Starting phenix.real_space_refine on Fri Jul 3 13:16:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fex_50344/07_2026/9fex_50344.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fex_50344/07_2026/9fex_50344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fex_50344/07_2026/9fex_50344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fex_50344/07_2026/9fex_50344.map" model { file = "/net/cci-nas-00/data/ceres_data/9fex_50344/07_2026/9fex_50344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fex_50344/07_2026/9fex_50344.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 85 5.16 5 Cl 5 4.86 5 C 9370 2.51 5 N 2285 2.21 5 O 2720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14465 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2776 Chain: "B" Number of atoms: 2761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2776 Chain: "C" Number of atoms: 2761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2776 Chain: "D" Number of atoms: 2761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2776 Chain: "E" Number of atoms: 2761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2776 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N AASN D 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN D 41 " occ=0.50 residue: pdb=" N AASN E 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN E 41 " occ=0.50 Time building chain proxies: 5.75, per 1000 atoms: 0.40 Number of scatterers: 14465 At special positions: 0 Unit cell: (100.434, 100.434, 127.712, 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) Cl 5 17.00 S 85 16.00 O 2720 8.00 N 2285 7.00 C 9370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " 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 ALPHA1-3 " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A 501 " - " ASN A 8 " " NAG B 502 " - " ASN B 8 " " NAG C 503 " - " ASN C 8 " " NAG D 503 " - " ASN D 8 " " NAG E 503 " - " ASN E 8 " " NAG F 1 " - " ASN A 80 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN C 80 " " NAG I 1 " - " ASN D 80 " " NAG J 1 " - " ASN E 80 " " NAG a 1 " - " ASN A 149 " " NAG b 1 " - " ASN B 149 " " NAG c 1 " - " ASN C 149 " " NAG d 1 " - " ASN D 149 " " NAG e 1 " - " ASN E 149 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3210 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 41.6% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.508A pdb=" N LEU A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 226 through 239 removed outlier: 3.915A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 272 Processing helix chain 'A' and resid 279 through 307 removed outlier: 4.577A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 446 Proline residue: A 432 - end of helix Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.509A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 226 through 239 removed outlier: 3.915A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 272 Processing helix chain 'B' and resid 279 through 307 removed outlier: 4.578A pdb=" N PHE B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 446 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.509A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 226 through 239 removed outlier: 3.915A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 272 Processing helix chain 'C' and resid 279 through 307 removed outlier: 4.578A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 446 Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.508A pdb=" N LEU D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 226 through 239 removed outlier: 3.915A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 272 Processing helix chain 'D' and resid 279 through 307 removed outlier: 4.578A pdb=" N PHE D 307 " --> pdb=" O ASN D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 446 Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.509A pdb=" N LEU E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 226 through 239 removed outlier: 3.915A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 272 Processing helix chain 'E' and resid 279 through 307 removed outlier: 4.578A pdb=" N PHE E 307 " --> pdb=" O ASN E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 446 Proline residue: E 432 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.293A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.767A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 42 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.998A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.293A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.767A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR B 176 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 42 