Starting phenix.real_space_refine on Mon Apr 6 01:31:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7z_72675/04_2026/9y7z_72675.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7z_72675/04_2026/9y7z_72675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y7z_72675/04_2026/9y7z_72675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7z_72675/04_2026/9y7z_72675.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y7z_72675/04_2026/9y7z_72675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7z_72675/04_2026/9y7z_72675.map" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9460 2.51 5 N 2305 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14480 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2803 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "B" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2803 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "C" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2803 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "D" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2803 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "E" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2803 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 93 Unusual residues: {'NAG': 2, 'PX4': 4} Inner-chain residues flagged as termini: ['pdbres="GLY A 505 "'] Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 93 Unusual residues: {'NAG': 2, 'PX4': 4} Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 93 Unusual residues: {'NAG': 2, 'PX4': 4} Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 93 Unusual residues: {'NAG': 2, 'PX4': 4} Inner-chain residues flagged as termini: ['pdbres="GLY D 505 "'] Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 93 Unusual residues: {'NAG': 2, 'PX4': 4} Inner-chain residues flagged as termini: ['pdbres="GLY E 503 "'] Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 3.28, per 1000 atoms: 0.23 Number of scatterers: 14480 At special positions: 0 Unit cell: (93.24, 91.56, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2625 8.00 N 2305 7.00 C 9460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 243 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 243 " distance=2.03 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 503 " - " ASN A 72 " " NAG A 504 " - " ASN A 103 " " NAG B 501 " - " ASN B 72 " " NAG B 502 " - " ASN B 103 " " NAG C 503 " - " ASN C 72 " " NAG C 504 " - " ASN C 103 " " NAG D 503 " - " ASN D 72 " " NAG D 504 " - " ASN D 103 " " NAG E 504 " - " ASN E 72 " " NAG E 505 " - " ASN E 103 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 521.0 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 25 sheets defined 40.3% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.812A pdb=" N LEU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 57 removed outlier: 4.261A pdb=" N GLY A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 120 through 127 removed outlier: 4.199A pdb=" N LEU A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.630A pdb=" N ILE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.508A pdb=" N VAL A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 278 Processing helix chain 'A' and resid 282 through 305 removed outlier: 3.650A pdb=" N ARG A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 410 through 443 removed outlier: 3.506A pdb=" N ASP A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'B' and resid 43 through 53 removed outlier: 3.812A pdb=" N LEU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 57 removed outlier: 4.261A pdb=" N GLY B 57 " --> pdb=" O ARG B 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 120 through 127 removed outlier: 4.199A pdb=" N LEU B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.629A pdb=" N ILE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 274 removed outlier: 3.507A pdb=" N VAL B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 278 Processing helix chain 'B' and resid 282 through 305 removed outlier: 3.650A pdb=" N ARG B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 410 through 443 removed outlier: 3.506A pdb=" N ASP B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'C' and resid 43 through 53 removed outlier: 3.812A pdb=" N LEU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 57 removed outlier: 4.261A pdb=" N GLY C 57 " --> pdb=" O ARG C 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 120 through 127 removed outlier: 4.198A pdb=" N LEU C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 removed outlier: 3.630A pdb=" N ILE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 274 removed outlier: 3.508A pdb=" N VAL C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 282 through 305 removed outlier: 3.650A pdb=" N ARG C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 343 Processing helix chain 'C' and resid 410 through 443 removed outlier: 3.506A pdb=" N ASP C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 424 " --> pdb=" O THR C 420 " (cutoff:3.500A) Proline residue: C 427 - end of