Starting phenix.real_space_refine on Sat Jul 4 09:13:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4o_70109/07_2026/9o4o_70109.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4o_70109/07_2026/9o4o_70109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o4o_70109/07_2026/9o4o_70109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4o_70109/07_2026/9o4o_70109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o4o_70109/07_2026/9o4o_70109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4o_70109/07_2026/9o4o_70109.map" } resolution = 2.53 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 9 9.91 5 S 104 5.16 5 C 11976 2.51 5 N 3276 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19201 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "A" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "I" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "B" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "C" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "K" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "D" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.39, per 1000 atoms: 0.23 Number of scatterers: 19201 At special positions: 0 Unit cell: (158.775, 158.775, 91.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 9 19.99 S 104 16.00 O 3836 8.00 N 3276 7.00 C 11976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.02 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 336 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 3 " " NAG O 1 " - " FUC O 3 " " NAG P 1 " - " FUC P 3 " NAG-ASN " NAG A 501 " - " ASN A 88 " " NAG A 502 " - " ASN A 234 " " NAG B 501 " - " ASN B 88 " " NAG B 502 " - " ASN B 234 " " NAG C 501 " - " ASN C 88 " " NAG C 502 " - " ASN C 234 " " NAG D 501 " - " ASN D 88 " " NAG D 502 " - " ASN D 234 " " NAG M 1 " - " ASN A 146 " " NAG N 1 " - " ASN B 146 " " NAG O 1 " - " ASN C 146 " " NAG P 1 " - " ASN D 146 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 880.3 milliseconds 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 52 sheets defined 3.2% alpha, 39.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 104 through 112 removed outlier: 4.438A pdb=" N LYS A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 412A through 414 Processing helix chain 'B' and resid 104 through 112 removed outlier: 4.438A pdb=" N LYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 412A through 414 Processing helix chain 'C' and resid 104 through 112 removed outlier: 4.438A pdb=" N LYS C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 412A through 414 Processing helix chain 'D' and resid 104 through 112 removed outlier: 4.438A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 412A through 414 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.502A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.731A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.731A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AA5, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.788A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL L 97 " --> pdb=" O ALA L 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.315A pdb=" N SER A 445 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS A 102 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.781A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER A 160 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE A 173 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.548A pdb=" N SER A 179 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 213 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR A 207 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AB2, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.522A pdb=" N LYS A 264 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 279 through 283 Processing sheet with id=AB4, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.423A pdb=" N ASN A 372 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY A 399 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 392 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.502A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.731A pdb=" N THR E 110 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.731A pdb=" N THR E 110 " --> pdb=" O GLU E 10 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 9 through 13 Processing sheet with id=AB9, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'I' and resid 45 through 48 removed outlier: 6.788A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL I 97 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY I 95B" --> pdb=" O ASP I 92 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.315A pdb=" N SER B 445 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS B 102 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.781A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER B 160 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE B 173 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.548A pdb=" N SER B 179 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP B 213 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR B 207 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AC6, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.522A pdb=" N LYS B 264 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 279 through 283 Processing sheet with id=AC8, first strand: chain 'B' and resid 353 through 356 removed outlier: 6.423A pdb=" N ASN B 372 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY B 399 