Starting phenix.real_space_refine on Thu Feb 5 19:15:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4o_70109/02_2026/9o4o_70109.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4o_70109/02_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_70109/02_2026/9o4o_70109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4o_70109/02_2026/9o4o_70109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o4o_70109/02_2026/9o4o_70109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4o_70109/02_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-2.0-5952/lib/python3.9/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, 31 Unusual residues: {' CA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.53, per 1000 atoms: 0.24 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: 1.48 Conformation dependent library (CDL) restraints added in 771.4 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: 0.65 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: 3.71 Time building geometry restraints manager: 1.91 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 2.510 nonbonded pdb=" O GLY B 297 " pdb="CA CA B 503 " model vdw 2.230 2.510 nonbonded pdb=" O GLY D 297 " pdb="CA CA D 503 " model vdw 2.230 2.510 nonbonded pdb=" O GLY A 297 " pdb="CA CA A 503 " model vdw 2.230 2.510 nonbonded pdb=" O ASN A 347 " pdb="CA CA A 503 " model vdw 2.233 2.510 ... (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: 11.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.390 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 covalent geometry : bond 0.00497 (19668) covalent geometry : angle 0.79188 (26768) SS BOND : bond 0.00366 ( 40) SS BOND : angle 1.98704 ( 80) hydrogen bonds : bond 0.21239 ( 616) hydrogen bonds : angle 9.98564 ( 1620) link_BETA1-4 : bond 0.00351 ( 4) link_BETA1-4 : angle 0.49530 ( 12) link_BETA1-6 : bond 0.00362 ( 4) link_BETA1-6 : angle 0.89053 ( 12) link_NAG-ASN : bond 0.00291 ( 12) link_NAG-ASN : angle 1.99762 ( 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 : 0.733 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: 0.5920 time to fit residues: 242.4658 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 : 0.600 ------------------------------------------------------------------------------- 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: 10.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.0470 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3577 r_free = 0.3577 target = 0.119009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.081694 restraints weight = 28292.489| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.21 r_work: 0.2872 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19728 Z= 0.128 Angle : 0.610 9.531 26908 Z= 0.323 Chirality : 0.049 0.262 2936 Planarity : 0.004 0.039 3468 Dihedral : 6.904 53.473 3076 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.97 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: 0.43 (0.16), residues: 2468 helix: -1.30 (0.75), residues: 24 sheet: 0.88 (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 A 252 PHE 0.015 0.002 PHE A 410 TRP 0.013 0.001 TRP D 295 HIS 0.005 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00281 (19668) covalent geometry : angle 0.60021 (26768) SS BOND : bond 0.00312 ( 40) SS BOND : angle 1.43483 ( 80) hydrogen bonds : bond 0.04195 ( 616) hydrogen bonds : angle 7.29328 ( 1620) link_BETA1-4 : bond 0.00674 ( 4) link_BETA1-4 : angle 1.26909 ( 12) link_BETA1-6 : bond 0.00375 ( 4) link_BETA1-6 : angle 1.42271 ( 12) link_NAG-ASN : bond 0.00279 ( 12) link_NAG-ASN : angle 2.15129 ( 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 304 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 0.746 Fit side-chains REVERT: H 105 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8995 (pm20) REVERT: L 27 ASN cc_start: 0.7755 (m110) cc_final: 0.7101 (m110) REVERT: L 35 TRP cc_start: 0.8261 (m100) cc_final: 0.7780 (m100) REVERT: L 73 LEU cc_start: 0.7803 (tt) cc_final: 0.7465 (tt) REVERT: E 105 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8992 (pm20) REVERT: I 27 ASN cc_start: 0.7757 (m110) cc_final: 