Starting phenix.real_space_refine on Sat Sep 12 11:14:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vm2_21236/09_2026/6vm2_21236.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vm2_21236/09_2026/6vm2_21236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vm2_21236/09_2026/6vm2_21236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vm2_21236/09_2026/6vm2_21236.map" model { file = "/net/cci-nas-00/data/ceres_data/6vm2_21236/09_2026/6vm2_21236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vm2_21236/09_2026/6vm2_21236.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vm2_21236/09_2026/6vm2_21236.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vm2_21236/09_2026/6vm2_21236.cif" } resolution = 3.34 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 100 5.16 5 C 10020 2.51 5 N 2440 2.21 5 O 2790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15355 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "E" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "C" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "B" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "D" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'IVM': 1, 'PIO': 1} Inner-chain residues flagged as termini: ['pdbres="GLY A 804 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'IVM': 1, 'PIO': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'IVM': 1, 'PIO': 1} Inner-chain residues flagged as termini: ['pdbres="GLY C 804 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'IVM': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'IVM': 1, 'PIO': 1} Inner-chain residues flagged as termini: ['pdbres="GLY D 902 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.36, per 1000 atoms: 0.22 Number of scatterers: 15355 At special positions: 0 Unit cell: (99.64, 97.52, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 5 15.00 O 2790 8.00 N 2440 7.00 C 10020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 504.9 milliseconds 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3480 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 39.1% alpha, 37.2% 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 33 through 41 removed outlier: 3.888A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 41 " --> pdb=" O PHE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.508A pdb=" N LEU A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 265 removed outlier: 3.764A pdb=" N SER A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.799A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 340 Processing helix chain 'A' and resid 395 through 444 removed outlier: 3.704A pdb=" N ASP A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'E' and resid 33 through 41 removed outlier: 3.888A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU E 41 " --> pdb=" O PHE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.508A pdb=" N LEU E 248 " --> pdb=" O MET E 244 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 265 removed outlier: 3.764A pdb=" N SER E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 295 removed outlier: 3.798A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 340 Processing helix chain 'E' and resid 395 through 444 removed outlier: 3.704A pdb=" N ASP E 411 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E 416 " --> pdb=" O THR E 412 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'C' and resid 33 through 41 removed outlier: 3.889A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 41 " --> pdb=" O PHE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.508A pdb=" N LEU C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 265 removed outlier: 3.764A pdb=" N SER C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 295 removed outlier: 3.798A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 340 Processing helix chain 'C' and resid 395 through 444 removed outlier: 3.704A pdb=" N ASP C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'B' and resid 33 through 41 removed outlier: 3.888A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 41 " --> pdb=" O PHE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.508A pdb=" N LEU B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 265 removed outlier: 3.762A pdb=" N SER B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 295 removed outlier: 3.799A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 340 Processing helix chain 'B' and resid 395 through 444 removed outlier: 3.703A pdb=" N ASP B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'D' and resid 33 through 41 removed outlier: 3.889A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 41 " --> pdb=" O PHE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.508A pdb=" N LEU D 248 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 265 removed outlier: 3.763A pdb=" N SER D 255 " --> pdb=" O MET D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.798A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 