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.998A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.294A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.768A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.998A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.294A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.768A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR D 176 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D 42 " --> pdb=" O THR D 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.997A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.294A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.767A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR E 176 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 42 " --> pdb=" O THR E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.997A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4310 1.34 - 1.46: 3723 1.46 - 1.58: 6572 1.58 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14755 Sorted by residual: bond pdb=" C1 MAN a 5 " pdb=" O5 MAN a 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" C1 MAN e 5 " pdb=" O5 MAN e 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C1 MAN d 5 " pdb=" O5 MAN d 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 MAN b 5 " pdb=" O5 MAN b 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C1 MAN c 5 " pdb=" O5 MAN c 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.42e+00 ... (remaining 14750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 19187 1.09 - 2.17: 637 2.17 - 3.26: 240 3.26 - 4.35: 22 4.35 - 5.44: 19 Bond angle restraints: 20105 Sorted by residual: angle pdb=" C TYR E 66 " pdb=" N TRP E 67 " pdb=" CA TRP E 67 " ideal model delta sigma weight residual 122.11 119.01 3.10 1.59e+00 3.96e-01 3.79e+00 angle pdb=" C TYR A 66 " pdb=" N TRP A 67 " pdb=" CA TRP A 67 " ideal model delta sigma weight residual 122.11 119.06 3.05 1.59e+00 3.96e-01 3.69e+00 angle pdb=" C TYR C 66 " pdb=" N TRP C 67 " pdb=" CA TRP C 67 " ideal model delta sigma weight residual 122.11 119.06 3.05 1.59e+00 3.96e-01 3.67e+00 angle pdb=" C TYR D 66 " pdb=" N TRP D 67 " pdb=" CA TRP D 67 " ideal model delta sigma weight residual 122.11 119.07 3.04 1.59e+00 3.96e-01 3.65e+00 angle pdb=" C TYR B 66 " pdb=" N TRP B 67 " pdb=" CA TRP B 67 " ideal model delta sigma weight residual 122.11 119.11 3.00 1.59e+00 3.96e-01 3.57e+00 ... (remaining 20100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 8910 21.07 - 42.14: 200 42.14 - 63.20: 20 63.20 - 84.27: 35 84.27 - 105.34: 20 Dihedral angle restraints: 9185 sinusoidal: 4155 harmonic: 5030 Sorted by residual: dihedral pdb=" O4 BMA c 3 " pdb=" C4 BMA c 3 " pdb=" C5 BMA c 3 " pdb=" O5 BMA c 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.63 105.34 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C5 BMA d 3 " pdb=" O5 BMA d 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.60 105.31 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.58 105.29 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 9182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1914 0.050 - 0.100: 340 0.100 - 0.150: 96 0.150 - 0.200: 12 0.200 - 0.249: 8 Chirality restraints: 2370 Sorted by residual: chirality pdb=" C5 BMA c 3 " pdb=" C4 BMA c 3 " pdb=" C6 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C5 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C6 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2367 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 275 " -0.016 5.00e-02 4.00e+02 2.38e-02 9.09e-01 pdb=" N PRO A 276 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 275 " 0.015 5.00e-02 4.00e+02 2.35e-02 8.85e-01 pdb=" N PRO D 276 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO D 276 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 276 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 275 " -0.015 5.00e-02 4.00e+02 2.35e-02 8.84e-01 pdb=" N PRO E 276 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " -0.013 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3190 2.79 - 3.32: 13527 3.32 - 3.84: 25437 3.84 - 4.37: 30932 4.37 - 4.90: 51432 Nonbonded interactions: 124518 Sorted by model distance: nonbonded pdb=" O LEU D 83 " pdb=" O HOH D 601 " model vdw 2.260 3.040 nonbonded pdb=" O LEU B 83 " pdb=" O HOH B 601 " model vdw 2.261 3.040 nonbonded pdb=" O PRO E 94 " pdb=" O HOH E 601 " model vdw 2.268 3.040 nonbonded pdb=" O LEU A 83 " pdb=" O HOH A 601 " model vdw 2.282 3.040 nonbonded pdb=" O LEU E 83 " pdb=" O HOH E 602 " model vdw 2.285 3.040 ... (remaining 124513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 40 or resid 42 through 65 or resid 67 through 13 \ 7 or resid 139 through 436 or resid 438 through 447)) selection = (chain 'B' and (resid 7 through 40 or resid 42 through 65 or resid 67 through 13 \ 7 or resid 139 through 436 or resid 438 through 447)) selection = (chain 'C' and (resid 7 through 40 or resid 42 through 65 or resid 67 through 13 \ 7 or resid 139 through 436 or resid 438 through 447)) selection = (chain 'D' and (resid 7 through 40 or resid 42 