0.7100 (m110) REVERT: I 35 TRP cc_start: 0.8263 (m100) cc_final: 0.7786 (m100) REVERT: I 73 LEU cc_start: 0.7802 (tt) cc_final: 0.7466 (tt) REVERT: F 105 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8993 (pm20) REVERT: J 27 ASN cc_start: 0.7759 (m110) cc_final: 0.7102 (m110) REVERT: J 35 TRP cc_start: 0.8261 (m100) cc_final: 0.7784 (m100) REVERT: J 73 LEU cc_start: 0.7806 (tt) cc_final: 0.7473 (tt) REVERT: G 105 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8999 (pm20) REVERT: K 27 ASN cc_start: 0.7759 (m110) cc_final: 0.7104 (m110) REVERT: K 35 TRP cc_start: 0.8263 (m100) cc_final: 0.7781 (m100) REVERT: K 73 LEU cc_start: 0.7801 (tt) cc_final: 0.7464 (tt) outliers start: 24 outliers final: 12 residues processed: 296 average time/residue: 0.5665 time to fit residues: 188.8992 Evaluate side-chains 255 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 239 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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: 5.9990 chunk 120 optimal weight: 6.9990 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: 0.2980 chunk 177 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3507 r_free = 0.3507 target = 0.114523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.076674 restraints weight = 28543.910| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.19 r_work: 0.2772 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19728 Z= 0.228 Angle : 0.647 14.111 26908 Z= 0.334 Chirality : 0.049 0.187 2936 Planarity : 0.004 0.040 3468 Dihedral : 6.463 50.581 3076 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.68 % Allowed : 9.37 % Favored : 87.95 % 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: 0.24 (0.16), residues: 2468 helix: -1.01 (0.77), residues: 24 sheet: 0.71 (0.16), residues: 924 loop : -0.12 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 61 TYR 0.011 0.001 TYR A 252 PHE 0.018 0.002 PHE D 121 TRP 0.015 0.002 TRP D 178 HIS 0.008 0.002 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00531 (19668) covalent geometry : angle 0.63724 (26768) SS BOND : bond 0.00394 ( 40) SS BOND : angle 1.45704 ( 80) hydrogen bonds : bond 0.03772 ( 616) hydrogen bonds : angle 6.84322 ( 1620) link_BETA1-4 : bond 0.00407 ( 4) link_BETA1-4 : angle 1.23115 ( 12) link_BETA1-6 : bond 0.00200 ( 4) link_BETA1-6 : angle 1.44653 ( 12) link_NAG-ASN : bond 0.00363 ( 12) link_NAG-ASN : angle 2.14090 ( 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 312 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 256 time to evaluate : 0.787 Fit side-chains REVERT: L 27 ASN cc_start: 0.7781 (m110) cc_final: 0.7471 (m110) REVERT: L 35 TRP cc_start: 0.8206 (m100) cc_final: 0.7704 (m100) REVERT: L 73 LEU cc_start: 0.7767 (tt) cc_final: 0.7507 (tt) REVERT: A 219 ARG cc_start: 0.8413 (mmt90) cc_final: 0.8198 (mmt90) REVERT: I 27 ASN cc_start: 0.7790 (m110) cc_final: 0.7481 (m110) REVERT: I 35 TRP cc_start: 0.8205 (m100) cc_final: 0.7707 (m100) REVERT: I 73 LEU cc_start: 0.7762 (tt) cc_final: 0.7502 (tt) REVERT: B 219 ARG cc_start: 0.8419 (mmt90) cc_final: 0.8206 (mmt90) REVERT: J 27 ASN cc_start: 0.7790 (m110) cc_final: 0.7482 (m110) REVERT: J 35 TRP cc_start: 0.8207 (m100) cc_final: 0.7709 (m100) REVERT: J 73 LEU cc_start: 0.7769 (tt) cc_final: 0.7508 (tt) REVERT: C 219 ARG cc_start: 0.8425 (mmt90) cc_final: 0.8212 (mmt90) REVERT: K 27 ASN cc_start: 0.7780 (m110) cc_final: 0.7469 (m110) REVERT: K 35 TRP cc_start: 0.8207 (m100) cc_final: 0.7706 (m100) REVERT: K 73 LEU cc_start: 0.7764 (tt) cc_final: 0.7503 (tt) REVERT: D 219 ARG cc_start: 0.8419 (mmt90) cc_final: 0.8206 (mmt90) outliers start: 56 outliers final: 24 residues processed: 284 average time/residue: 0.6169 time to fit residues: 197.1666 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 : 0.646 ------------------------------------------------------------------------------- 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: 6.9990 chunk 172 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3527 r_free = 0.3527 target = 0.115765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.078072 restraints weight = 