340 Processing helix chain 'D' and resid 395 through 444 removed outlier: 3.704A pdb=" N ASP D 411 " --> pdb=" O ALA D 407 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 109 removed outlier: 4.425A pdb=" N LEU A 142 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.553A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.610A pdb=" N LYS A 224 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 108 through 109 removed outlier: 4.425A pdb=" N LEU E 142 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL E 61 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU E 193 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 127 through 132 removed outlier: 3.553A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE E 132 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ARG E 155 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AB1, first strand: chain 'E' and resid 224 through 225 removed outlier: 3.609A pdb=" N LYS E 224 " --> pdb=" O PHE E 231 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 109 removed outlier: 4.425A pdb=" N LEU C 142 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 132 removed outlier: 3.552A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB6, first strand: chain 'C' and resid 224 through 225 removed outlier: 3.609A pdb=" N LYS C 224 " --> pdb=" O PHE C 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 108 through 109 removed outlier: 4.424A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.553A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AC1, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AC2, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.610A pdb=" N LYS B 224 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 108 through 109 removed outlier: 4.425A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.552A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC6, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC7, first strand: chain 'D' and resid 224 through 225 removed outlier: 3.610A pdb=" N LYS D 224 " --> pdb=" O PHE D 231 " (cutoff:3.500A) 895 hydrogen bonds defined for protein. 2640 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: 2.68 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2370 1.30 - 1.43: 4291 1.43 - 1.56: 8834 1.56 - 1.69: 70 1.69 - 1.82: 175 Bond restraints: 15740 Sorted by residual: bond pdb=" C43 IVM E 901 " pdb=" C44 IVM E 901 " ideal model delta sigma weight residual 1.330 1.694 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" C43 IVM C 805 " pdb=" C44 IVM C 805 " ideal model delta sigma weight residual 1.330 1.693 -0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" C43 IVM B 602 " pdb=" C44 IVM B 602 " ideal model delta sigma weight residual 1.330 1.693 -0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" C43 IVM D 901 " pdb=" C44 IVM D 901 " ideal model delta sigma weight residual 1.330 1.693 -0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" C43 IVM A 805 " pdb=" C44 IVM A 805 " ideal model delta sigma weight residual 1.330 1.693 -0.363 2.00e-02 2.50e+03 3.29e+02 ... (remaining 15735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.92: 21197 7.92 - 15.85: 118 15.85 - 23.77: 5 23.77 - 31.70: 5 31.70 - 39.62: 15 Bond angle restraints: 21340 Sorted by residual: angle pdb=" C7 IVM E 901 " pdb=" C6 IVM E 901 " pdb=" O14 IVM E 901 " ideal model delta sigma weight residual 106.56 66.94 39.62 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C7 IVM B 602 " pdb=" C6 IVM B 602 " pdb=" O14 IVM B 602 " ideal model delta sigma weight residual 106.56 66.94 39.62 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C7 IVM C 805 " pdb=" C6 IVM C 805 " pdb=" O14 IVM C 805 " ideal model delta sigma weight residual 106.56 66.96 39.60 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C7 IVM D 901 " pdb=" C6 IVM D 901 " pdb=" O14 IVM D 901 " ideal model delta sigma weight residual 106.56 66.98 39.58 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C7 IVM A 805 " pdb=" C6 IVM A 805 " pdb=" O14 IVM A 805 " ideal model delta sigma weight residual 106.56 66.99 39.57 3.00e+00 1.11e-01 1.74e+02 ... (remaining 21335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 8555 21.79 - 43.59: 880 43.59 - 65.38: 225 65.38 - 87.17: 35 87.17 - 108.96: 115 Dihedral angle restraints: 9810 sinusoidal: 4455 harmonic: 5355 Sorted by residual: dihedral pdb=" C26 IVM D 901 " pdb=" C25 IVM D 901 " pdb=" O7 IVM D 901 " pdb=" C30 IVM D 901 " ideal model delta sinusoidal sigma weight residual 56.57 -52.39 108.96 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C26 IVM E 901 " pdb=" C25 IVM E 901 " pdb=" O7 IVM E 901 " pdb=" C30 IVM E 901 " ideal model delta sinusoidal sigma weight residual 56.57 -52.37 108.94 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C26 IVM C 805 " pdb=" C25 IVM C 805 " pdb=" O7 IVM C 805 " pdb=" C30 IVM C 805 " ideal model delta