helix Processing helix chain 'D' and resid 43 through 53 removed outlier: 3.812A pdb=" N LEU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 57 removed outlier: 4.261A pdb=" N GLY D 57 " --> pdb=" O ARG D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 54 through 57' Processing helix chain 'D' and resid 105 through 108 Processing helix chain 'D' and resid 120 through 127 removed outlier: 4.198A pdb=" N LEU D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 removed outlier: 3.631A pdb=" N ILE D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 274 removed outlier: 3.507A pdb=" N VAL D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 278 Processing helix chain 'D' and resid 282 through 305 removed outlier: 3.650A pdb=" N ARG D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 343 Processing helix chain 'D' and resid 410 through 443 removed outlier: 3.506A pdb=" N ASP D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 424 " --> pdb=" O THR D 420 " (cutoff:3.500A) Proline residue: D 427 - end of helix Processing helix chain 'E' and resid 43 through 53 removed outlier: 3.813A pdb=" N LEU E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 57 removed outlier: 4.261A pdb=" N GLY E 57 " --> pdb=" O ARG E 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 57' Processing helix chain 'E' and resid 105 through 108 Processing helix chain 'E' and resid 120 through 127 removed outlier: 4.198A pdb=" N LEU E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP E 125 " --> pdb=" O SER E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 261 removed outlier: 3.630A pdb=" N ILE E 259 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 removed outlier: 3.508A pdb=" N VAL E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 278 Processing helix chain 'E' and resid 282 through 305 removed outlier: 3.650A pdb=" N ARG E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 343 Processing helix chain 'E' and resid 410 through 443 removed outlier: 3.506A pdb=" N ASP E 419 " --> pdb=" O ALA E 415 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA E 424 " --> pdb=" O THR E 420 " (cutoff:3.500A) Proline residue: E 427 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.570A pdb=" N LEU A 152 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 142 removed outlier: 6.540A pdb=" N THR A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR A 167 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE A 142 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ARG A 165 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA5, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 119 removed outlier: 4.569A pdb=" N LEU B 152 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 137 through 142 removed outlier: 6.541A pdb=" N THR B 169 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA B 140 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B 167 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE B 142 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ARG B 165 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AA9, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB2, first strand: chain 'C' and resid 116 through 119 removed outlier: 4.570A pdb=" N LEU C 152 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 137 through 142 removed outlier: 6.540A pdb=" N THR C 169 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA C 140 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C 167 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE C 142 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ARG C 165 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB5, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB6, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AB7, first strand: chain 'D' and resid 116 through 119 removed outlier: 4.569A pdb=" N LEU D 152 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 137 through 142 removed outlier: 6.540A pdb=" N THR D 169 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA D 140 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR D 167 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE D 142 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ARG D 165 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 132 through 134 Processing sheet with id=AC1, first strand: chain 'D' and resid 132 through 134 Processing sheet with id=AC2, first strand: chain 'D' and resid 234 through 235 Processing sheet with id=AC3, first strand: chain 'E' and resid 116 through 119 removed outlier: 4.570A pdb=" N LEU E 152 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.540A pdb=" N THR E 169 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA E 140 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR E 167 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE E 142 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ARG E 165 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 132 through 134 Processing sheet with id=AC6, first strand: chain 'E' and resid 132 through 134 Processing sheet with id=AC7, first strand: chain 'E' and resid 234 through 235 860 hydrogen bonds defined for protein. 