28386.730| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.18 r_work: 0.2796 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19728 Z= 0.150 Angle : 0.590 12.228 26908 Z= 0.307 Chirality : 0.047 0.175 2936 Planarity : 0.004 0.040 3468 Dihedral : 5.974 46.552 3076 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.10 % Allowed : 11.47 % Favored : 86.42 % 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: 0.15 (0.16), residues: 2468 helix: -1.11 (0.82), residues: 24 sheet: 0.56 (0.16), residues: 924 loop : -0.11 (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 D 252 PHE 0.022 0.002 PHE E 63 TRP 0.013 0.001 TRP B 178 HIS 0.005 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00339 (19668) covalent geometry : angle 0.58050 (26768) SS BOND : bond 0.00317 ( 40) SS BOND : angle 1.35368 ( 80) hydrogen bonds : bond 0.03285 ( 616) hydrogen bonds : angle 6.50263 ( 1620) link_BETA1-4 : bond 0.00575 ( 4) link_BETA1-4 : angle 1.24675 ( 12) link_BETA1-6 : bond 0.00225 ( 4) link_BETA1-6 : angle 1.42918 ( 12) link_NAG-ASN : bond 0.00308 ( 12) link_NAG-ASN : angle 2.08526 ( 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 312 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 0.762 Fit side-chains REVERT: L 27 ASN cc_start: 0.7820 (m110) cc_final: 0.7517 (m110) REVERT: L 35 TRP cc_start: 0.8162 (m100) cc_final: 0.7637 (m100) REVERT: L 73 LEU cc_start: 0.7783 (tt) cc_final: 0.7542 (tt) REVERT: I 27 ASN cc_start: 0.7833 (m110) cc_final: 0.7531 (m110) REVERT: I 35 TRP cc_start: 0.8161 (m100) cc_final: 0.7637 (m100) REVERT: I 73 LEU cc_start: 0.7783 (tt) cc_final: 0.7539 (tt) REVERT: J 27 ASN cc_start: 0.7829 (m110) cc_final: 0.7525 (m110) REVERT: J 35 TRP cc_start: 0.8162 (m100) cc_final: 0.7638 (m100) REVERT: J 73 LEU cc_start: 0.7784 (tt) cc_final: 0.7538 (tt) REVERT: K 27 ASN cc_start: 0.7819 (m110) cc_final: 0.7515 (m110) REVERT: K 35 TRP cc_start: 0.8159 (m100) cc_final: 0.7634 (m100) REVERT: K 73 LEU cc_start: 0.7779 (tt) cc_final: 0.7534 (tt) outliers start: 44 outliers final: 28 residues processed: 288 average time/residue: 0.5992 time to fit residues: 193.9202 Evaluate side-chains 284 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 20 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 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 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: 0.0170 chunk 52 optimal weight: 0.4980 chunk 200 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 232 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN A 226 GLN A 313 GLN E 105 GLN B 226 GLN B 313 GLN F 105 GLN C 226 GLN C 313 GLN G 105 GLN D 226 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 = 0.3554 r_free = 0.3554 target = 0.117515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.079959 restraints weight = 28098.131| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.19 r_work: 0.2834 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19728 Z= 0.112 Angle : 0.584 11.828 26908 Z= 0.298 Chirality : 0.046 0.164 2936 Planarity : 0.004 0.040 3468 Dihedral : 5.474 38.842 3076 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.29 % Allowed : 12.81 % Favored : 84.89 % 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: 0.13 (0.16), residues: 2468 helix: -1.05 (0.86), residues: 24 sheet: 0.52 (0.16), residues: 920 loop : -0.10 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 61 TYR 0.012 0.001 TYR A 252 PHE 0.025 0.002 PHE E 63 TRP 0.012 0.001 TRP F 47 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00253 (19668) covalent geometry : angle 0.57660 (26768) SS BOND : bond 0.00204 ( 40) SS BOND : angle 1.13602 ( 80) hydrogen bonds : bond 0.03005 ( 616) hydrogen bonds : angle 6.20949 ( 1620) link_BETA1-4 : bond 0.00421 ( 4) link_BETA1-4 : angle 1.07874 ( 12) link_BETA1-6 : bond 0.00264 ( 4) link_BETA1-6 : angle 1.34217 ( 12) link_NAG-ASN : bond 0.00269 ( 12) link_NAG-ASN : angle 1.95751 ( 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 328 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 0.675 Fit side-chains REVERT: H 39 GLN cc_start: 0.7942 (tt0) cc_final: 0.7675 (tt0) REVERT: L 27 ASN