sinusoidal sigma weight residual 56.57 -52.37 108.94 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 9807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 2370 0.213 - 0.426: 60 0.426 - 0.639: 5 0.639 - 0.852: 0 0.852 - 1.065: 5 Chirality restraints: 2440 Sorted by residual: chirality pdb=" C6 IVM A 805 " pdb=" C11 IVM A 805 " pdb=" C7 IVM A 805 " pdb=" O14 IVM A 805 " both_signs ideal model delta sigma weight residual False 2.53 1.46 1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" C6 IVM B 602 " pdb=" C11 IVM B 602 " pdb=" C7 IVM B 602 " pdb=" O14 IVM B 602 " both_signs ideal model delta sigma weight residual False 2.53 1.47 1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" C6 IVM C 805 " pdb=" C11 IVM C 805 " pdb=" C7 IVM C 805 " pdb=" O14 IVM C 805 " both_signs ideal model delta sigma weight residual False 2.53 1.47 1.06 2.00e-01 2.50e+01 2.83e+01 ... (remaining 2437 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C37 IVM C 805 " 0.301 2.00e-02 2.50e+03 3.23e-01 1.31e+03 pdb=" C38 IVM C 805 " -0.593 2.00e-02 2.50e+03 pdb=" C39 IVM C 805 " 0.279 2.00e-02 2.50e+03 pdb=" C40 IVM C 805 " -0.024 2.00e-02 2.50e+03 pdb=" C47 IVM C 805 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM A 805 " 0.301 2.00e-02 2.50e+03 3.23e-01 1.31e+03 pdb=" C38 IVM A 805 " -0.593 2.00e-02 2.50e+03 pdb=" C39 IVM A 805 " 0.280 2.00e-02 2.50e+03 pdb=" C40 IVM A 805 " -0.024 2.00e-02 2.50e+03 pdb=" C47 IVM A 805 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM D 901 " 0.301 2.00e-02 2.50e+03 3.23e-01 1.31e+03 pdb=" C38 IVM D 901 " -0.593 2.00e-02 2.50e+03 pdb=" C39 IVM D 901 " 0.279 2.00e-02 2.50e+03 pdb=" C40 IVM D 901 " -0.024 2.00e-02 2.50e+03 pdb=" C47 IVM D 901 " 0.037 2.00e-02 2.50e+03 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4374 2.82 - 3.34: 13523 3.34 - 3.86: 24987 3.86 - 4.38: 28151 4.38 - 4.90: 49652 Nonbonded interactions: 120687 Sorted by model distance: nonbonded pdb=" O GLY C 43 " pdb=" OG SER C 46 " model vdw 2.295 3.040 nonbonded pdb=" O GLY A 43 " pdb=" OG SER A 46 " model vdw 2.296 3.040 nonbonded pdb=" O GLY B 43 " pdb=" OG SER B 46 " model vdw 2.297 3.040 nonbonded pdb=" O GLY E 43 " pdb=" OG SER E 46 " model vdw 2.297 3.040 nonbonded pdb=" O GLY D 43 " pdb=" OG SER D 46 " model vdw 2.297 3.040 ... (remaining 120682 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 31 through 444) selection = (chain 'B' and resid 31 through 444) selection = (chain 'C' and resid 31 through 444) selection = (chain 'D' and resid 31 through 444) selection = (chain 'E' and resid 31 through 444) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.790 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 : 0.017 0.364 15745 Z= 0.783 Angle : 1.863 39.624 21355 Z= 0.805 Chirality : 0.096 1.065 2440 Planarity : 0.025 0.323 2605 Dihedral : 22.187 108.964 6330 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 14.68 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.33 (0.16), residues: 1790 helix: -1.66 (0.15), residues: 665 sheet: -0.13 (0.23), residues: 375 loop : -2.09 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 89 TYR 0.040 0.004 TYR C 325 PHE 0.023 0.003 PHE C 169 TRP 0.028 0.004 TRP E 118 HIS 0.026 0.005 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.01670 / 0.78 (15740) covalent geometry : angle 1.86323 / 0.80 (21340) hydrogen bonds : bond 0.15257 / 9.90 ( 750) hydrogen bonds : angle 7.35817 / 4.99 ( 2640) link_BETA1-4 : bond 0.00383 / 0.22 ( 5) link_BETA1-4 : angle 2.06038 / 1.07 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 115 ASP cc_start: 0.7696 (p0) cc_final: 0.7495 (p0) REVERT: C 263 TRP cc_start: 0.8877 (m-10) cc_final: 0.8497 (m-10) REVERT: B 262 SER cc_start: 0.9489 (m) cc_final: 0.9243 (p) REVERT: D 221 TYR cc_start: 0.8273 (p90) cc_final: 0.8053 (p90) REVERT: D 262 SER cc_start: 0.9440 (m) cc_final: 0.9176 (p) REVERT: D 263 TRP cc_start: 0.8930 (m-10) cc_final: 0.8628 (m-10) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1623 time to fit residues: 43.7126 Evaluate side-chains 134 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0970 chunk 149 optimal weight: 0.8980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 133 HIS A 168 ASN A 201 GLN A 225 HIS A 269 ASN A 290 GLN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 133 HIS E 168 ASN E 201 GLN E 225 HIS E 269 ASN E 290 GLN ** E 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 133 HIS C 168 ASN C 201 GLN C 225 HIS C 269 ASN C 290 GLN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 133 HIS B 168 ASN B 201 GLN B 225 HIS B 269 ASN B 290 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 133 HIS D 168 ASN D 201 GLN D 225 HIS D 290 GLN ** D 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.060189 restraints weight = 42430.767| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.67 r_work: 0.2784 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15745 Z= 0.155 Angle : 0.812 