2475 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2250 1.31 - 1.44: 4125 1.44 - 1.57: 8190 1.57 - 1.70: 95 1.70 - 1.83: 150 Bond restraints: 14810 Sorted by residual: bond pdb=" C23 PX4 D 506 " pdb=" O7 PX4 D 506 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C23 PX4 E 502 " pdb=" O7 PX4 E 502 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C23 PX4 C 502 " pdb=" O7 PX4 C 502 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C23 PX4 C 506 " pdb=" O7 PX4 C 506 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C23 PX4 B 506 " pdb=" O7 PX4 B 506 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 14805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 19415 1.74 - 3.47: 328 3.47 - 5.21: 226 5.21 - 6.94: 1 6.94 - 8.68: 20 Bond angle restraints: 19990 Sorted by residual: angle pdb=" C24 PX4 C 506 " pdb=" C23 PX4 C 506 " pdb=" O7 PX4 C 506 " ideal model delta sigma weight residual 111.45 120.13 -8.68 3.00e+00 1.11e-01 8.36e+00 angle pdb=" C24 PX4 A 507 " pdb=" C23 PX4 A 507 " pdb=" O7 PX4 A 507 " ideal model delta sigma weight residual 111.45 120.09 -8.64 3.00e+00 1.11e-01 8.30e+00 angle pdb=" C24 PX4 B 506 " pdb=" C23 PX4 B 506 " pdb=" O7 PX4 B 506 " ideal model delta sigma weight residual 111.45 120.09 -8.64 3.00e+00 1.11e-01 8.30e+00 angle pdb=" C24 PX4 E 502 " pdb=" C23 PX4 E 502 " pdb=" O7 PX4 E 502 " ideal model delta sigma weight residual 111.45 120.08 -8.63 3.00e+00 1.11e-01 8.28e+00 angle pdb=" C24 PX4 D 507 " pdb=" C23 PX4 D 507 " pdb=" O7 PX4 D 507 " ideal model delta sigma weight residual 111.45 120.07 -8.62 3.00e+00 1.11e-01 8.26e+00 ... (remaining 19985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 8217 17.59 - 35.19: 628 35.19 - 52.78: 100 52.78 - 70.37: 45 70.37 - 87.96: 10 Dihedral angle restraints: 9000 sinusoidal: 3885 harmonic: 5115 Sorted by residual: dihedral pdb=" CG ARG D 343 " pdb=" CD ARG D 343 " pdb=" NE ARG D 343 " pdb=" CZ ARG D 343 " ideal model delta sinusoidal sigma weight residual 90.00 130.53 -40.53 2 1.50e+01 4.44e-03 9.01e+00 dihedral pdb=" CG ARG E 343 " pdb=" CD ARG E 343 " pdb=" NE ARG E 343 " pdb=" CZ ARG E 343 " ideal model delta sinusoidal sigma weight residual 90.00 130.53 -40.53 2 1.50e+01 4.44e-03 9.01e+00 dihedral pdb=" CG ARG A 343 " pdb=" CD ARG A 343 " pdb=" NE ARG A 343 " pdb=" CZ ARG A 343 " ideal model delta sinusoidal sigma weight residual 90.00 130.52 -40.52 2 1.50e+01 4.44e-03 9.01e+00 ... (remaining 8997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1410 0.031 - 0.062: 581 0.062 - 0.093: 139 0.093 - 0.124: 104 0.124 - 0.154: 11 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 72 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" C1 NAG D 503 " pdb=" ND2 ASN D 72 " pdb=" C2 NAG D 503 " pdb=" O5 NAG D 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" C1 NAG A 503 " pdb=" ND2 ASN A 72 " pdb=" C2 NAG A 503 " pdb=" O5 NAG A 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2242 not shown) Planarity restraints: 2480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 120 " 0.023 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO E 121 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 120 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO D 121 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 120 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 121 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.020 5.00e-02 4.00e+02 ... (remaining 2477 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 3192 2.78 - 3.31: 13342 3.31 - 3.84: 23140 3.84 - 4.37: 28795 4.37 - 4.90: 50116 Nonbonded interactions: 118585 Sorted by model distance: nonbonded pdb=" O THR B 146 " pdb=" OG1 THR B 147 " model vdw 2.256 3.040 nonbonded pdb=" O THR A 146 " pdb=" OG1 THR A 147 " model vdw 2.257 3.040 nonbonded pdb=" O THR E 146 " pdb=" OG1 THR E 147 " model vdw 2.257 3.040 nonbonded pdb=" O THR C 146 " pdb=" OG1 THR C 147 " model vdw 2.257 3.040 nonbonded pdb=" O THR D 146 " pdb=" OG1 THR D 147 " model vdw 2.257 3.040 ... (remaining 118580 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 450 or (resid 506 and (name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name C31 \ or name C32 or name O7 or name O8 )))) selection = (chain 'B' and (resid 42 through 450 or resid 506)) selection = (chain 'C' and (resid 42 through 450 or resid 506)) selection = (chain 'D' and (resid 42 through 450 or (resid 506 and (name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name C31 \ or name C32 or name O7 or name O8 )))) selection = (chain 'E' and (resid 42 through 450 or (resid 506 and (name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name C31 \ or name C32 or name O7 or name O8 )))) } 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: 1.750 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.770 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 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 : 0.007 0.088 14830 Z= 0.358 