cc_start: 0.7793 (m110) cc_final: 0.7476 (m110) REVERT: L 35 TRP cc_start: 0.8097 (m100) cc_final: 0.7590 (m100) REVERT: L 73 LEU cc_start: 0.7725 (tt) cc_final: 0.7524 (tt) REVERT: A 230 CYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8901 (p) REVERT: A 259 LYS cc_start: 0.9348 (mttp) cc_final: 0.9135 (mttm) REVERT: E 39 GLN cc_start: 0.7942 (tt0) cc_final: 0.7675 (tt0) REVERT: I 27 ASN cc_start: 0.7804 (m110) cc_final: 0.7486 (m110) REVERT: I 35 TRP cc_start: 0.8100 (m100) cc_final: 0.7593 (m100) REVERT: I 73 LEU cc_start: 0.7725 (tt) cc_final: 0.7522 (tt) REVERT: B 230 CYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8896 (p) REVERT: B 259 LYS cc_start: 0.9350 (mttp) cc_final: 0.9134 (mttm) REVERT: F 39 GLN cc_start: 0.7944 (tt0) cc_final: 0.7678 (tt0) REVERT: J 27 ASN cc_start: 0.7796 (m110) cc_final: 0.7477 (m110) REVERT: J 35 TRP cc_start: 0.8097 (m100) cc_final: 0.7590 (m100) REVERT: J 73 LEU cc_start: 0.7728 (tt) cc_final: 0.7521 (tt) REVERT: C 230 CYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8906 (p) REVERT: C 259 LYS cc_start: 0.9348 (mttp) cc_final: 0.9134 (mttm) REVERT: G 39 GLN cc_start: 0.7941 (tt0) cc_final: 0.7676 (tt0) REVERT: K 27 ASN cc_start: 0.7788 (m110) cc_final: 0.7468 (m110) REVERT: K 35 TRP cc_start: 0.8095 (m100) cc_final: 0.7589 (m100) REVERT: K 73 LEU cc_start: 0.7726 (tt) cc_final: 0.7521 (tt) REVERT: D 230 CYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8901 (p) REVERT: D 259 LYS cc_start: 0.9343 (mttp) cc_final: 0.9128 (mttm) outliers start: 48 outliers final: 24 residues processed: 308 average time/residue: 0.6481 time to fit residues: 223.2261 Evaluate side-chains 296 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 105 GLN Chi-restraints excluded: chain A residue 127 LEU 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 89 VAL Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain B residue 127 LEU 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 89 VAL Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain C residue 127 LEU 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 89 VAL Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain D residue 127 LEU 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: 2.9990 chunk 96 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 219 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 226 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.072701 restraints weight = 28634.942| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.18 r_work: 0.2719 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 19728 Z= 0.317 Angle : 0.700 16.518 26908 Z= 0.356 Chirality : 0.051 0.202 2936 Planarity : 0.005 0.040 3468 Dihedral : 5.844 37.265 3076 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.72 % Allowed : 13.58 % Favored : 84.70 % 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: 0.00 (0.16), residues: 2468 helix: -1.52 (0.67), residues: 24 sheet: 0.61 (0.17), residues: 876 loop : -0.30 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 12 TYR 0.012 0.001 TYR A 252 PHE 0.022 0.003 PHE E 63 TRP 0.018 0.002 TRP A 97 HIS 0.012 0.002 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00730 (19668) covalent geometry : angle 0.69067 (26768) SS BOND : bond 0.00505 ( 40) SS BOND : angle 1.55662 ( 80) hydrogen bonds : bond 0.03720 ( 616) hydrogen bonds : angle 6.58390 ( 1620) link_BETA1-4 : bond 0.00382 ( 4) link_BETA1-4 : angle 1.09120 ( 12) link_BETA1-6 : bond 0.00229 ( 4) link_BETA1-6 : angle 1.55465 ( 12) link_NAG-ASN : bond 0.00490 ( 12) link_NAG-ASN : angle 2.24282 ( 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 300 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.572 Fit side-chains REVERT: H 38 ARG cc_start: 0.8714 (ppt-90) cc_final: 0.7832 (ptp90) REVERT: H 79 TYR cc_start: 0.8532 (m-80) cc_final: 0.8243 (m-80) REVERT: L 35 TRP cc_start: 0.8238 (m100) cc_final: 0.7766 (m100) REVERT: A 230 CYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8867 (p) REVERT: E 38 ARG cc_start: 0.8712 (ppt-90) cc_final: 0.7830 (ptp90) REVERT: E 79 TYR cc_start: 0.8532 (m-80) cc_final: 0.8241 (m-80) REVERT: I 35 TRP cc_start: 0.8240 (m100) cc_final: 0.7768 (m100) REVERT: B 230 CYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8860 (p) REVERT: F 38 ARG cc_start: 0.8709 (ppt-90) cc_final: 0.7827 (ptp90) REVERT: F 79 TYR cc_start: 0.8530 (m-80) cc_final: 0.8240 (m-80) REVERT: J 35 TRP cc_start: 0.8241 (m100) cc_final: 0.7769 (m100) REVERT: C 230 CYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8874 (p) REVERT: G 38 ARG cc_start: 0.8711 (ppt-90) cc_final: 0.7828 (ptp90) REVERT: G 79 TYR cc_start: 0.8532 (m-80) cc_final: 0.8244 (m-80) REVERT: K 35 TRP cc_start: 0.8241 (m100) cc_final: 0.7767 (m100) REVERT: D 230 CYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8867 (p) outliers start: 36 outliers final: 28 residues processed: 284 average time/residue: 0.5986 time to fit residues: 190.9063 Evaluate side-chains 284 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 62 GLU 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 20 VAL Chi-restraints excluded: chain E residue 62 GLU 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 62 GLU 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 62 GLU 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: 10.0000 chunk 115 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 39 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 chunk 206 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN E 105 GLN F 105 GLN G 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.077399 restraints weight = 28171.165| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.17 r_work: 0.2792 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19728 Z= 0.136 Angle : 0.608 12.637 26908 Z= 0.313 Chirality : 0.047 0.175 2936 Planarity : 0.004 0.040 3468 Dihedral : 5.337 33.721 3076 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.29 % Allowed : 13.19 % Favored : 84.51 % 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: -0.02 (0.16), residues: 2468 helix: -1.21 (0.79), residues: 24 sheet: 0.51 (0.16), residues: 892 loop : -0.26 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 219 TYR 0.012 0.001 TYR A 252 PHE 0.023 0.002 PHE E 63 TRP 0.020 0.001 TRP G 47 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00309 (19668) covalent geometry : angle 0.60013 (26768) SS BOND : bond 0.00317 ( 40) SS BOND : angle 1.22087 ( 80) hydrogen bonds : bond 0.03127 ( 616) hydrogen bonds : angle 6.26154 ( 1620) link_BETA1-4 : bond 0.00356 ( 4) link_BETA1-4 : angle 1.04217 ( 12) link_BETA1-6 : bond 0.00155 ( 4) link_BETA1-6 : angle 1.37133 ( 12) link_NAG-ASN : bond 0.00328 ( 12) link_NAG-ASN : angle 2.05629 ( 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 312 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 0.476 Fit side-chains REVERT: H 38 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7856 (ptp90) REVERT: H 39 GLN cc_start: 0.8004 (tt0) cc_final: 0.7736 (tt0) REVERT: H 62 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8066 (pt0) REVERT: L 35 TRP cc_start: 0.8080 (m100) cc_final: 0.7573 (m100) REVERT: A 230 CYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8916 (p) REVERT: E 38 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7862 (ptp90) REVERT: E 39 GLN cc_start: 0.8009 (tt0) cc_final: 0.7742 (tt0) REVERT: E 62 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: I 35 TRP cc_start: 0.8083 (m100) cc_final: 0.7576 (m100) REVERT: B 230 CYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8908 (p) REVERT: F 38 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7852 (ptp90) REVERT: F 39 GLN cc_start: 0.8004 (tt0) cc_final: 0.7735 (tt0) REVERT: F 62 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8074 (pt0) REVERT: J 35 TRP cc_start: 0.8081 (m100) cc_final: 0.7574 (m100) REVERT: C 230 CYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8908 (p) REVERT: G 38 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7852 (ptp90) REVERT: G 39 GLN cc_start: 0.7999 (tt0) cc_final: 0.7731 (tt0) REVERT: G 62 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8067 (pt0) REVERT: K 35 TRP cc_start: 0.8080 (m100) cc_final: 0.7573 (m100) REVERT: D 230 CYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8910 (p) outliers start: 48 outliers final: 20 residues processed: 284 average time/residue: 0.5818 time to fit residues: 185.8517 Evaluate side-chains 276 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 62 GLU Chi-restraints excluded: chain H residue 89 VAL 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 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 62 GLU Chi-restraints excluded: chain E residue 89 VAL 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 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 62 GLU Chi-restraints excluded: chain F residue 89 VAL 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 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 62 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 336 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 40 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 43 optimal weight: 0.0270 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN A 226 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN B 226 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN C 226 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN D 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.076717 restraints weight = 28086.819| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.18 r_work: 0.2776 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19728 Z= 0.169 Angle : 0.634 13.240 26908 Z= 0.321 Chirality : 0.048 0.178 2936 Planarity : 0.004 0.044 3468 Dihedral : 5.281 33.863 3076 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: 0.09 (0.16), residues: 2468 helix: -1.28 (0.80), residues: 24 sheet: 0.59 (0.17), residues: 872 loop : -0.19 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 54 TYR 0.012 0.001 TYR A 252 PHE 0.024 0.002 PHE E 63 TRP 0.026 0.001 TRP H 47 HIS 0.006 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00393 (19668) covalent geometry : angle 0.62608 (26768) SS BOND : bond 0.00307 ( 40) SS BOND : angle 1.26323 ( 80) hydrogen bonds : bond 0.03174 ( 616) hydrogen bonds : angle 6.20657 ( 1620) link_BETA1-4 : bond 0.00383 ( 4) link_BETA1-4 : angle 0.98683 ( 12) link_BETA1-6 : bond 0.00131 ( 4) link_BETA1-6 : angle 1.43507 ( 12) link_NAG-ASN : bond 0.00329 ( 12) link_NAG-ASN : angle 2.02614 ( 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: 32 poor density : 244 time to evaluate : 0.614 Fit side-chains REVERT: H 38 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7955 (ptp90) REVERT: H 62 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8143 (pt0) REVERT: L 35 TRP cc_start: 0.8075 (m100) cc_final: 0.7603 (m100) REVERT: A 230 CYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8925 (p) REVERT: E 38 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7955 (ptp90) REVERT: E 62 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8147 (pt0) REVERT: I 35 TRP cc_start: 0.8071 (m100) cc_final: 0.7599 (m100) REVERT: B 230 CYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8914 (p) REVERT: F 38 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7943 (ptp90) REVERT: F 62 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8148 (pt0) REVERT: J 35 TRP cc_start: 0.8074 (m100) cc_final: 0.7601 (m100) REVERT: C 230 CYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8911 (p) REVERT: G 38 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7950 (ptp90) REVERT: G 62 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: K 35 TRP cc_start: 0.8073 (m100) cc_final: 0.7601 (m100) REVERT: D 230 CYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8912 (p) outliers start: 32 outliers final: 20 residues processed: 256 average time/residue: 0.6293 time to fit residues: 180.4518 Evaluate side-chains 272 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 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 H residue 62 GLU Chi-restraints excluded: chain H residue 89 VAL 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 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 62 GLU Chi-restraints excluded: chain E residue 89 VAL 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 