9.817 21355 Z= 0.378 Chirality : 0.051 0.309 2440 Planarity : 0.004 0.029 2605 Dihedral : 15.178 83.214 2725 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.77 % Allowed : 16.33 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.18), residues: 1790 helix: 0.88 (0.18), residues: 645 sheet: 0.32 (0.24), residues: 395 loop : -1.78 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 220 TYR 0.025 0.002 TYR C 221 PHE 0.015 0.001 PHE C 319 TRP 0.014 0.001 TRP A 118 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (15740) covalent geometry : angle 0.81176 / 0.38 (21340) hydrogen bonds : bond 0.05133 / 3.25 ( 750) hydrogen bonds : angle 5.11022 / 3.50 ( 2640) link_BETA1-4 : bond 0.00762 / 0.51 ( 5) link_BETA1-4 : angle 0.99021 / 0.62 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.9021 (mpp) cc_final: 0.8734 (mpp) REVERT: A 80 MET cc_start: 0.9447 (mtt) cc_final: 0.9164 (mmm) REVERT: A 113 MET cc_start: 0.8802 (ppp) cc_final: 0.8458 (ppp) REVERT: E 113 MET cc_start: 0.8834 (ppp) cc_final: 0.8531 (ppp) REVERT: E 221 TYR cc_start: 0.8530 (p90) cc_final: 0.8328 (p90) REVERT: E 263 TRP cc_start: 0.8765 (m-10) cc_final: 0.8445 (m-10) REVERT: C 42 MET cc_start: 0.9067 (mpp) cc_final: 0.8822 (mpp) REVERT: C 113 MET cc_start: 0.8935 (ppp) cc_final: 0.8586 (ppp) REVERT: C 187 MET cc_start: 0.8840 (mmm) cc_final: 0.8613 (tpt) REVERT: C 235 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8724 (pt0) REVERT: C 244 MET cc_start: 0.8910 (tpp) cc_final: 0.8688 (tpp) REVERT: C 263 TRP cc_start: 0.8927 (m-10) cc_final: 0.8596 (m-10) REVERT: B 113 MET cc_start: 0.9006 (ppp) cc_final: 0.8751 (ppp) REVERT: B 235 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8797 (pt0) REVERT: D 113 MET cc_start: 0.8880 (ppp) cc_final: 0.8518 (ppp) REVERT: D 187 MET cc_start: 0.8612 (tpt) cc_final: 0.7963 (tpp) REVERT: D 221 TYR cc_start: 0.8527 (p90) cc_final: 0.8205 (p90) REVERT: D 235 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: D 263 TRP cc_start: 0.8936 (m-10) cc_final: 0.8648 (m-10) REVERT: D 411 ASP cc_start: 0.9091 (m-30) cc_final: 0.8865 (t0) outliers start: 29 outliers final: 3 residues processed: 179 average time/residue: 0.1210 time to fit residues: 33.0111 Evaluate side-chains 135 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 264 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 53 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.078993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060708 restraints weight = 43184.390| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.56 r_work: 0.2787 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15745 Z= 0.134 Angle : 0.652 7.154 21355 Z= 0.320 Chirality : 0.045 0.197 2440 Planarity : 0.004 0.025 2605 Dihedral : 10.071 68.123 2725 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.83 % Allowed : 17.06 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.19), residues: 1790 helix: 1.92 (0.19), residues: 645 sheet: 0.60 (0.25), residues: 390 loop : -1.53 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.022 0.002 TYR B 221 PHE 0.018 0.001 PHE C 319 TRP 0.008 0.001 TRP A 118 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15740) covalent geometry : angle 0.65199 / 0.32 (21340) hydrogen bonds : bond 0.04290 / 2.71 ( 750) hydrogen bonds : angle 4.56554 / 3.13 ( 2640) link_BETA1-4 : bond 0.00912 / 0.52 ( 5) link_BETA1-4 : angle 1.11744 / 0.72 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.9516 (mtt) cc_final: 0.9290 (mtt) REVERT: A 113 MET cc_start: 0.8848 (ppp) cc_final: 0.8455 (ppp) REVERT: E 113 MET cc_start: 0.8946 (ppp) cc_final: 0.8526 (ppp) REVERT: E 187 MET cc_start: 0.8860 (mmt) cc_final: 0.8476 (mmm) REVERT: E 399 MET cc_start: 0.8098 (mmm) cc_final: 0.7554 (mmp) REVERT: C 113 MET cc_start: 0.8982 (ppp) cc_final: 0.8514 (ppp) REVERT: C 187 MET cc_start: 0.8977 (mmm) cc_final: 0.8549 (mmm) REVERT: C 235 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8733 (pt0) REVERT: C 244 MET cc_start: 0.8983 (tpp) cc_final: 0.8532 (tpp) REVERT: B 80 MET cc_start: 0.9491 (OUTLIER) cc_final: 0.9056 (mmm) REVERT: B 113 MET cc_start: 0.9009 (ppp) cc_final: 0.8665 (ppp) REVERT: B 187 MET cc_start: 0.8773 (tpt) cc_final: 0.8197 (tpt) REVERT: B 399 MET cc_start: 0.8266 (mmm) cc_final: 0.7956 (mmp) REVERT: D 113 MET cc_start: 0.8872 (ppp) cc_final: 0.8446 (ppp) REVERT: D 187 MET cc_start: 0.8724 (tpt) cc_final: 0.8065 (tpp) REVERT: D 221 TYR cc_start: 0.8498 (p90) cc_final: 0.8139 (p90) REVERT: D 263 TRP cc_start: 0.9051 (m-10) cc_final: 0.8679 (m-10) REVERT: D 411 ASP cc_start: 0.9139 (m-30) cc_final: 0.8906 (t70) outliers start: 30 outliers final: 11 residues processed: 165 average time/residue: 0.1207 time to fit residues: 30.5984 Evaluate side-chains 144 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 431 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 31 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 152 optimal weight: 