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 392 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.502A pdb=" N THR F 77 " --> pdb=" O ASP F 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.731A pdb=" N THR F 110 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.731A pdb=" N THR F 110 " --> pdb=" O GLU F 10 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 9 through 13 Processing sheet with id=AD4, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AD5, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.788A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL J 97 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY J 95B" --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.315A pdb=" N SER C 445 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS C 102 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.781A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER C 160 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE C 173 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.548A pdb=" N SER C 179 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 213 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR C 207 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AE1, first strand: chain 'C' and resid 223 through 224 removed outlier: 3.522A pdb=" N LYS C 264 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 279 through 283 Processing sheet with id=AE3, first strand: chain 'C' and resid 353 through 356 removed outlier: 6.423A pdb=" N ASN C 372 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY C 399 " --> pdb=" O ASN C 372 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 392 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.502A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.731A pdb=" N THR G 110 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.731A pdb=" N THR G 110 " --> pdb=" O GLU G 10 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 9 through 13 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.788A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL K 97 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY K 95B" --> pdb=" O ASP K 92 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.315A pdb=" N SER D 445 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS D 102 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.781A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER D 160 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE D 173 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.548A pdb=" N SER D 179 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP D 213 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR D 207 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 223 through 224 Processing sheet with id=AF5, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.522A pdb=" N LYS D 264 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 279 through 283 Processing sheet with id=AF7, first strand: chain 'D' and resid 353 through 356 removed outlier: 6.423A pdb=" N ASN D 372 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY D 399 " --> pdb=" O ASN D 372 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 392 " --> pdb=" O TRP D 378 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1620 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: 3.86 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6272 1.35 - 1.47: 5192 1.47 - 1.59: 8076 1.59 - 1.72: 0 1.72 - 1.84: 128 Bond restraints: 19668 Sorted by residual: bond pdb=" C1 NAG B 502 " pdb=" O5 NAG B 502 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1 NAG D 502 " pdb=" O5 NAG D 502 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1 NAG A 502 " pdb=" O5 NAG A 502 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1 NAG C 502 " pdb=" O5 NAG C 502 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C LEU A 464 " pdb=" N PRO A 465 " ideal model delta sigma weight residual 1.334 1.378 -0.045 2.34e-02 1.83e+03 3.62e+00 ... (remaining 19663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 25084 1.46 - 2.92: 1360 2.92 - 4.39: 232 4.39 - 5.85: 76 5.85 - 7.31: 16 Bond angle restraints: 26768 Sorted by residual: angle pdb=" C LEU K 95 " pdb=" N ASN K 95A" pdb=" CA ASN K 95A" ideal model delta sigma weight residual 122.82 127.67 -4.85 1.42e+00 4.96e-01 1.17e+01 angle pdb=" C LEU L 95 " pdb=" N ASN L 95A" pdb=" CA ASN L 95A" ideal model delta sigma weight residual 122.82 127.67 -4.85 1.42e+00 4.96e-01 1.17e+01 angle pdb=" C LEU I 95 " pdb=" N ASN I 95A" pdb=" CA ASN I 95A" ideal model delta sigma weight residual 122.82 127.67 -4.85 1.42e+00 4.96e-01 1.17e+01 angle pdb=" C LEU J 95 " pdb=" N ASN J 95A" pdb=" CA ASN J 95A" ideal model delta sigma weight residual 122.82 127.67 -4.85 1.42e+00 4.96e-01 1.17e+01 angle pdb=" N GLY D 339 " pdb=" CA GLY D 339 " pdb=" C GLY D 339 " ideal model delta sigma weight residual 112.34 106.43 5.91 2.04e+00 2.40e-01 8.39e+00 ... (remaining 26763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 10756 16.65 - 33.30: 848 33.30 - 49.95: 136 49.95 - 66.60: 40 66.60 - 83.26: 28 Dihedral angle restraints: 11808 sinusoidal: 4808 harmonic: 7000 Sorted by residual: dihedral pdb=" CA THR H 94 " pdb=" C THR H 94 " pdb=" N ASP H 95 " pdb=" CA ASP H 95 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA THR G 94 " pdb=" C THR G 94 " pdb=" N ASP G 95 " pdb=" CA ASP G 95 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA THR F 94 " pdb=" C THR F 94 " pdb=" N ASP F 95 " pdb=" CA ASP