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 62 GLU Chi-restraints excluded: chain F residue 89 VAL 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 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 62 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 336 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 116 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.077927 restraints weight = 29503.515| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.32 r_work: 0.2862 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19728 Z= 0.174 Angle : 0.626 13.485 26908 Z= 0.319 Chirality : 0.047 0.178 2936 Planarity : 0.004 0.040 3468 Dihedral : 5.213 34.122 3076 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.72 % Allowed : 14.53 % 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: 0.18 (0.17), residues: 2468 helix: -1.26 (0.79), residues: 24 sheet: 0.67 (0.17), residues: 844 loop : -0.12 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 61 TYR 0.011 0.001 TYR A 252 PHE 0.022 0.002 PHE E 63 TRP 0.032 0.001 TRP H 47 HIS 0.006 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00404 (19668) covalent geometry : angle 0.61828 (26768) SS BOND : bond 0.00294 ( 40) SS BOND : angle 1.26668 ( 80) hydrogen bonds : bond 0.03213 ( 616) hydrogen bonds : angle 6.18961 ( 1620) link_BETA1-4 : bond 0.00367 ( 4) link_BETA1-4 : angle 0.97785 ( 12) link_BETA1-6 : bond 0.00126 ( 4) link_BETA1-6 : angle 1.42375 ( 12) link_NAG-ASN : bond 0.00362 ( 12) link_NAG-ASN : angle 2.03628 ( 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 280 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.758 Fit side-chains REVERT: H 38 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7643 (ptp90) REVERT: H 62 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: L 35 TRP cc_start: 0.8067 (m100) cc_final: 0.7573 (m100) REVERT: A 230 CYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8883 (p) REVERT: E 38 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7628 (ptp90) REVERT: E 62 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8175 (pt0) REVERT: I 35 TRP cc_start: 0.8067 (m100) cc_final: 0.7573 (m100) REVERT: B 230 CYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8874 (p) REVERT: F 38 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7651 (ptp90) REVERT: F 62 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: J 35 TRP cc_start: 0.8072 (m100) cc_final: 0.7579 (m100) REVERT: C 230 CYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8873 (p) REVERT: G 38 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7655 (ptp90) REVERT: G 62 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8182 (pt0) REVERT: K 35 TRP cc_start: 0.8068 (m100) cc_final: 0.7576 (m100) REVERT: D 230 CYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8877 (p) outliers start: 36 outliers final: 24 residues processed: 260 average time/residue: 0.6161 time to fit residues: 180.3166 Evaluate side-chains 272 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 62 GLU Chi-restraints excluded: chain H residue 89 VAL 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 62 GLU Chi-restraints excluded: chain E residue 89 VAL 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 4 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 89 VAL 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 4 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 89 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 234 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 210 optimal weight: 0.0060 chunk 151 optimal weight: 2.9990 chunk 219 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3556 r_free = 0.3556 target = 0.116329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.078348 restraints weight = 29505.417| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.31 r_work: 0.2853 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19728 Z= 0.166 Angle : 0.623 13.301 26908 Z= 0.317 Chirality : 0.047 0.176 2936 Planarity : 0.004 0.040 3468 Dihedral : 5.142 33.894 3076 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.72 % Allowed : 14.53 % 