0.0000 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN A 269 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN E 329 ASN ** E 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN C 149 ASN C 269 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** D 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.057380 restraints weight = 43682.760| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.55 r_work: 0.2699 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15745 Z= 0.212 Angle : 0.671 8.418 21355 Z= 0.333 Chirality : 0.046 0.208 2440 Planarity : 0.004 0.031 2605 Dihedral : 8.141 53.179 2725 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.63 % Allowed : 15.84 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.19), residues: 1790 helix: 2.49 (0.19), residues: 645 sheet: 0.79 (0.25), residues: 390 loop : -1.30 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 437 TYR 0.025 0.002 TYR B 221 PHE 0.020 0.001 PHE C 319 TRP 0.008 0.001 TRP B 92 HIS 0.005 0.002 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (15740) covalent geometry : angle 0.67060 / 0.33 (21340) hydrogen bonds : bond 0.04446 / 2.80 ( 750) hydrogen bonds : angle 4.55571 / 3.14 ( 2640) link_BETA1-4 : bond 0.00581 / 0.34 ( 5) link_BETA1-4 : angle 1.13730 / 0.73 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.9502 (mtt) cc_final: 0.9290 (mtt) REVERT: A 113 MET cc_start: 0.8885 (ppp) cc_final: 0.8407 (ppp) REVERT: A 399 MET cc_start: 0.8351 (mmm) cc_final: 0.8002 (mmp) REVERT: E 113 MET cc_start: 0.8940 (ppp) cc_final: 0.8532 (ppp) REVERT: E 187 MET cc_start: 0.8874 (mmt) cc_final: 0.8417 (mmm) REVERT: E 262 SER cc_start: 0.9651 (m) cc_final: 0.9306 (p) REVERT: E 399 MET cc_start: 0.8289 (mmm) cc_final: 0.7774 (mmp) REVERT: C 113 MET cc_start: 0.8979 (ppp) cc_final: 0.8521 (ppp) REVERT: C 187 MET cc_start: 0.9007 (mmm) cc_final: 0.8784 (mmm) REVERT: B 80 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.9071 (mmm) REVERT: B 399 MET cc_start: 0.8345 (mmm) cc_final: 0.8060 (mmp) REVERT: D 113 MET cc_start: 0.8889 (ppp) cc_final: 0.8467 (ppp) REVERT: D 187 MET cc_start: 0.8826 (tpt) cc_final: 0.8117 (tpp) REVERT: D 221 TYR cc_start: 0.8441 (p90) cc_final: 0.8083 (p90) REVERT: D 263 TRP cc_start: 0.9140 (m-10) cc_final: 0.8886 (m-10) outliers start: 43 outliers final: 14 residues processed: 165 average time/residue: 0.1184 time to fit residues: 30.2596 Evaluate side-chains 141 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 431 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 24 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 31 optimal weight: 0.0050 chunk 138 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.078121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.060637 restraints weight = 43341.665| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.32 r_work: 0.2809 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15745 Z= 0.119 Angle : 0.610 7.886 21355 Z= 0.298 Chirality : 0.044 0.204 2440 Planarity : 0.003 0.032 2605 Dihedral : 7.407 54.063 2725 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.96 % Allowed : 16.15 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.19), residues: 1790 helix: 2.62 (0.19), residues: 670 sheet: 0.98 (0.25), residues: 390 loop : -1.23 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 220 TYR 0.022 0.002 TYR E 221 PHE 0.020 0.001 PHE E 319 TRP 0.007 0.001 TRP C 263 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (15740) covalent geometry : angle 0.60887 / 0.30 (21340) hydrogen bonds : bond 0.03970 / 2.51 ( 750) hydrogen bonds : angle 4.25808 / 2.92 ( 2640) link_BETA1-4 : bond 0.00837 / 0.49 ( 5) link_BETA1-4 : angle 1.22714 / 0.79 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8887 (ppp) cc_final: 0.8476 (ppp) REVERT: A 263 TRP cc_start: 0.9021 (m-10) cc_final: 0.8596 (m-10) REVERT: A 399 MET cc_start: 0.8240 (mmm) cc_final: 0.7852 (mmp) REVERT: E 113 MET cc_start: 0.8958 (ppp) cc_final: 0.8590 (ppp) REVERT: E 187 MET cc_start: 0.8870 (mmt) cc_final: 0.8622 (mmm) REVERT: E 262 SER cc_start: 0.9662 (m) cc_final: 0.9307 (p) REVERT: E 399 MET cc_start: 0.8206 (mmm) cc_final: 0.7746 (mmp) REVERT: C 113 MET cc_start: 0.8934 (ppp) cc_final: 0.8495 (ppp) REVERT: C 244 MET cc_start: 0.8718 (tpp) cc_final: 0.8407 (tpp) REVERT: B 80 MET cc_start: 0.9581 (OUTLIER) cc_final: 0.9182 (mmm) REVERT: B 113 MET cc_start: 0.8991 (ppp) cc_final: 0.8660 (ppp) REVERT: B 187 MET cc_start: 0.8850 (tpt) cc_final: 0.8409 (tpt) REVERT: B 399 MET cc_start: 0.8285 (mmm) cc_final: 0.7927 (mmp) REVERT: D 113 MET cc_start: 0.8902 (ppp) cc_final: 0.8505 (ppp) REVERT: D 187 MET cc_start: 0.8893 (tpt) cc_final: 0.8297 (tpp) REVERT: D 221 TYR cc_start: 0.8330 (p90) cc_final: 0.8054 (p90) REVERT: D 399 MET cc_start: 0.8181 (mmt) cc_final: 0.7820 (mmp) REVERT: D 411 ASP cc_start: 0.9164 (m-30) cc_final: 0.8947 (t0) outliers start: 32 outliers final: 20 residues processed: 156 average time/residue: 0.1211 time to fit residues: 29.0194 Evaluate side-chains 151 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 333 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 44 optimal weight: 0.0770 chunk 78 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 overall best weight: 2.