Angle : 0.737 8.675 20040 Z= 0.326 Chirality : 0.041 0.154 2245 Planarity : 0.003 0.036 2470 Dihedral : 13.277 87.964 5650 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1710 helix: 1.42 (0.21), residues: 580 sheet: 0.48 (0.28), residues: 355 loop : -0.00 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 99 TYR 0.018 0.001 TYR E 257 PHE 0.008 0.001 PHE E 82 TRP 0.004 0.001 TRP B 102 HIS 0.002 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00725 (14810) covalent geometry : angle 0.72550 (19990) SS BOND : bond 0.00214 ( 10) SS BOND : angle 2.20822 ( 20) hydrogen bonds : bond 0.23060 ( 715) hydrogen bonds : angle 8.18560 ( 2475) link_NAG-ASN : bond 0.00689 ( 10) link_NAG-ASN : angle 3.00085 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.509 Fit side-chains REVERT: A 191 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 260 GLN cc_start: 0.9263 (tp40) cc_final: 0.8889 (tp40) REVERT: C 318 ASP cc_start: 0.8682 (m-30) cc_final: 0.8344 (m-30) REVERT: C 416 LYS cc_start: 0.9049 (ttmm) cc_final: 0.8842 (tmmt) REVERT: D 318 ASP cc_start: 0.8614 (m-30) cc_final: 0.8339 (m-30) REVERT: E 318 ASP cc_start: 0.8584 (m-30) cc_final: 0.8329 (m-30) outliers start: 0 outliers final: 1 residues processed: 208 average time/residue: 0.5904 time to fit residues: 134.5841 Evaluate side-chains 160 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 413 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 = 0.3263 r_free = 0.3263 target = 0.094636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.071094 restraints weight = 24523.209| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.68 r_work: 0.2712 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14830 Z= 0.141 Angle : 0.621 6.710 20040 Z= 0.312 Chirality : 0.043 0.177 2245 Planarity : 0.004 0.031 2470 Dihedral : 8.654 57.911 2312 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.22 % Allowed : 9.04 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1710 helix: 2.45 (0.21), residues: 575 sheet: 0.74 (0.28), residues: 355 loop : -0.27 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 93 TYR 0.023 0.001 TYR D 335 PHE 0.011 0.001 PHE A 133 TRP 0.012 0.001 TRP D 102 HIS 0.001 0.000 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00306 (14810) covalent geometry : angle 0.59879 (19990) SS BOND : bond 0.00350 ( 10) SS BOND : angle 1.44051 ( 20) hydrogen bonds : bond 0.04962 ( 715) hydrogen bonds : angle 5.22324 ( 2475) link_NAG-ASN : bond 0.00901 ( 10) link_NAG-ASN : angle 4.12894 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.427 Fit side-chains REVERT: A 120 ASP cc_start: 0.8581 (t0) cc_final: 0.8362 (t0) REVERT: B 300 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8917 (mt0) REVERT: C 89 THR cc_start: 0.9057 (p) cc_final: 0.8674 (t) REVERT: C 300 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8865 (mt0) REVERT: C 338 VAL cc_start: 0.9115 (t) cc_final: 0.8889 (m) REVERT: C 344 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8443 (mm-40) REVERT: C 416 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8683 (tmmt) REVERT: D 318 ASP cc_start: 0.9123 (m-30) cc_final: 0.8851 (m-30) REVERT: D 338 VAL cc_start: 0.9055 (t) cc_final: 0.8843 (m) REVERT: E 52 MET cc_start: 0.8227 (pmm) cc_final: 0.7612 (pp-130) REVERT: E 300 GLN cc_start: 0.9108 (tp40) cc_final: 0.8850 (mt0) REVERT: E 318 ASP cc_start: 0.9094 (m-30) cc_final: 0.8860 (m-30) outliers start: 19 outliers final: 2 residues processed: 201 average time/residue: 0.5708 time to fit residues: 126.1896 Evaluate side-chains 180 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 GLN Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain D residue 419 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.094116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.070487 restraints weight = 24693.193| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.64 r_work: 0.2696 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14830 Z= 0.159 Angle : 0.584 6.610 20040 Z= 0.293 Chirality : 0.042 0.230 2245 Planarity : 0.003 0.028 2470 Dihedral : 8.160 57.623 2312 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.73 % Allowed : 10.06 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1710 helix: 2.44 (0.20), residues: 605 sheet: 0.87 (0.28), residues: 355 loop : -0.30 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 93 TYR 0.022 0.001 TYR A 335 PHE 0.010 0.001 PHE A 133 TRP 0.010 0.001 TRP D 102 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00370 (14810) covalent geometry : angle 0.56602 (19990) SS BOND : bond 0.00378 ( 10) SS BOND : angle 1.30252 ( 20) hydrogen bonds : bond 0.04590 ( 715) hydrogen bonds : angle 5.00412 ( 2475) link_NAG-ASN : bond 0.00749 ( 10) link_NAG-ASN : angle 3.59260 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.576 Fit side-chains REVERT: A 416 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8671 (tmmt) REVERT: B 300 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8926 (mt0) REVERT: B 344 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8298 (mm-40) REVERT: B 416 LYS cc_start: 0.9083 (ttmm) cc_final: 0.8693 (tmmt) REVERT: B 446 HIS cc_start: 0.8097 (t-90) cc_final: 0.7883 (t-90) REVERT: C 89 THR cc_start: 0.9021 (p) cc_final: 0.8618 (t) REVERT: C 300 GLN cc_start: 0.9117 (tp40) cc_final: 0.8875 (mt0) REVERT: C 344 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8373 (mm-40) REVERT: C 416 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8664 (tmmt) REVERT: D 318 ASP cc_start: 0.9124 (m-30) cc_final: 0.8829 (m-30) REVERT: D 416 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8660 (tmmt) REVERT: E 181 MET cc_start: 0.9180 (mtm) cc_final: 0.8979 (mtm) REVERT: E 300 GLN cc_start: 0.9146 (tp40) cc_final: 0.8839 (mt0) REVERT: E 318 ASP cc_start: 0.9096 (m-30) cc_final: 0.8854 (m-30) REVERT: E 343 ARG cc_start: 0.8282 (ttm110) cc_final: 0.8052 (ttm110) REVERT: E 416 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8707 (tmmt) outliers start: 27 outliers final: 11 residues processed: 192 average time/residue: 0.5757 time to fit residues: 121.5678 Evaluate side-chains 188 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 300 GLN Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain E residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 5 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.069453 restraints weight = 24725.835| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.66 r_work: 0.2680 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14830 Z= 0.200 Angle : 0.611 9.012 20040 Z= 0.303 Chirality : 0.043 0.227 2245 Planarity : 0.003 0.031 2470 Dihedral : 7.836 58.857 2312 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.67 % Allowed : 11.41 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1710 helix: 2.39 (0.20), residues: 605 sheet: 0.83 (0.28), residues: 355 loop : -0.35 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 93 TYR 0.022 0.002 TYR D 335 PHE 0.011 0.001 PHE A 133 TRP 0.010 0.001 TRP D 102 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00471 (14810) covalent geometry : angle 0.59713 (19990) SS BOND : bond 0.00408 ( 10) SS BOND : angle 1.33904 ( 20) hydrogen bonds : bond 0.04396 ( 715) hydrogen bonds : angle 4.95720 ( 2475) link_NAG-ASN : bond 0.00689 ( 10) link_NAG-ASN : angle 3.28119 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.517 Fit side-chains REVERT: A 416 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8707 (tmmt) REVERT: B 344 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8433 (mm-40) REVERT: B 416 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8690 (tmmt) REVERT: B 446 HIS cc_start: 0.8084 (t-90) cc_final: 0.7835 (t-90) REVERT: C 89 THR cc_start: 0.9009 (p) cc_final: 0.8603 (t) REVERT: C 344 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8305 (mm-40) REVERT: C 416 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8689 (tmmt) REVERT: D 318 ASP cc_start: 0.9123 (m-30) cc_final: 0.8843 (m-30) REVERT: D 416 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8681 (tmmt) REVERT: E 125 ASP cc_start: 0.8903 (m-30) cc_final: 0.8584 (t0) REVERT: E 174 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8617 (mtt) REVERT: E 300 GLN cc_start: 0.9148 (tp40) cc_final: 0.8806 (mt0) REVERT: E 318 ASP cc_start: 0.9096 (m-30) cc_final: 0.8853 (m-30) REVERT: E 416 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8680 (tmmt) outliers start: 26 outliers final: 11 residues processed: 189 average time/residue: 0.5858 time to fit residues: 121.8212 Evaluate side-chains 185 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 174 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 53 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 153 optimal weight: 0.3980 chunk 157 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.071791 restraints weight = 24403.586| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.62 r_work: 0.2735 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14830 Z= 0.106 Angle : 0.561 8.464 20040 Z= 0.279 Chirality : 0.042 0.236 2245 Planarity : 0.003 0.027 2470 Dihedral : 7.301 54.755 2312 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.92 % Allowed : 12.24 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1710 helix: 2.51 (0.20), residues: 600 sheet: 0.98 (0.28), residues: 355 loop : -0.33 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 93 TYR 0.023 0.001 TYR D 335 PHE 0.011 0.001 PHE A 133 TRP 0.009 0.001 TRP D 102 HIS 0.001 0.000 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00227 (14810) covalent geometry : angle 0.55206 (19990) SS BOND : bond 0.00335 ( 10) SS BOND : angle 1.06231 ( 20) hydrogen bonds : bond 0.03841 ( 715) hydrogen bonds : angle 4.64612 ( 2475) link_NAG-ASN : bond 0.00745 ( 10) link_NAG-ASN : angle 2.58999 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 125 ASP cc_start: 0.8655 (p0) cc_final: 0.8337 (t0) REVERT: A 416 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8678 (tmmt) REVERT: B 344 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8420 (mm-40) REVERT: B 416 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8697 (tmmt) REVERT: B 446 HIS cc_start: 0.8097 (t-90) cc_final: 0.7830 (t-90) REVERT: C 89 THR cc_start: 0.9086 (p) cc_final: 0.8682 (t) REVERT: C 344 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8443 (mm-40) REVERT: C 416 LYS cc_start: 0.9051 (ttmm) cc_final: 0.8683 (tmmt) REVERT: D 318 ASP cc_start: 0.9112 (m-30) cc_final: 0.8879 (m-30) REVERT: D 416 LYS cc_start: 0.9091 (ttmm) cc_final: 0.8694 (tmmt) REVERT: E 89 THR cc_start: 0.9146 (p) cc_final: 0.8858 (t) REVERT: E 125 ASP cc_start: 0.8891 (m-30) cc_final: 0.8545 (OUTLIER) REVERT: E 174 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8453 (mtt) REVERT: E 300 GLN cc_start: 0.9146 (tp40) cc_final: 0.8884 (mt0) REVERT: E 416 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8686 (tmmt) outliers start: 30 outliers final: 12 residues processed: 208 average time/residue: 0.5331 time to fit residues: 122.3792 Evaluate side-chains 196 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 413 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 142 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 155 optimal weight: 0.4980 chunk 132 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.070436 restraints weight = 24421.274| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.62 r_work: 0.2710 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14830 Z= 0.152 Angle : 0.586 10.043 20040 Z= 0.289 Chirality : 0.042 0.218 2245 Planarity : 0.003 0.026 2470 Dihedral : 7.179 54.532 2312 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.92 % Allowed : 13.14 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1710 helix: 2.46 (0.20), residues: 600 sheet: 0.96 (0.28), residues: 355 loop : -0.33 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 93 TYR 0.022 0.001 TYR B 335 PHE 0.011 0.001 PHE A 133 TRP 0.009 0.001 TRP D 102 HIS 0.001 0.000 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00356 (14810) covalent geometry : angle 0.57869 (19990) SS BOND : bond 0.00367 ( 10) SS BOND : angle 1.16714 ( 20) hydrogen bonds : bond 0.03927 ( 715) hydrogen bonds : angle 4.68149 ( 2475) link_NAG-ASN : bond 0.00559 ( 10) link_NAG-ASN : angle 2.27768 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.8667 (p0) cc_final: 0.8323 (t0) REVERT: A 416 LYS cc_start: 0.9051 (ttmm) cc_final: 0.8703 (tmmt) REVERT: B 344 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8386 (mm-40) REVERT: B 416 LYS cc_start: 0.9064 (ttmm) cc_final: 0.8707 (tmmt) REVERT: B 446 HIS cc_start: 0.8092 (t-90) cc_final: 0.7817 (t-90) REVERT: C 89 THR cc_start: 0.9071 (p) cc_final: 0.8670 (t) REVERT: C 344 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8436 (mm-40) REVERT: C 416 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8699 (tmmt) REVERT: D 52 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7804 (ptt) REVERT: D 123 MET cc_start: 0.7867 (ppp) cc_final: 0.7105 (ppp) REVERT: D 318 ASP cc_start: 0.9124 (m-30) cc_final: 0.8884 (m-30) REVERT: D 416 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8719 (tmmt) REVERT: E 89 THR cc_start: 0.9153 (p) cc_final: 0.8868 (t) REVERT: E 125 ASP cc_start: 0.8845 (m-30) cc_final: 0.8523 (OUTLIER) REVERT: E 174 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8534 (mtt) REVERT: E 300 GLN cc_start: 0.9178 (tp40) cc_final: 0.8883 (mt0) REVERT: E 416 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8693 (tmmt) outliers start: 30 outliers final: 17 residues processed: 204 average time/residue: 0.5512 time to fit residues: 124.0847 Evaluate side-chains 198 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 413 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 GLN D 260 GLN D 300 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.072005 restraints weight = 24313.050| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.61 r_work: 0.2735 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14830 Z= 0.113 Angle : 0.581 12.512 20040 Z= 0.282 Chirality : 0.041 0.172 2245 Planarity : 0.003 0.027 2470 Dihedral : 6.805 51.881 2312 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.67 % Allowed : 13.78 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1710 helix: 2.44 (0.20), residues: 600 sheet: 1.05 (0.27), residues: 355 loop : -0.31 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 93 TYR 0.022 0.001 TYR B 335 PHE 0.011 0.001 PHE A 133 TRP 0.008 0.001 TRP A 102 HIS 0.001 0.000 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00254 (14810) covalent geometry : angle 0.57616 (19990) SS BOND : bond 0.00335 ( 10) SS BOND : angle 1.06329 ( 20) hydrogen bonds : bond 0.03697 ( 715) hydrogen bonds : angle 4.52794 ( 2475) link_NAG-ASN : bond 0.00597 ( 10) link_NAG-ASN : angle 1.86991 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.8695 (p0) cc_final: 0.8319 (t0) REVERT: A 416 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8679 (tmmt) REVERT: A 446 HIS cc_start: 0.8135 (t-90) cc_final: 0.7920 (t-90) REVERT: B 344 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8426 (mm-40) REVERT: B 416 LYS cc_start: 0.9064 (ttmm) cc_final: 0.8708 (tmmt) REVERT: B 