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: 0.12 (0.17), residues: 2468 helix: -1.23 (0.81), residues: 24 sheet: 0.62 (0.17), residues: 884 loop : -0.17 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 61 TYR 0.011 0.001 TYR D 252 PHE 0.021 0.002 PHE E 63 TRP 0.039 0.002 TRP G 47 HIS 0.006 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00386 (19668) covalent geometry : angle 0.61548 (26768) SS BOND : bond 0.00283 ( 40) SS BOND : angle 1.25922 ( 80) hydrogen bonds : bond 0.03215 ( 616) hydrogen bonds : angle 6.14873 ( 1620) link_BETA1-4 : bond 0.00375 ( 4) link_BETA1-4 : angle 0.97132 ( 12) link_BETA1-6 : bond 0.00143 ( 4) link_BETA1-6 : angle 1.42338 ( 12) link_NAG-ASN : bond 0.00346 ( 12) link_NAG-ASN : angle 2.00976 ( 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 284 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.662 Fit side-chains REVERT: H 38 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7678 (ptp90) REVERT: H 62 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: L 35 TRP cc_start: 0.8067 (m100) cc_final: 0.7590 (m100) REVERT: A 230 CYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8878 (p) REVERT: E 38 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7663 (ptp90) REVERT: E 62 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: I 35 TRP cc_start: 0.8068 (m100) cc_final: 0.7593 (m100) REVERT: B 230 CYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8870 (p) REVERT: F 38 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7677 (ptp90) REVERT: F 62 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: J 35 TRP cc_start: 0.8072 (m100) cc_final: 0.7596 (m100) REVERT: C 230 CYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8866 (p) REVERT: G 38 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7688 (ptp90) REVERT: G 62 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: K 35 TRP cc_start: 0.8068 (m100) cc_final: 0.7593 (m100) REVERT: D 230 CYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8877 (p) outliers start: 36 outliers final: 24 residues processed: 264 average time/residue: 0.5726 time to fit residues: 170.8754 Evaluate side-chains 276 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 62 GLU Chi-restraints excluded: chain H residue 89 VAL 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 62 GLU Chi-restraints excluded: chain E residue 89 VAL 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 4 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 89 VAL 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 4 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 89 VAL 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=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: 10.0000 chunk 175 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 199 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.076352 restraints weight = 29610.122| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.31 r_work: 0.2821 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19728 Z= 0.241 Angle : 0.659 15.097 26908 Z= 0.335 Chirality : 0.049 0.190 2936 Planarity : 0.005 0.040 3468 Dihedral : 5.350 34.933 3076 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.72 % Allowed : 14.53 % 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: 0.14 (0.17), residues: 2468 helix: -1.36 (0.74), residues: 24 sheet: 0.69 (0.17), residues: 868 loop : -0.18 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 61 TYR 0.011 0.001 TYR A 252 PHE 0.021 0.002 PHE F 63 TRP 0.051 0.002 TRP H 47 HIS 0.009 0.002 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00559 (19668) covalent geometry : angle 0.65038 (26768) SS BOND : bond 0.00384 ( 40) SS BOND : angle 1.41541 ( 80) hydrogen bonds : bond 0.03450 ( 616) hydrogen bonds : angle 6.30371 ( 1620) link_BETA1-4 : bond 0.00278 ( 4) link_BETA1-4 : angle 0.98570 ( 12) link_BETA1-6 : bond 0.00002 ( 4) link_BETA1-6 : angle 1.50712 ( 12) link_NAG-ASN : bond 0.00477 ( 12) link_NAG-ASN : angle 2.15193 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7424.39 seconds wall clock time: 127 minutes 8.33 seconds (7628.33 seconds total)