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN E 269 ASN E 329 ASN C 139 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN D 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.076435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057691 restraints weight = 45085.300| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.51 r_work: 0.2715 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15745 Z= 0.238 Angle : 0.664 8.566 21355 Z= 0.332 Chirality : 0.045 0.209 2440 Planarity : 0.004 0.059 2605 Dihedral : 7.263 53.349 2725 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.12 % Allowed : 15.66 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.19), residues: 1790 helix: 2.61 (0.19), residues: 670 sheet: 1.16 (0.26), residues: 365 loop : -1.22 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 437 TYR 0.024 0.002 TYR C 325 PHE 0.020 0.002 PHE A 319 TRP 0.008 0.001 TRP C 118 HIS 0.005 0.002 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (15740) covalent geometry : angle 0.66393 / 0.33 (21340) hydrogen bonds : bond 0.04431 / 2.77 ( 750) hydrogen bonds : angle 4.52633 / 3.12 ( 2640) link_BETA1-4 : bond 0.00733 / 0.42 ( 5) link_BETA1-4 : angle 1.19854 / 0.77 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8963 (ppp) cc_final: 0.8657 (ppp) REVERT: A 399 MET cc_start: 0.8304 (mmm) cc_final: 0.7913 (mmp) REVERT: E 113 MET cc_start: 0.8987 (ppp) cc_final: 0.8566 (ppp) REVERT: E 187 MET cc_start: 0.8955 (mmt) cc_final: 0.8737 (mmm) REVERT: E 262 SER cc_start: 0.9671 (m) cc_final: 0.9351 (p) REVERT: E 399 MET cc_start: 0.8244 (mmm) cc_final: 0.7862 (mmp) REVERT: E 420 LEU cc_start: 0.9353 (tp) cc_final: 0.9131 (tt) REVERT: C 113 MET cc_start: 0.8947 (ppp) cc_final: 0.8506 (ppp) REVERT: C 244 MET cc_start: 0.8761 (tpp) cc_final: 0.8281 (tpp) REVERT: B 80 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.9210 (mmm) REVERT: B 113 MET cc_start: 0.9040 (ppp) cc_final: 0.8636 (ppp) REVERT: B 399 MET cc_start: 0.8452 (mmm) cc_final: 0.8071 (mmp) REVERT: D 113 MET cc_start: 0.8898 (ppp) cc_final: 0.8464 (ppp) REVERT: D 187 MET cc_start: 0.8995 (tpt) cc_final: 0.8420 (tpp) REVERT: D 221 TYR cc_start: 0.8401 (p90) cc_final: 0.8107 (p90) REVERT: D 399 MET cc_start: 0.8491 (mmt) cc_final: 0.8095 (mmp) outliers start: 51 outliers final: 27 residues processed: 164 average time/residue: 0.1156 time to fit residues: 29.5426 Evaluate side-chains 151 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 431 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 124 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 135 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058097 restraints weight = 43383.118| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.29 r_work: 0.2765 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15745 Z= 0.141 Angle : 0.620 8.167 21355 Z= 0.305 Chirality : 0.044 0.216 2440 Planarity : 0.003 0.031 2605 Dihedral : 7.025 53.431 2725 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.51 % Allowed : 16.51 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.19), residues: 1790 helix: 2.69 (0.19), residues: 670 sheet: 1.20 (0.26), residues: 365 loop : -1.25 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 437 TYR 0.024 0.002 TYR B 221 PHE 0.020 0.001 PHE A 319 TRP 0.008 0.001 TRP D 263 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15740) covalent geometry : angle 0.61880 / 0.30 (21340) hydrogen bonds : bond 0.04119 / 2.59 ( 750) hydrogen bonds : angle 4.31936 / 2.97 ( 2640) link_BETA1-4 : bond 0.00734 / 0.43 ( 5) link_BETA1-4 : angle 1.27510 / 0.82 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8950 (ppp) cc_final: 0.8572 (ppp) REVERT: A 399 MET cc_start: 0.8318 (mmm) cc_final: 0.7925 (mmp) REVERT: E 113 MET cc_start: 0.8936 (ppp) cc_final: 0.8605 (ppp) REVERT: E 262 SER cc_start: 0.9667 (m) cc_final: 0.9335 (p) REVERT: E 399 MET cc_start: 0.8205 (mmm) cc_final: 0.7841 (mmp) REVERT: E 420 LEU cc_start: 0.9315 (tp) cc_final: 0.9109 (tt) REVERT: C 113 MET cc_start: 0.8901 (ppp) cc_final: 0.8509 (ppp) REVERT: C 244 MET cc_start: 0.8629 (tpp) cc_final: 0.8322 (tpp) REVERT: B 80 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.9203 (mmm) REVERT: B 113 MET cc_start: 0.8972 (ppp) cc_final: 0.8612 (ppp) REVERT: B 187 MET cc_start: 0.8907 (tpt) cc_final: 0.8455 (tpt) REVERT: B 399 MET cc_start: 0.8443 (mmm) cc_final: 0.8047 (mmp) REVERT: D 113 MET cc_start: 0.8903 (ppp) cc_final: 0.8525 (ppp) REVERT: D 187 MET cc_start: 0.8980 (tpt) cc_final: 0.8626 (tpt) REVERT: D 221 TYR cc_start: 0.8312 (p90) cc_final: 0.8014 (p90) REVERT: D 399 MET cc_start: 0.8476 (mmt) cc_final: 0.8072 (mmp) outliers start: 41 outliers final: 24 residues processed: 154 average time/residue: 0.1085 time to fit residues: 26.1790 Evaluate side-chains 153 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 333 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 127 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.075970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058378 restraints weight = 43960.737| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.34 r_work: 0.2779 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15745 Z= 0.130 Angle : 0.617 9.260 21355 Z= 0.301 Chirality : 0.044 0.199 2440 Planarity : 0.003 0.033 2605 Dihedral : 6.812 54.051 2725 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.90 % Allowed : 17.25 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.19), residues: 1790 helix: 2.74 (0.19), residues: 670 sheet: 1.25 (0.26), residues: 365 loop : -1.24 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 437 TYR 0.022 0.002 TYR E 221 PHE 0.018 0.001 PHE D 319 TRP 0.009 0.001 TRP D 263 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15740) covalent geometry : angle 0.61623 / 0.30 (21340) hydrogen bonds : bond 0.03965 / 2.50 ( 750) hydrogen bonds : angle 4.19387 / 2.88 ( 2640) link_BETA1-4 : bond 0.00728 / 0.42 ( 5) link_BETA1-4 : angle 1.28667 / 0.83 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8906 (ppp) cc_final: 0.8647 (ppp) REVERT: A 399 MET cc_start: 0.8330 (mmm) cc_final: 0.7937 (mmp) REVERT: E 113 MET cc_start: 0.9016 (ppp) cc_final: 0.8709 (ppp) REVERT: E 262 SER cc_start: 0.9648 (m) cc_final: 0.9300 (p) REVERT: E 399 MET cc_start: 0.8251 (mmm) cc_final: 0.7910 (mmp) REVERT: E 420 LEU cc_start: 0.9309 (tp) cc_final: 0.9098 (tt) REVERT: C 113 MET cc_start: 0.8874 (ppp) cc_final: 0.8515 (ppp) REVERT: C 187 MET cc_start: 0.9086 (tpt) cc_final: 0.8870 (mmm) REVERT: C 244 MET cc_start: 0.8687 (tpp) cc_final: 0.8375 (tpp) REVERT: B 80 MET cc_start: 0.9603 (OUTLIER) cc_final: 0.9211 (mmm) REVERT: B 113 MET cc_start: 0.8956 (ppp) cc_final: 0.8609 (ppp) REVERT: B 187 MET cc_start: 0.8897 (tpt) cc_final: 0.8441 (tpt) REVERT: B 221 TYR cc_start: 0.8555 (p90) cc_final: 0.8310 (p90) REVERT: B 399 MET cc_start: 0.8452 (mmm) cc_final: 0.8060 (mmp) REVERT: D 113 MET cc_start: 0.8884 (ppp) cc_final: 0.8533 (ppp) REVERT: D 187 MET cc_start: 0.8951 (tpt) cc_final: 0.8566 (tpt) REVERT: D 221 TYR cc_start: 0.8278 (p90) cc_final: 0.8002 (p90) REVERT: D 300 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8978 (mttm) REVERT: D 399 MET cc_start: 0.8487 (mmt) cc_final: 0.8094 (mmp) REVERT: D 411 ASP cc_start: 0.9182 (m-30) cc_final: 0.8951 (t0) outliers start: 31 outliers final: 27 residues processed: 148 average time/residue: 0.1184 time to fit residues: 27.2087 Evaluate side-chains 159 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 333 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 128 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.075976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.058486 restraints weight = 43485.466| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.35 r_work: 0.2779 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15745 Z= 0.132 Angle : 0.613 9.067 21355 Z= 0.299 Chirality : 0.044 0.221 2440 Planarity : 0.003 0.031 2605 Dihedral : 6.654 54.820 2725 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.26 % Allowed : 17.00 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.20), residues: 1790 helix: 2.72 (0.19), residues: 670 sheet: 0.93 (0.25), residues: 395 loop : -1.29 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 437 TYR 0.022 0.002 TYR E 221 PHE 0.018 0.001 PHE D 319 TRP 0.009 0.001 TRP D 263 HIS 0.004 0.001 HIS D 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (15740) covalent geometry : angle 0.61268 / 0.30 (21340) hydrogen bonds : bond 0.03888 / 2.45 ( 750) hydrogen bonds : angle 4.13192 / 2.84 ( 2640) link_BETA1-4 : bond 0.00708 / 0.41 ( 5) link_BETA1-4 : angle 1.31725 / 0.85 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8966 (ppp) cc_final: 0.8649 (ppp) REVERT: A 399 MET cc_start: 0.8347 (mmm) cc_final: 0.7957 (mmp) REVERT: E 113 MET cc_start: 0.8983 (ppp) cc_final: 0.8702 (ppp) REVERT: E 262 SER cc_start: 0.9649 (m) cc_final: 0.9293 (p) REVERT: E 311 MET cc_start: 0.9467 (mmm) cc_final: 0.9204 (mmt) REVERT: E 399 MET cc_start: 0.8375 (mmm) cc_final: 0.8015 (mmp) REVERT: E 420 LEU cc_start: 0.9326 (tp) cc_final: 0.9109 (tt) REVERT: C 113 MET cc_start: 0.8855 (ppp) cc_final: 0.8518 (ppp) REVERT: C 187 MET cc_start: 0.9094 (tpt) cc_final: 0.8888 (mmm) REVERT: C 244 MET cc_start: 0.8703 (tpp) cc_final: 0.8399 (tpp) REVERT: B 80 MET cc_start: 0.9613 (OUTLIER) cc_final: 0.9212 (mmm) REVERT: B 113 MET cc_start: 0.8950 (ppp) cc_final: 0.8627 (ppp) REVERT: B 187 MET cc_start: 0.8905 (tpt) cc_final: 0.8469 (tpt) REVERT: B 221 TYR cc_start: 0.8533 (p90) cc_final: 0.8274 (p90) REVERT: B 399 MET cc_start: 0.8471 (mmm) cc_final: 0.8083 (mmp) REVERT: D 113 MET cc_start: 0.8879 (ppp) cc_final: 0.8544 (ppp) REVERT: D 187 MET cc_start: 0.8990 (tpt) cc_final: 0.8626 (tpt) REVERT: D 221 TYR cc_start: 0.8356 (p90) cc_final: 0.8078 (p90) REVERT: D 263 TRP cc_start: 0.9189 (m-10) cc_final: 0.8919 (m-10) REVERT: D 300 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9004 (mttm) REVERT: D 399 MET cc_start: 0.8481 (mmt) cc_final: 0.8087 (mmp) REVERT: D 411 ASP cc_start: 0.9173 (m-30) cc_final: 0.8947 (t0) outliers start: 37 outliers final: 31 residues processed: 155 average time/residue: 0.1182 time to fit residues: 28.3849 Evaluate side-chains 166 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 333 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 109 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 chunk 131 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 chunk 152 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN E 70 ASN C 70 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.077038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.059493 restraints weight = 43599.895| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.38 r_work: 0.2810 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15745 Z= 0.112 Angle : 0.609 10.254 21355 Z= 0.294 Chirality : 0.044 0.284 2440 Planarity : 0.003 0.033 2605 Dihedral : 6.535 59.698 2725 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.90 % Allowed : 17.80 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.20), residues: 1790 helix: 2.74 (0.18), residues: 670 sheet: 0.98 (0.25), residues: 395 loop : -1.25 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 437 TYR 0.021 0.002 TYR E 221 PHE 0.017 0.001 PHE D 319 TRP 0.009 0.001 TRP C 263 HIS 0.004 0.001 HIS D 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (15740) covalent geometry : angle 0.60813 / 0.29 (21340) hydrogen bonds : bond 0.03724 / 2.38 ( 750) hydrogen bonds : angle 3.99028 / 2.73 ( 2640) link_BETA1-4 : bond 0.00696 / 0.40 ( 5) link_BETA1-4 : angle 1.30534 / 0.84 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9029 (ppp) cc_final: 0.8631 (ppp) REVERT: A 263 TRP cc_start: 0.9052 (m-10) cc_final: 0.8629 (m-10) REVERT: A 399 MET cc_start: 0.8343 (mmm) cc_final: 0.7954 (mmp) REVERT: E 113 MET cc_start: 0.8975 (ppp) cc_final: 0.8681 (ppp) REVERT: E 187 MET cc_start: 0.8743 (mmm) cc_final: 0.8486 (mmm) REVERT: E 311 MET cc_start: 0.9479 (mmm) cc_final: 0.9221 (mmt) REVERT: E 399 MET cc_start: 0.8328 (mmm) cc_final: 0.7962 (mmp) REVERT: E 420 LEU cc_start: 0.9319 (tp) cc_final: 0.9106 (tt) REVERT: C 113 MET cc_start: 0.8848 (ppp) cc_final: 0.8529 (ppp) REVERT: C 187 MET cc_start: 0.9095 (tpt) cc_final: 0.8871 (mmm) REVERT: C 244 MET cc_start: 0.8735 (tpp) cc_final: 0.8396 (tpp) REVERT: B 80 MET cc_start: 0.9570 (OUTLIER) cc_final: 0.9152 (mmm) REVERT: B 113 MET cc_start: 0.8929 (ppp) cc_final: 0.8594 (ppp) REVERT: B 187 MET cc_start: 0.8906 (tpt) cc_final: 0.8435 (tpt) REVERT: B 221 TYR cc_start: 0.8526 (p90) cc_final: 0.8268 (p90) REVERT: B 399 MET cc_start: 0.8482 (mmm) cc_final: 0.8093 (mmp) REVERT: D 113 MET cc_start: 0.8863 (ppp) cc_final: 0.8598 (ppp) REVERT: D 187 MET cc_start: 0.8948 (tpt) cc_final: 0.8547 (tpt) REVERT: D 221 TYR cc_start: 0.8356 (p90) cc_final: 0.8082 (p90) REVERT: D 300 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.8970 (mttm) REVERT: D 399 MET cc_start: 0.8482 (mmt) cc_final: 0.8091 (mmp) REVERT: D 411 ASP cc_start: 0.9129 (m-30) cc_final: 0.8911 (t0) outliers start: 31 outliers final: 28 residues processed: 155 average time/residue: 0.1154 time to fit residues: 27.7536 Evaluate side-chains 165 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 333 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.077714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.060518 restraints weight = 43220.010| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.30 r_work: 0.2815 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15745 Z= 0.113 Angle : 0.607 9.100 21355 Z= 0.293 Chirality : 0.044 0.286 2440 Planarity : 0.003 0.032 2605 Dihedral : 6.381 58.868 2725 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.96 % Allowed : 17.68 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.20), residues: 1790 helix: 2.74 (0.19), residues: 670 sheet: 1.04 (0.25), residues: 395 loop : -1.21 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 437 TYR 0.020 0.002 TYR E 221 PHE 0.016 0.001 PHE D 319 TRP 0.010 0.001 TRP C 263 HIS 0.004 0.001 HIS D 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15740) covalent geometry : angle 0.60589 / 0.29 (21340) hydrogen bonds : bond 0.03677 / 2.34 ( 750) hydrogen bonds : angle 3.95683 / 2.71 ( 2640) link_BETA1-4 : bond 0.00735 / 0.43 ( 5) link_BETA1-4 : angle 1.28665 / 0.83 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.62 seconds wall clock time: 49 minutes 55.02 seconds (2995.02 seconds total)