446 HIS cc_start: 0.8077 (t-90) cc_final: 0.7788 (t-90) REVERT: C 89 THR cc_start: 0.9054 (p) cc_final: 0.8649 (t) REVERT: C 344 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8443 (mm-40) REVERT: D 318 ASP cc_start: 0.9112 (m-30) cc_final: 0.8877 (m-30) REVERT: D 446 HIS cc_start: 0.8160 (t-90) cc_final: 0.7910 (t-90) REVERT: E 89 THR cc_start: 0.9129 (p) cc_final: 0.8830 (t) REVERT: E 125 ASP cc_start: 0.8906 (m-30) cc_final: 0.8527 (t0) REVERT: E 174 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8393 (mtt) REVERT: E 300 GLN cc_start: 0.9148 (tp40) cc_final: 0.8860 (mt0) outliers start: 26 outliers final: 15 residues processed: 204 average time/residue: 0.5492 time to fit residues: 123.7072 Evaluate side-chains 198 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 413 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 99 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 128 optimal weight: 0.0070 chunk 52 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 GLN D 300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.095371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.071934 restraints weight = 24337.287| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.60 r_work: 0.2730 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14830 Z= 0.126 Angle : 0.602 13.392 20040 Z= 0.289 Chirality : 0.042 0.212 2245 Planarity : 0.003 0.027 2470 Dihedral : 6.690 50.811 2310 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.60 % Allowed : 13.97 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1710 helix: 2.41 (0.20), residues: 600 sheet: 1.08 (0.27), residues: 355 loop : -0.31 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 93 TYR 0.021 0.001 TYR B 335 PHE 0.011 0.001 PHE B 133 TRP 0.008 0.001 TRP D 102 HIS 0.001 0.000 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00292 (14810) covalent geometry : angle 0.59830 (19990) SS BOND : bond 0.00340 ( 10) SS BOND : angle 1.10164 ( 20) hydrogen bonds : bond 0.03714 ( 715) hydrogen bonds : angle 4.52687 ( 2475) link_NAG-ASN : bond 0.00517 ( 10) link_NAG-ASN : angle 1.77062 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.9568 (tp) cc_final: 0.9346 (tm) REVERT: A 446 HIS cc_start: 0.8149 (t-90) cc_final: 0.7941 (t-90) REVERT: B 174 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8848 (mtt) REVERT: B 344 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8397 (mm-40) REVERT: B 416 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8709 (tmmt) REVERT: B 446 HIS cc_start: 0.8067 (t-90) cc_final: 0.7782 (t-90) REVERT: C 89 THR cc_start: 0.9042 (p) cc_final: 0.8633 (t) REVERT: C 344 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8400 (mm-40) REVERT: C 416 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8652 (tmmt) REVERT: D 89 THR cc_start: 0.9138 (p) cc_final: 0.8904 (p) REVERT: D 125 ASP cc_start: 0.8508 (p0) cc_final: 0.8214 (t0) REVERT: D 318 ASP cc_start: 0.9114 (m-30) cc_final: 0.8877 (m-30) REVERT: D 416 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8680 (tmmt) REVERT: D 446 HIS cc_start: 0.8162 (t-90) cc_final: 0.7944 (t-90) REVERT: E 89 THR cc_start: 0.9127 (p) cc_final: 0.8827 (t) REVERT: E 125 ASP cc_start: 0.8876 (m-30) cc_final: 0.8512 (t0) REVERT: E 174 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: E 300 GLN cc_start: 0.9142 (tp40) cc_final: 0.8840 (mt0) REVERT: E 416 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8702 (tmmt) outliers start: 25 outliers final: 11 residues processed: 199 average time/residue: 0.5280 time to fit residues: 116.0898 Evaluate side-chains 196 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 413 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 22 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 17 optimal weight: 0.0970 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 GLN D 149 ASN D 300 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.073105 restraints weight = 24429.458| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.61 r_work: 0.2754 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 14830 Z= 0.108 Angle : 0.614 15.337 20040 Z= 0.291 Chirality : 0.041 0.249 2245 Planarity : 0.003 0.027 2470 Dihedral : 6.489 48.409 2310 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.09 % Allowed : 15.00 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1710 helix: 2.31 (0.20), residues: 595 sheet: 1.14 (0.28), residues: 355 loop : -0.32 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 93 TYR 0.021 0.001 TYR B 335 PHE 0.011 0.001 PHE A 133 TRP 0.009 0.001 TRP A 102 HIS 0.001 0.000 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00246 (14810) covalent geometry : angle 0.61114 (19990) SS BOND : bond 0.00318 ( 10) SS BOND : angle 1.03549 ( 20) hydrogen bonds : bond 0.03614 ( 715) hydrogen bonds : angle 4.46849 ( 2475) link_NAG-ASN : bond 0.00560 ( 10) link_NAG-ASN : angle 1.60359 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8620 (tmmt) REVERT: A 446 HIS cc_start: 0.8181 (t-90) cc_final: 0.7940 (t-90) REVERT: B 174 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8819 (mtt) REVERT: B 344 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8432 (mm-40) REVERT: B 416 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8709 (tmmt) REVERT: B 446 HIS cc_start: 0.8069 (t-90) cc_final: 0.7786 (t-90) REVERT: C 89 THR cc_start: 0.9061 (p) cc_final: 0.8649 (t) REVERT: C 318 ASP cc_start: 0.9114 (m-30) cc_final: 0.8822 (m-30) REVERT: C 344 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8427 (mm-40) REVERT: C 416 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8646 (tmmt) REVERT: D 89 THR cc_start: 0.9158 (p) cc_final: 0.8930 (p) REVERT: D 125 ASP cc_start: 0.8528 (p0) cc_final: 0.8306 (t0) REVERT: D 318 ASP cc_start: 0.9082 (m-30) cc_final: 0.8853 (m-30) REVERT: E 89 THR cc_start: 0.9137 (p) cc_final: 0.8839 (t) REVERT: E 174 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: E 300 GLN cc_start: 0.9126 (tp40) cc_final: 0.8801 (mt0) outliers start: 17 outliers final: 10 residues processed: 202 average time/residue: 0.5246 time to fit residues: 117.2315 Evaluate side-chains 199 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 413 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 GLN D 300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.070180 restraints weight = 24617.352| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.69 r_work: 0.2688 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14830 Z= 0.193 Angle : 0.669 16.546 20040 Z= 0.318 Chirality : 0.043 0.248 2245 Planarity : 0.003 0.026 2470 Dihedral : 6.758 51.386 2310 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.90 % Allowed : 15.71 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1710 helix: 2.21 (0.20), residues: 605 sheet: 1.01 (0.27), residues: 355 loop : -0.36 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 93 TYR 0.021 0.001 TYR E 335 PHE 0.010 0.001 PHE A 133 TRP 0.009 0.001 TRP D 273 HIS 0.002 0.000 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00458 (14810) covalent geometry : angle 0.66429 (19990) SS BOND : bond 0.00394 ( 10) SS BOND : angle 1.25346 ( 20) hydrogen bonds : bond 0.03990 ( 715) hydrogen bonds : angle 4.70124 ( 2475) link_NAG-ASN : bond 0.00426 ( 10) link_NAG-ASN : angle 1.91347 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8448 (pmm) cc_final: 0.7532 (ppp) REVERT: A 416 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8653 (tmmt) REVERT: A 446 HIS cc_start: 0.8138 (t-90) cc_final: 0.7917 (t-90) REVERT: B 174 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8861 (mtt) REVERT: B 344 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8362 (mm-40) REVERT: B 416 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8709 (tmmt) REVERT: B 446 HIS cc_start: 0.8026 (t-90) cc_final: 0.7781 (t-90) REVERT: C 89 THR cc_start: 0.9006 (p) cc_final: 0.8592 (t) REVERT: C 125 ASP cc_start: 0.8889 (m-30) cc_final: 0.8567 (t0) REVERT: C 344 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8424 (mm-40) REVERT: C 416 LYS cc_start: 0.9106 (ttmm) cc_final: 0.8649 (tmmt) REVERT: D 125 ASP cc_start: 0.8566 (p0) cc_final: 0.8202 (OUTLIER) REVERT: D 318 ASP cc_start: 0.9125 (m-30) cc_final: 0.8865 (m-30) REVERT: D 446 HIS cc_start: 0.8179 (t-90) cc_final: 0.7975 (t-90) REVERT: E 89 THR cc_start: 0.9114 (p) cc_final: 0.8799 (t) REVERT: E 125 ASP cc_start: 0.8867 (m-30) cc_final: 0.8436 (t0) REVERT: E 174 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8513 (mtt) REVERT: E 300 GLN cc_start: 0.9155 (tp40) cc_final: 0.8834 (mt0) REVERT: E 416 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8674 (tmmt) outliers start: 14 outliers final: 10 residues processed: 198 average time/residue: 0.5583 time to fit residues: 122.0939 Evaluate side-chains 197 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 413 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 138 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 GLN D 300 GLN E 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.072611 restraints weight = 24265.843| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.62 r_work: 0.2742 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 14830 Z= 0.114 Angle : 0.641 16.037 20040 Z= 0.302 Chirality : 0.042 0.246 2245 Planarity : 0.003 0.027 2470 Dihedral : 6.482 48.388 2310 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.03 % Allowed : 15.71 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1710 helix: 2.27 (0.20), residues: 600 sheet: 1.07 (0.27), residues: 355 loop : -0.29 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 93 TYR 0.021 0.001 TYR B 335 PHE 0.011 0.001 PHE D 329 TRP 0.009 0.001 TRP D 102 HIS 0.001 0.000 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00268 (14810) covalent geometry : angle 0.63780 (19990) SS BOND : bond 0.00310 ( 10) SS BOND : angle 1.03048 ( 20) hydrogen bonds : bond 0.03694 ( 715) hydrogen bonds : angle 4.52678 ( 2475) link_NAG-ASN : bond 0.00569 ( 10) link_NAG-ASN : angle 1.58595 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4466.09 seconds wall clock time: 76 minutes 53.41 seconds (4613.41 seconds total)