (0.64), residues: 24 sheet: 1.06 (0.22), residues: 548 loop : -1.02 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 179 HIS 0.003 0.001 HIS D 297 PHE 0.013 0.001 PHE A 121 TYR 0.007 0.001 TYR C 282 ARG 0.005 0.000 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 12) link_NAG-ASN : angle 1.73391 ( 36) hydrogen bonds : bond 0.03283 ( 386) hydrogen bonds : angle 5.67177 ( 1032) SS BOND : bond 0.00209 ( 32) SS BOND : angle 1.82648 ( 64) covalent geometry : bond 0.00244 (12452) covalent geometry : angle 0.52307 (16924) *********************** 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 86 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 1.369 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: 0.8754 (OUTLIER) cc_final: 0.8454 (mt) REVERT: B 426 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8403 (mt) REVERT: C 220 ARG cc_start: 0.8307 (mtt-85) cc_final: 0.7422 (mtp85) REVERT: C 426 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8439 (mt) REVERT: D 426 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8449 (mt) outliers start: 18 outliers final: 11 residues processed: 82 average time/residue: 0.2114 time to fit residues: 27.6177 Evaluate side-chains 75 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 426 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 101 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 139 optimal weight: 0.2980 chunk 103 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 143 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.093797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.082344 restraints weight = 16340.398| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.38 r_work: 0.2709 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12496 Z= 0.127 Angle : 0.567 9.780 17024 Z= 0.296 Chirality : 0.048 0.213 1796 Planarity : 0.004 0.039 2188 Dihedral : 5.430 56.583 1916 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.81 % Allowed : 8.96 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1540 helix: -2.41 (0.57), residues: 24 sheet: 1.23 (0.22), residues: 520 loop : -0.97 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 179 HIS 0.005 0.001 HIS D 297 PHE 0.014 0.002 PHE C 121 TYR 0.008 0.001 TYR D 344 ARG 0.004 0.000 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 12) link_NAG-ASN : angle 1.84236 ( 36) hydrogen bonds : bond 0.03633 ( 386) hydrogen bonds : angle 5.75962 ( 1032) SS BOND : bond 0.00227 ( 32) SS BOND : angle 1.74017 ( 64) covalent geometry : bond 0.00311 (12452) covalent geometry : angle 0.55248 (16924) *********************** 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 83 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 1.793 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: 0.8780 (OUTLIER) cc_final: 0.8500 (mt) REVERT: B 426 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8468 (mt) REVERT: C 220 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.7319 (mtp85) REVERT: C 426 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8521 (mt) REVERT: D 426 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8502 (mt) outliers start: 24 outliers final: 14 residues processed: 82 average time/residue: 0.1973 time to fit residues: 27.6305 Evaluate side-chains 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 97 optimal weight: 0.1980 chunk 136 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3030 r_free = 0.3030 target = 0.096369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.083732 restraints weight = 16231.915| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.57 r_work: 0.2741 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 12496 Z= 0.100 Angle : 0.551 11.356 17024 Z= 0.286 Chirality : 0.047 0.214 1796 Planarity : 0.004 0.038 2188 Dihedral : 5.307 55.660 1916 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.28 % Allowed : 9.34 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1540 helix: -2.03 (0.67), residues: 24 sheet: 1.09 (0.22), residues: 552 loop : -0.95 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 179 HIS 0.002 0.001 HIS D 297 PHE 0.011 0.001 PHE D 121 TYR 0.007 0.001 TYR C 282 ARG 0.004 0.000 ARG B 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 12) link_NAG-ASN : angle 1.63598 ( 36) hydrogen bonds : bond 0.03080 ( 386) hydrogen bonds : angle 5.58368 ( 1032) SS BOND : bond 0.00710 ( 32) SS BOND : angle 2.80097 ( 64) covalent geometry : bond 0.00239 (12452) covalent geometry : angle 0.51970 (16924) *********************** 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 76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8230 (mt) REVERT: B 426 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8182 (mt) REVERT: C 426 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8249 (mt) REVERT: D 426 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8242 (mt) outliers start: 17 outliers final: 13 residues processed: 74 average time/residue: 0.1858 time to fit residues: 22.9324 Evaluate side-chains 76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 15 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.2993 r_free = 0.2993 target = 0.093874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.081194 restraints weight = 16327.442| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.58 r_work: 0.2710 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 12496 Z= 0.144 Angle : 0.598 10.417 17024 Z= 0.310 Chirality : 0.048 0.214 1796 Planarity : 0.004 0.038 2188 Dihedral : 5.470 56.727 1916 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.58 % Allowed : 9.