F 95 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 11805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1788 0.041 - 0.081: 792 0.081 - 0.122: 244 0.122 - 0.162: 100 0.162 - 0.203: 12 Chirality restraints: 2936 Sorted by residual: chirality pdb=" CA LEU B 464 " pdb=" N LEU B 464 " pdb=" C LEU B 464 " pdb=" CB LEU B 464 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA LEU A 464 " pdb=" N LEU A 464 " pdb=" C LEU A 464 " pdb=" CB LEU A 464 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA LEU D 464 " pdb=" N LEU D 464 " pdb=" C LEU D 464 " pdb=" CB LEU D 464 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2933 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 66 " 0.264 9.50e-02 1.11e+02 1.18e-01 9.54e+00 pdb=" NE ARG H 66 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG H 66 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG H 66 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG H 66 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 66 " -0.264 9.50e-02 1.11e+02 1.18e-01 9.54e+00 pdb=" NE ARG G 66 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG G 66 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG G 66 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G 66 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 66 " 0.264 9.50e-02 1.11e+02 1.18e-01 9.54e+00 pdb=" NE ARG E 66 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG E 66 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG E 66 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 66 " 0.004 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2844 2.76 - 3.30: 18496 3.30 - 3.83: 33828 3.83 - 4.37: 42652 4.37 - 4.90: 73212 Nonbonded interactions: 171032 Sorted by model distance: nonbonded pdb=" O GLY C 297 " pdb="CA CA C 503 " model vdw 2.230 3.250 nonbonded pdb=" O GLY B 297 " pdb="CA CA B 503 " model vdw 2.230 3.250 nonbonded pdb=" O GLY D 297 " pdb="CA CA D 503 " model vdw 2.230 3.250 nonbonded pdb=" O GLY A 297 " pdb="CA CA A 503 " model vdw 2.230 3.250 nonbonded pdb=" O ASN A 347 " pdb="CA CA A 503 " model vdw 2.233 3.250 ... (remaining 171027 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 83 through 504) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 10.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 18.640 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: 0.010 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 0.005 0.067 19728 Z= 0.206 Angle : 0.801 7.309 26908 Z= 0.412 Chirality : 0.053 0.203 2936 Planarity : 0.008 0.118 3468 Dihedral : 12.884 83.255 7248 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.57 % Allowed : 1.34 % Favored : 98.09 % 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: 0.20 (0.16), residues: 2468 helix: -1.68 (0.86), residues: 24 sheet: 0.74 (0.17), residues: 872 loop : -0.15 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 66 TYR 0.011 0.002 TYR I 49 PHE 0.040 0.003 PHE F 63 TRP 0.014 0.002 TRP A 295 HIS 0.006 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (19668) covalent geometry : angle 0.79188 / 0.41 (26768) SS BOND : bond 0.00366 / 0.24 ( 40) SS BOND : angle 1.98704 / 1.32 ( 80) hydrogen bonds : bond 0.21239 / 14.26 ( 616) hydrogen bonds : angle 9.98564 / 7.26 ( 1620) link_BETA1-4 : bond 0.00351 / 0.18 ( 4) link_BETA1-4 : angle 0.49530 / 0.26 ( 12) link_BETA1-6 : bond 0.00362 / 0.18 ( 4) link_BETA1-6 : angle 0.89053 / 0.51 ( 12) link_NAG-ASN : bond 0.00291 / 0.19 ( 12) link_NAG-ASN : angle 1.99762 / 1.05 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 356 time to evaluate : 0.766 Fit side-chains REVERT: L 27 ASN cc_start: 0.7690 (m110) cc_final: 0.7183 (m110) REVERT: L 35 TRP cc_start: 0.8103 (m100) cc_final: 0.7533 (m100) REVERT: L 73 LEU cc_start: 0.7928 (tt) cc_final: 0.7447 (tp) REVERT: I 27 ASN cc_start: 0.7690 (m110) cc_final: 0.7185 (m110) REVERT: I 35 TRP cc_start: 0.8103 (m100) cc_final: 0.7533 (m100) REVERT: I 73 LEU cc_start: 0.7928 (tt) cc_final: 0.7447 (tp) REVERT: J 27 ASN cc_start: 0.7688 (m110) cc_final: 0.7184 (m110) REVERT: J 35 TRP cc_start: 0.8101 (m100) cc_final: 0.7532 (m100) REVERT: J 73 LEU cc_start: 0.7925 (tt) cc_final: 0.7447 (tp) REVERT: K 27 ASN cc_start: 0.7692 (m110) cc_final: 0.7185 (m110) REVERT: K 35 TRP cc_start: 0.8103 (m100) cc_final: 0.7532 (m100) REVERT: K 73 LEU cc_start: 0.7925 (tt) cc_final: 0.7447 (tp) outliers start: 12 outliers final: 0 residues processed: 364 average time/residue: 0.6060 time to fit residues: 249.7813 Evaluate side-chains 280 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 0.0670 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0030 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.0470 overall best weight: 0.2626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN L 34 ASN A 184 HIS A 294 ASN ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 450 ASN E 105 GLN I 34 ASN B 184 HIS B 294 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 450 ASN F 105 GLN J 34 ASN C 184 HIS C 294 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN C 450 ASN G 105 GLN K 34 ASN D 184 HIS D 294 ASN ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN D 450 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.120728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.083893 restraints weight = 28293.032| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.16 r_work: 0.2906 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19728 Z= 0.119 Angle : 0.608 8.890 26908 Z= 0.324 Chirality : 0.049 0.260 2936 Planarity : 0.004 0.040 3468 Dihedral : 6.909 53.407 3076 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.15 % Allowed : 9.37 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.42 (0.16), residues: 2468 helix: -1.31 (0.74), residues: 24 sheet: 0.87 (0.16), residues: 920 loop : -0.01 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 54 TYR 0.012 0.001 TYR D 252 PHE 0.013 0.002 PHE A 410 TRP 0.014 0.001 TRP A 295 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (19668) covalent geometry : angle 0.59943 / 0.32 (26768) SS BOND : bond 0.00250 / 0.16 ( 40) SS BOND : angle 1.29678 / 0.81 ( 80) hydrogen bonds : bond 0.03984 / 2.70 ( 616) hydrogen bonds : angle 7.35937 / 5.34 ( 1620) link_BETA1-4 : bond 0.00714 / 0.36 ( 4) link_BETA1-4 : angle 1.19583 / 0.68 ( 12) link_BETA1-6 : bond 0.00271 / 0.14 ( 4) link_BETA1-6 : angle 1.32540 / 0.74 ( 12) link_NAG-ASN : bond 0.00270 / 0.17 ( 12) link_NAG-ASN : angle 2.15305 / 1.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 300 time to evaluate : 0.779 Fit side-chains REVERT: H 105 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.9000 (pm20) REVERT: L 27 ASN cc_start: 0.7756 (m110) cc_final: 0.7129 (m110) REVERT: L 35 TRP cc_start: 0.8241 (m100) cc_final: 0.7769 (m100) REVERT: L 73 LEU cc_start: 0.7837 (tt) cc_final: 0.7505 (tt) REVERT: A 259 LYS cc_start: 0.9333 (mttp) cc_final: 0.9121 (mttm) REVERT: E 105 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8997 (pm20) REVERT: I 27 ASN cc_start: 0.7759 (m110) cc_final: 0.7130 (m110) REVERT: I 35 TRP cc_start: 0.8243 (m100) cc_final: 0.7774 (m100) REVERT: I 73 LEU cc_start: 0.7831 (tt) cc_final: 0.7501 (tt) REVERT: B 259 LYS cc_start: 0.9340 (mttp) cc_final: 0.9130 (mttm) REVERT: F 105 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8996 (pm20) REVERT: J 27 ASN cc_start: 0.7760 (m110) cc_final: 0.7132 (m110) REVERT: J 35 TRP cc_start: 0.8243 (m100) cc_final: 0.7775 (m100) REVERT: J 73 LEU cc_start: 0.7830 (tt) cc_final: 0.7503 (tt) REVERT: C 259 LYS cc_start: 0.9337 (mttp) cc_final: 0.9124 (mttm) REVERT: G 105 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.9000 (pm20) REVERT: K 27 ASN cc_start: 0.7762 (m110) cc_final: 0.7135 (m110) REVERT: K 35 TRP cc_start: 0.8240 (m100) cc_final: 0.7769 (m100) REVERT: K 73 LEU cc_start: 0.7828 (tt) cc_final: 0.7497 (tt) REVERT: D 259 LYS cc_start: 0.9328 (mttp) cc_final: 0.9112 (mttm) outliers start: 24 outliers final: 12 residues processed: 316 average time/residue: 0.6112 time to fit residues: 218.8196 Evaluate side-chains 272 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 256 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 336 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 159 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 177 optimal weight: 0.0050 chunk 215 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 226 GLN A 313 GLN A 450 ASN I 34 ASN B 226 GLN B 313 GLN B 450 ASN J 34 ASN C 226 GLN C 313 GLN C 450 ASN K 34 ASN D 226 GLN D 313 GLN D 450 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.115294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.076968 restraints weight = 28343.006| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.19 r_work: 0.2781 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19728 Z= 0.248 Angle : 0.665 15.381 26908 Z= 0.342 Chirality : 0.050 0.203 2936 Planarity : 0.005 0.040 3468 Dihedral : 6.500 50.434 3076 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.29 % Allowed : 10.33 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.21 (0.16), residues: 2468 helix: -1.03 (0.77), residues: 24 sheet: 0.67 (0.16), residues: 924 loop : -0.12 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 61 TYR 0.012 0.001 TYR C 252 PHE 0.018 0.002 PHE C 121 TRP 0.016 0.002 TRP B 97 HIS 0.008 0.002 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.25 (19668) covalent geometry : angle 0.65529 / 0.34 (26768) SS BOND : bond 0.00884 / 0.50 ( 40) SS BOND : angle 1.52791 / 0.98 ( 80) hydrogen bonds : bond 0.03825 / 2.63 ( 616) hydrogen bonds : angle 6.86719 / 4.98 ( 1620) link_BETA1-4 : bond 0.00093 / 0.05 ( 4) link_BETA1-4 : angle 1.23134 / 0.69 ( 12) link_BETA1-6 : bond 0.00308 / 0.15 ( 4) link_BETA1-6 : angle 1.60233 / 0.88 ( 12) link_NAG-ASN : bond 0.00390 / 0.27 ( 12) link_NAG-ASN : angle 2.15922 / 1.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 260 time to evaluate : 0.717 Fit side-chains REVERT: L 27 ASN cc_start: 0.7806 (m110) cc_final: 0.7483 (m110) REVERT: L 35 TRP cc_start: 0.8208 (m100) cc_final: 0.7680 (m100) REVERT: L 73 LEU cc_start: 0.7810 (tt) cc_final: 0.7545 (tt) REVERT: A 219 ARG cc_start: 0.8439 (mmt90) cc_final: 0.8229 (mmt90) REVERT: I 27 ASN cc_start: 0.7816 (m110) cc_final: 0.7494 (m110) REVERT: I 35 TRP cc_start: 0.8211 (m100) cc_final: 0.7689 (m100) REVERT: I 73 LEU cc_start: 0.7805 (tt) cc_final: 0.7540 (tt) REVERT: B 219 ARG cc_start: 0.8447 (mmt90) cc_final: 0.8238 (mmt90) REVERT: J 27 ASN cc_start: 0.7819 (m110) cc_final: 0.7498 (m110) REVERT: J 35 TRP cc_start: 0.8210 (m100) cc_final: 0.7689 (m100) REVERT: J 73 LEU cc_start: 0.7804 (tt) cc_final: 0.7539 (tt) REVERT: C 219 ARG cc_start: 0.8449 (mmt90) cc_final: 0.8240 (mmt90) REVERT: K 27 ASN cc_start: 0.7806 (m110) cc_final: 0.7485 (m110) REVERT: K 35 TRP cc_start: 0.8210 (m100) cc_final: 0.7684 (m100) REVERT: K 73 LEU cc_start: 0.7804 (tt) cc_final: 0.7539 (tt) REVERT: D 219 ARG cc_start: 0.8446 (mmt90) cc_final: 0.8238 (mmt90) outliers start: 48 outliers final: 24 residues processed: 280 average time/residue: 0.5645 time to fit residues: 179.1538 Evaluate side-chains 268 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 342 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 12 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN A 313 GLN E 105 GLN B 313 GLN F 105 GLN C 313 GLN G 105 GLN D 313 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.074480 restraints weight = 28759.098| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.19 r_work: 0.2754 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19728 Z= 0.253 Angle : 0.654 15.117 26908 Z= 0.337 Chirality : 0.050 0.192 2936 Planarity : 0.004 0.040 3468 Dihedral : 6.235 47.672 3076 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.87 % Allowed : 10.90 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.03 (0.16), residues: 2468 helix: -1.20 (0.73), residues: 24 sheet: 0.48 (0.16), residues: 924 loop : -0.20 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 12 TYR 0.012 0.001 TYR B 252 PHE 0.020 0.002 PHE B 121 TRP 0.017 0.002 TRP E 47 HIS 0.009 0.002 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (19668) covalent geometry : angle 0.64386 / 0.33 (26768) SS BOND : bond 0.00407 / 0.28 ( 40) SS BOND : angle 1.51478 / 0.98 ( 80) hydrogen bonds : bond 0.03626 / 2.50 ( 616) hydrogen bonds : angle 6.64266 / 4.80 ( 1620) link_BETA1-4 : bond 0.00365 / 0.18 ( 4) link_BETA1-4 : angle 1.28917 / 0.73 ( 12) link_BETA1-6 : bond 0.00042 / 0.02 ( 4) link_BETA1-6 : angle 1.49696 / 0.83 ( 12) link_NAG-ASN : bond 0.00424 / 0.29 ( 12) link_NAG-ASN : angle 2.25335 / 1.36 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 268 time to evaluate : 0.753 Fit side-chains REVERT: H 6 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: H 39 GLN cc_start: 0.7993 (tt0) cc_final: 0.7739 (tt0) REVERT: L 27 ASN cc_start: 0.7820 (m110) cc_final: 0.7494 (m110) REVERT: L 35 TRP cc_start: 0.8242 (m100) cc_final: 0.7718 (m100) REVERT: E 6 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: E 39 GLN cc_start: 0.7996 (tt0) cc_final: 0.7740 (tt0) REVERT: I 27 ASN cc_start: 0.7825 (m110) cc_final: 0.7498 (m110) REVERT: I 35 TRP cc_start: 0.8243 (m100) cc_final: 0.7720 (m100) REVERT: F 39 GLN cc_start: 0.7983 (tt0) cc_final: 0.7725 (tt0) REVERT: J 27 ASN cc_start: 0.7830 (m110) cc_final: 0.7505 (m110) REVERT: J 35 TRP cc_start: 0.8242 (m100) cc_final: 0.7721 (m100) REVERT: G 39 GLN cc_start: 0.7985 (tt0) cc_final: 0.7728 (tt0) REVERT: K 27 ASN cc_start: 0.7820 (m110) cc_final: 0.7493 (m110) REVERT: K 35 TRP cc_start: 0.8243 (m100) cc_final: 0.7718 (m100) outliers start: 60 outliers final: 32 residues processed: 308 average time/residue: 0.6285 time to fit residues: 218.1980 Evaluate side-chains 302 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 342 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 184 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 223 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN A 313 GLN A 450 ASN E 105 GLN B 313 GLN B 450 ASN F 105 GLN C 313 GLN C 450 ASN G 105 GLN D 313 GLN D 450 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.114236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.075984 restraints weight = 28087.035| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.17 r_work: 0.2763 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19728 Z= 0.211 Angle : 0.631 14.621 26908 Z= 0.325 Chirality : 0.048 0.190 2936 Planarity : 0.004 0.039 3468 Dihedral : 5.933 43.510 3076 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.49 % Allowed : 12.43 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.09 (0.16), residues: 2468 helix: -1.19 (0.75), residues: 24 sheet: 0.47 (0.16), residues: 884 loop : -0.10 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 54 TYR 0.013 0.001 TYR D 252 PHE 0.024 0.002 PHE H 63 TRP 0.015 0.001 TRP C 178 HIS 0.009 0.002 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (19668) covalent geometry : angle 0.62158 / 0.32 (26768) SS BOND : bond 0.00360 / 0.24 ( 40) SS BOND : angle 1.38703 / 0.89 ( 80) hydrogen bonds : bond 0.03412 / 2.35 ( 616) hydrogen bonds : angle 6.44557 / 4.66 ( 1620) link_BETA1-4 : bond 0.00403 / 0.20 ( 4) link_BETA1-4 : angle 1.22649 / 0.69 ( 12) link_BETA1-6 : bond 0.00059 / 0.03 ( 4) link_BETA1-6 : angle 1.50998 / 0.84 ( 12) link_NAG-ASN : bond 0.00406 / 0.28 ( 12) link_NAG-ASN : angle 2.23045 / 1.35 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 0.791 Fit side-chains REVERT: H 38 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7948 (ptp90) REVERT: H 72 ASP cc_start: 0.7911 (t70) cc_final: 0.7605 (p0) REVERT: L 35 TRP cc_start: 0.8120 (m100) cc_final: 0.7593 (m100) REVERT: A 230 CYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8890 (p) REVERT: E 38 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7947 (ptp90) REVERT: E 72 ASP cc_start: 0.7908 (t70) cc_final: 0.7603 (p0) REVERT: I 35 TRP cc_start: 0.8124 (m100) cc_final: 0.7597 (m100) REVERT: B 230 CYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8887 (p) REVERT: F 38 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7941 (ptp90) REVERT: F 72 ASP cc_start: 0.7909 (t70) cc_final: 0.7604 (p0) REVERT: J 35 TRP cc_start: 0.8122 (m100) cc_final: 0.7597 (m100) REVERT: C 230 CYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8891 (p) REVERT: G 38 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7947 (ptp90) REVERT: G 72 ASP cc_start: 0.7909 (t70) cc_final: 0.7603 (p0) REVERT: K 35 TRP cc_start: 0.8127 (m100) cc_final: 0.7599 (m100) REVERT: D 230 CYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8887 (p) outliers start: 52 outliers final: 28 residues processed: 288 average time/residue: 0.5878 time to fit residues: 191.9004 Evaluate side-chains 288 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 342 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 71 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 124 optimal weight: 0.0770 chunk 2 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN H 105 GLN A 313 GLN E 39 GLN E 105 GLN B 313 GLN F 39 GLN F 105 GLN C 313 GLN G 39 GLN G 105 GLN D 313 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.077443 restraints weight = 27867.110| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.11 r_work: 0.2787 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19728 Z= 0.160 Angle : 0.608 13.568 26908 Z= 0.314 Chirality : 0.047 0.180 2936 Planarity : 0.004 0.039 3468 Dihedral : 5.643 38.644 3076 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.39 % Allowed : 13.48 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.01 (0.16), residues: 2468 helix: -1.14 (0.78), residues: 24 sheet: 0.48 (0.16), residues: 892 loop : -0.21 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.012 0.001 TYR C 252 PHE 0.026 0.002 PHE H 63 TRP 0.014 0.001 TRP E 47 HIS 0.006 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (19668) covalent geometry : angle 0.59896 / 0.31 (26768) SS BOND : bond 0.00353 / 0.22 ( 40) SS BOND : angle 1.28654 / 0.82 ( 80) hydrogen bonds : bond 0.03208 / 2.21 ( 616) hydrogen bonds : angle 6.35264 / 4.60 ( 1620) link_BETA1-4 : bond 0.00465 / 0.23 ( 4) link_BETA1-4 : angle 1.13293 / 0.64 ( 12) link_BETA1-6 : bond 0.00144 / 0.07 ( 4) link_BETA1-6 : angle 1.46490 / 0.82 ( 12) link_NAG-ASN : bond 0.00333 / 0.23 ( 12) link_NAG-ASN : angle 2.13767 / 1.29 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 276 time to evaluate : 0.795 Fit side-chains REVERT: H 38 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7957 (ptp90) REVERT: H 72 ASP cc_start: 0.7963 (t70) cc_final: 0.7629 (p0) REVERT: L 35 TRP cc_start: 0.8112 (m100) cc_final: 0.7563 (m100) REVERT: A 230 CYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8929 (p) REVERT: E 38 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7952 (ptp90) REVERT: E 72 ASP cc_start: 0.7961 (t70) cc_final: 0.7627 (p0) REVERT: I 35 TRP cc_start: 0.8113 (m100) cc_final: 0.7564 (m100) REVERT: B 230 CYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8921 (p) REVERT: F 23 LYS cc_start: 0.8474 (tppt) cc_final: 0.8243 (tppt) REVERT: F 38 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7957 (ptp90) REVERT: F 72 ASP cc_start: 0.7959 (t70) cc_final: 0.7626 (p0) REVERT: J 35 TRP cc_start: 0.8112 (m100) cc_final: 0.7563 (m100) REVERT: C 230 CYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8922 (p) REVERT: G 23 LYS cc_start: 0.8475 (tppt) cc_final: 0.8243 (tppt) REVERT: G 38 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7952 (ptp90) REVERT: G 72 ASP cc_start: 0.7965 (t70) cc_final: 0.7631 (p0) REVERT: K 35 TRP cc_start: 0.8114 (m100) cc_final: 0.7566 (m100) REVERT: D 230 CYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8915 (p) outliers start: 50 outliers final: 26 residues processed: 294 average time/residue: 0.6133 time to fit residues: 203.8139 Evaluate side-chains 286 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 342 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 198 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 143 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN L 34 ASN A 226 GLN A 313 GLN E 105 GLN I 34 ASN B 226 GLN B 313 GLN F 105 GLN J 34 ASN C 226 GLN C 313 GLN G 105 GLN K 34 ASN D 226 GLN D 313 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.076429 restraints weight = 29694.049| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.32 r_work: 0.2822 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19728 Z= 0.250 Angle : 0.646 15.715 26908 Z= 0.331 Chirality : 0.049 0.194 2936 Planarity : 0.004 0.039 3468 Dihedral : 5.700 35.195 3076 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.10 % Allowed : 13.96 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.03 (0.16), residues: 2468 helix: -1.38 (0.73), residues: 24 sheet: 0.44 (0.16), residues: 896 loop : -0.22 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 219 TYR 0.012 0.001 TYR C 252 PHE 0.023 0.002 PHE E 63 TRP 0.018 0.001 TRP E 47 HIS 0.009 0.002 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 (19668) covalent geometry : angle 0.63634 / 0.33 (26768) SS BOND : bond 0.00404 / 0.27 ( 40) SS BOND : angle 1.43459 / 0.93 ( 80) hydrogen bonds : bond 0.03469 / 2.40 ( 616) hydrogen bonds : angle 6.41122 / 4.63 ( 1620) link_BETA1-4 : bond 0.00277 / 0.14 ( 4) link_BETA1-4 : angle 1.08209 / 0.61 ( 12) link_BETA1-6 : bond 0.00003 / 0.00 ( 4) link_BETA1-6 : angle 1.54777 / 0.86 ( 12) link_NAG-ASN : bond 0.00457 / 0.31 ( 12) link_NAG-ASN : angle 2.23210 / 1.34 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.769 Fit side-chains REVERT: H 23 LYS cc_start: 0.8324 (tppt) cc_final: 0.8109 (tppt) REVERT: H 38 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7916 (ptp90) REVERT: H 62 GLU cc_start: 0.8464 (pt0) cc_final: 0.7892 (pt0) REVERT: L 35 TRP cc_start: 0.8099 (m100) cc_final: 0.7627 (m100) REVERT: E 23 LYS cc_start: 0.8325 (tppt) cc_final: 0.8111 (tppt) REVERT: E 38 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7906 (ptp90) REVERT: E 62 GLU cc_start: 0.8466 (pt0) cc_final: 0.7892 (pt0) REVERT: I 35 TRP cc_start: 0.8093 (m100) cc_final: 0.7625 (m100) REVERT: F 38 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7912 (ptp90) REVERT: F 62 GLU cc_start: 0.8473 (pt0) cc_final: 0.7898 (pt0) REVERT: J 35 TRP cc_start: 0.8102 (m100) cc_final: 0.7630 (m100) REVERT: G 38 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7921 (ptp90) REVERT: G 62 GLU cc_start: 0.8469 (pt0) cc_final: 0.7895 (pt0) REVERT: K 35 TRP cc_start: 0.8103 (m100) cc_final: 0.7630 (m100) outliers start: 44 outliers final: 26 residues processed: 264 average time/residue: 0.5495 time to fit residues: 164.6471 Evaluate side-chains 262 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 342 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 40 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN A 313 GLN E 105 GLN B 313 GLN F 105 GLN C 313 GLN G 105 GLN D 313 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.076996 restraints weight = 29606.968| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.26 r_work: 0.2845 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19728 Z= 0.236 Angle : 0.666 15.288 26908 Z= 0.338 Chirality : 0.049 0.193 2936 Planarity : 0.004 0.039 3468 Dihedral : 5.652 35.468 3076 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.63 % Allowed : 14.63 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.04 (0.16), residues: 2468 helix: -1.34 (0.75), residues: 24 sheet: 0.43 (0.16), residues: 892 loop : -0.23 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 219 TYR 0.013 0.001 TYR H 91 PHE 0.026 0.002 PHE G 63 TRP 0.026 0.002 TRP F 47 HIS 0.009 0.002 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (19668) covalent geometry : angle 0.65528 / 0.33 (26768) SS BOND : bond 0.00417 / 0.28 ( 40) SS BOND : angle 1.67868 / 1.08 ( 80) hydrogen bonds : bond 0.03412 / 2.36 ( 616) hydrogen bonds : angle 6.38615 / 4.62 ( 1620) link_BETA1-4 : bond 0.00273 / 0.14 ( 4) link_BETA1-4 : angle 1.07280 / 0.61 ( 12) link_BETA1-6 : bond 0.00018 / 0.01 ( 4) link_BETA1-6 : angle 1.53289 / 0.86 ( 12) link_NAG-ASN : bond 0.00459 / 0.31 ( 12) link_NAG-ASN : angle 2.23695 / 1.34 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 0.678 Fit side-chains REVERT: H 38 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7888 (ptp90) REVERT: H 62 GLU cc_start: 0.8499 (pt0) cc_final: 0.7948 (pt0) REVERT: H 72 ASP cc_start: 0.7870 (t70) cc_final: 0.7544 (p0) REVERT: L 35 TRP cc_start: 0.8128 (m100) cc_final: 0.7645 (m100) REVERT: E 38 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7878 (ptp90) REVERT: E 62 GLU cc_start: 0.8499 (pt0) cc_final: 0.7944 (pt0) REVERT: E 72 ASP cc_start: 0.7881 (t70) cc_final: 0.7556 (p0) REVERT: I 35 TRP cc_start: 0.8128 (m100) cc_final: 0.7646 (m100) REVERT: F 38 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7903 (ptp90) REVERT: F 62 GLU cc_start: 0.8505 (pt0) cc_final: 0.7951 (pt0) REVERT: F 72 ASP cc_start: 0.7866 (t70) cc_final: 0.7515 (p0) REVERT: J 35 TRP cc_start: 0.8128 (m100) cc_final: 0.7646 (m100) REVERT: G 38 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7911 (ptp90) REVERT: G 62 GLU cc_start: 0.8504 (pt0) cc_final: 0.7953 (pt0) REVERT: G 72 ASP cc_start: 0.7876 (t70) cc_final: 0.7523 (p0) REVERT: K 35 TRP cc_start: 0.8129 (m100) cc_final: 0.7646 (m100) outliers start: 34 outliers final: 24 residues processed: 258 average time/residue: 0.5388 time to fit residues: 156.9420 Evaluate side-chains 268 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 342 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 116 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN A 313 GLN E 105 GLN B 313 GLN F 105 GLN C 313 GLN G 105 GLN D 313 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.079104 restraints weight = 29355.465| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.30 r_work: 0.2896 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19728 Z= 0.142 Angle : 0.615 13.089 26908 Z= 0.315 Chirality : 0.047 0.174 2936 Planarity : 0.004 0.039 3468 Dihedral : 5.290 34.281 3076 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.53 % Allowed : 14.53 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.06 (0.17), residues: 2468 helix: -1.16 (0.84), residues: 24 sheet: 0.49 (0.17), residues: 892 loop : -0.15 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 61 TYR 0.012 0.001 TYR C 252 PHE 0.024 0.002 PHE E 63 TRP 0.028 0.001 TRP E 47 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (19668) covalent geometry : angle 0.60525 / 0.31 (26768) SS BOND : bond 0.00309 / 0.20 ( 40) SS BOND : angle 1.45663 / 0.92 ( 80) hydrogen bonds : bond 0.03106 / 2.14 ( 616) hydrogen bonds : angle 6.16998 / 4.46 ( 1620) link_BETA1-4 : bond 0.00362 / 0.18 ( 4) link_BETA1-4 : angle 0.99507 / 0.56 ( 12) link_BETA1-6 : bond 0.00252 / 0.13 ( 4) link_BETA1-6 : angle 1.42792 / 0.80 ( 12) link_NAG-ASN : bond 0.00335 / 0.23 ( 12) link_NAG-ASN : angle 2.04208 / 1.22 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 0.827 Fit side-chains REVERT: H 38 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7794 (ptp90) REVERT: H 62 GLU cc_start: 0.8553 (pt0) cc_final: 0.8019 (pt0) REVERT: H 72 ASP cc_start: 0.7846 (t70) cc_final: 0.7540 (p0) REVERT: L 35 TRP cc_start: 0.8077 (m100) cc_final: 0.7634 (m100) REVERT: E 38 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7785 (ptp90) REVERT: E 62 GLU cc_start: 0.8555 (pt0) cc_final: 0.8021 (pt0) REVERT: E 72 ASP cc_start: 0.7838 (t70) cc_final: 0.7537 (p0) REVERT: I 35 TRP cc_start: 0.8077 (m100) cc_final: 0.7636 (m100) REVERT: F 23 LYS cc_start: 0.8344 (tppt) cc_final: 0.8125 (tppt) REVERT: F 38 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7791 (ptp90) REVERT: F 62 GLU cc_start: 0.8561 (pt0) cc_final: 0.8025 (pt0) REVERT: F 72 ASP cc_start: 0.7827 (t70) cc_final: 0.7521 (p0) REVERT: J 35 TRP cc_start: 0.8079 (m100) cc_final: 0.7630 (m100) REVERT: G 23 LYS cc_start: 0.8341 (tppt) cc_final: 0.8121 (tppt) REVERT: G 38 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7813 (ptp90) REVERT: G 62 GLU cc_start: 0.8557 (pt0) cc_final: 0.8021 (pt0) REVERT: G 72 ASP cc_start: 0.7844 (t70) cc_final: 0.7532 (p0) REVERT: K 35 TRP cc_start: 0.8073 (m100) cc_final: 0.7625 (m100) outliers start: 32 outliers final: 20 residues processed: 284 average time/residue: 0.6123 time to fit residues: 196.9497 Evaluate side-chains 272 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 342 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 234 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 192 optimal weight: 0.4980 chunk 146 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 219 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN A 313 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 313 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN C 313 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN D 313 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.079765 restraints weight = 29437.669| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.31 r_work: 0.2910 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19728 Z= 0.136 Angle : 0.635 15.821 26908 Z= 0.316 Chirality : 0.047 0.171 2936 Planarity : 0.004 0.038 3468 Dihedral : 5.120 33.464 3076 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.15 % Allowed : 15.30 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.16 (0.17), residues: 2468 helix: -1.22 (0.85), residues: 24 sheet: 0.57 (0.17), residues: 872 loop : -0.09 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 61 TYR 0.011 0.001 TYR B 252 PHE 0.024 0.002 PHE E 63 TRP 0.035 0.001 TRP E 47 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (19668) covalent geometry : angle 0.62636 / 0.31 (26768) SS BOND : bond 0.00312 / 0.21 ( 40) SS BOND : angle 1.41429 / 0.90 ( 80) hydrogen bonds : bond 0.03022 / 2.07 ( 616) hydrogen bonds : angle 6.08062 / 4.39 ( 1620) link_BETA1-4 : bond 0.00437 / 0.22 ( 4) link_BETA1-4 : angle 0.95944 / 0.54 ( 12) link_BETA1-6 : bond 0.00200 / 0.10 ( 4) link_BETA1-6 : angle 1.39651 / 0.78 ( 12) link_NAG-ASN : bond 0.00306 / 0.21 ( 12) link_NAG-ASN : angle 1.96623 / 1.18 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.770 Fit side-chains REVERT: H 38 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8085 (ptp90) REVERT: H 62 GLU cc_start: 0.8563 (pt0) cc_final: 0.8061 (pt0) REVERT: H 72 ASP cc_start: 0.7815 (t70) cc_final: 0.7557 (p0) REVERT: L 35 TRP cc_start: 0.8084 (m100) cc_final: 0.7618 (m100) REVERT: E 38 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8072 (ptp90) REVERT: E 62 GLU cc_start: 0.8563 (pt0) cc_final: 0.8063 (pt0) REVERT: E 72 ASP cc_start: 0.7815 (t70) cc_final: 0.7557 (p0) REVERT: I 35 TRP cc_start: 0.8083 (m100) cc_final: 0.7623 (m100) REVERT: F 38 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8077 (ptp90) REVERT: F 62 GLU cc_start: 0.8570 (pt0) cc_final: 0.8065 (pt0) REVERT: F 72 ASP cc_start: 0.7852 (t70) cc_final: 0.7582 (p0) REVERT: J 35 TRP cc_start: 0.8084 (m100) cc_final: 0.7621 (m100) REVERT: G 38 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8090 (ptp90) REVERT: G 62 GLU cc_start: 0.8569 (pt0) cc_final: 0.8065 (pt0) REVERT: G 72 ASP cc_start: 0.7855 (t70) cc_final: 0.7584 (p0) REVERT: K 35 TRP cc_start: 0.8082 (m100) cc_final: 0.7619 (m100) outliers start: 24 outliers final: 20 residues processed: 260 average time/residue: 0.6153 time to fit residues: 180.8817 Evaluate side-chains 263 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 342 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 59 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** 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 = 0.3544 r_free = 0.3544 target = 0.115476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077115 restraints weight = 29685.661| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.33 r_work: 0.2857 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19728 Z= 0.234 Angle : 0.673 15.351 26908 Z= 0.337 Chirality : 0.049 0.191 2936 Planarity : 0.004 0.039 3468 Dihedral : 5.388 35.109 3076 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.15 % Allowed : 15.87 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.12 (0.17), residues: 2468 helix: -1.36 (0.75), residues: 24 sheet: 0.53 (0.17), residues: 856 loop : -0.10 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 61 TYR 0.011 0.001 TYR F 91 PHE 0.023 0.002 PHE F 63 TRP 0.043 0.002 TRP E 47 HIS 0.009 0.002 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (19668) covalent geometry : angle 0.66351 / 0.33 (26768) SS BOND : bond 0.00438 / 0.30 ( 40) SS BOND : angle 1.55829 / 1.00 ( 80) hydrogen bonds : bond 0.03388 / 2.34 ( 616) hydrogen bonds : angle 6.26111 / 4.52 ( 1620) link_BETA1-4 : bond 0.00297 / 0.15 ( 4) link_BETA1-4 : angle 0.98368 / 0.56 ( 12) link_BETA1-6 : bond 0.00028 / 0.01 ( 4) link_BETA1-6 : angle 1.50995 / 0.84 ( 12) link_NAG-ASN : bond 0.00469 / 0.32 ( 12) link_NAG-ASN : angle 2.16148 / 1.29 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7990.18 seconds wall clock time: 136 minutes 52.14 seconds (8212.14 seconds total)