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1540 helix: -2.29 (0.59), residues: 24 sheet: 1.26 (0.22), residues: 520 loop : -0.94 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 179 HIS 0.004 0.001 HIS D 297 PHE 0.014 0.002 PHE D 121 TYR 0.008 0.001 TYR D 344 ARG 0.007 0.000 ARG C 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 12) link_NAG-ASN : angle 1.79445 ( 36) hydrogen bonds : bond 0.03655 ( 386) hydrogen bonds : angle 5.74632 ( 1032) SS BOND : bond 0.00581 ( 32) SS BOND : angle 2.78051 ( 64) covalent geometry : bond 0.00364 (12452) covalent geometry : angle 0.56839 (16924) *********************** 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 83 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8335 (mt) REVERT: B 426 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8293 (mt) REVERT: C 426 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8360 (mt) REVERT: D 426 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8381 (mt) outliers start: 21 outliers final: 17 residues processed: 80 average time/residue: 0.1817 time to fit residues: 24.3884 Evaluate side-chains 83 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 45 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.2901 r_free = 0.2901 target = 0.088621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.076968 restraints weight = 16520.476| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 1.39 r_work: 0.2657 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 12496 Z= 0.210 Angle : 0.693 10.855 17024 Z= 0.358 Chirality : 0.051 0.214 1796 Planarity : 0.005 0.039 2188 Dihedral : 5.921 58.280 1916 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.58 % Allowed : 9.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1540 helix: -2.88 (0.39), residues: 24 sheet: 1.10 (0.23), residues: 492 loop : -1.11 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 179 HIS 0.006 0.001 HIS D 297 PHE 0.014 0.002 PHE A 121 TYR 0.009 0.001 TYR D 344 ARG 0.007 0.001 ARG C 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 12) link_NAG-ASN : angle 2.14968 ( 36) hydrogen bonds : bond 0.04483 ( 386) hydrogen bonds : angle 6.02711 ( 1032) SS BOND : bond 0.00551 ( 32) SS BOND : angle 3.00891 ( 64) covalent geometry : bond 0.00533 (12452) covalent geometry : angle 0.66276 (16924) ********************** 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 84 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 1.403 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: 0.8885 (OUTLIER) cc_final: 0.8625 (mt) REVERT: B 426 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8600 (mt) REVERT: C 426 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 150 LYS cc_start: 0.8372 (ptpt) cc_final: 0.8162 (ptpt) REVERT: D 426 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8632 (mt) outliers start: 21 outliers final: 17 residues processed: 81 average time/residue: 0.1958 time to fit residues: 26.3461 Evaluate side-chains 84 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 32 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.2982 r_free = 0.2982 target = 0.093266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.080737 restraints weight = 16177.665| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.56 r_work: 0.2694 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12496 Z= 0.129 Angle : 0.600 10.589 17024 Z= 0.312 Chirality : 0.048 0.214 1796 Planarity : 0.004 0.040 2188 Dihedral : 5.664 56.883 1916 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.58 % Allowed : 9.56 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1540 helix: -2.50 (0.49), residues: 24 sheet: 1.14 (0.23), residues: 520 loop : -0.99 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 179 HIS 0.004 0.001 HIS D 297 PHE 0.012 0.002 PHE D 422 TYR 0.008 0.001 TYR D 344 ARG 0.004 0.000 ARG C 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 12) link_NAG-ASN : angle 1.89819 ( 36) hydrogen bonds : bond 0.03609 ( 386) hydrogen bonds : angle 5.80535 ( 1032) SS BOND : bond 0.00475 ( 32) SS BOND : angle 2.82147 ( 64) covalent geometry : bond 0.00321 (12452) covalent geometry : angle 0.56999 (16924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5553.11 seconds wall clock time: 98 minutes 15.64 seconds (5895.64 seconds total)