through 65 or resid 67 through 13 \ 7 or resid 139 through 436 or resid 438 through 447)) selection = (chain 'E' and (resid 7 through 40 or resid 42 through 65 or resid 67 through 13 \ 7 or resid 139 through 436 or resid 438 through 447)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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=0.50 max=1.00 mean=0.99 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 17.860 Find NCS groups from input model: 0.420 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: 0.000 Load rotamer database and sin/cos tables:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 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 : 0.003 0.032 14800 Z= 0.161 Angle : 0.546 5.437 20235 Z= 0.259 Chirality : 0.045 0.249 2370 Planarity : 0.003 0.024 2440 Dihedral : 11.648 105.341 5960 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.66 % Allowed : 2.32 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.22), residues: 1690 helix: 2.82 (0.21), residues: 635 sheet: 1.28 (0.25), residues: 395 loop : 0.74 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 129 TYR 0.012 0.001 TYR B 299 PHE 0.011 0.001 PHE B 293 TRP 0.007 0.001 TRP A 67 HIS 0.002 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (14755) covalent geometry : angle 0.53742 / 0.26 (20105) SS BOND : bond 0.00272 / 0.18 ( 5) SS BOND : angle 0.49644 / 0.34 ( 10) hydrogen bonds : bond 0.09138 / 5.97 ( 770) hydrogen bonds : angle 4.47332 / 3.10 ( 2490) link_ALPHA1-3 : bond 0.00130 / 0.09 ( 5) link_ALPHA1-3 : angle 1.31014 / 0.91 ( 15) link_ALPHA1-6 : bond 0.00298 / 0.19 ( 5) link_ALPHA1-6 : angle 0.97451 / 0.70 ( 15) link_BETA1-4 : bond 0.00273 / 0.18 ( 15) link_BETA1-4 : angle 1.54412 / 1.06 ( 45) link_NAG-ASN : bond 0.00062 / 0.04 ( 15) link_NAG-ASN : angle 1.28232 / 0.92 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 349 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8319 (t80) cc_final: 0.8011 (t80) REVERT: C 9 MET cc_start: 0.8500 (mtp) cc_final: 0.8076 (mtp) REVERT: D 52 GLU cc_start: 0.8166 (mp0) cc_final: 0.7934 (mp0) REVERT: E 224 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7925 (tp40) outliers start: 10 outliers final: 2 residues processed: 354 average time/residue: 0.6317 time to fit residues: 243.0404 Evaluate side-chains 239 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 236 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 224 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN B C 41 ASN B D 41 ASN B E 41 ASN B E 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.059021 restraints weight = 122678.943| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 5.32 r_work: 0.2467 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2464 r_free = 0.2464 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.2464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14800 Z= 0.133 Angle : 0.623 9.242 20235 Z= 0.310 Chirality : 0.045 0.179 2370 Planarity : 0.004 0.034 2440 Dihedral : 10.458 79.790 2761 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.98 % Allowed : 14.30 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.22), residues: 1690 helix: 2.35 (0.21), residues: 635 sheet: 1.37 (0.26), residues: 380 loop : 0.58 (0.27), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 425 TYR 0.028 0.002 TYR E 277 PHE 0.011 0.001 PHE C 63 TRP 0.030 0.001 TRP B 241 HIS 0.003 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14755) covalent geometry : angle 0.61059 / 0.31 (20105) SS BOND : bond 0.00191 / 0.12 ( 5) SS BOND : angle 0.27902 / 0.20 ( 10) hydrogen bonds : bond 0.03665 / 2.42 ( 770) hydrogen bonds : angle 4.20612 / 2.94 ( 2490) link_ALPHA1-3 : bond 0.00857 / 0.55 ( 5) link_ALPHA1-3 : angle 2.30628 / 1.52 ( 15) link_ALPHA1-6 : bond 0.00585 / 0.38 ( 5) link_ALPHA1-6 : angle 2.04290 / 1.41 ( 15) link_BETA1-4 : bond 0.00316 / 0.21 ( 15) link_BETA1-4 : angle 1.63188 / 1.11 ( 45) link_NAG-ASN : bond 0.00181 / 0.11 ( 15) link_NAG-ASN : angle 1.40242 / 1.04 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.9456 (mtmm) cc_final: 0.9251 (mmmm) REVERT: A 190 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8804 (tt0) REVERT: B 14 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8763 (pp20) REVERT: B 17 ASP cc_start: 0.8962 (m-30) cc_final: 0.8726 (m-30) REVERT: B 99 LEU cc_start: 0.9413 (tp) cc_final: 0.9052 (mt) REVERT: B 218 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8412 (pp) REVERT: B 224 GLN cc_start: 0.9064 (tp40) cc_final: 0.8489 (mm110) REVERT: B 244 TYR cc_start: 0.8331 (p90) cc_final: 0.8011 (p90) REVERT: B 309 GLN cc_start: 0.8330 (tp40) cc_final: 0.7936 (pm20) REVERT: C 9 MET cc_start: 0.8066 (mtp) cc_final: 0.7568 (mtp) REVERT: C 14 GLU cc_start: 0.8989 (pt0) cc_final: 0.8685 (pp20) REVERT: C 79 LEU cc_start: 0.8791 (mt) cc_final: 0.8563 (mm) REVERT: C 218 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8268 (pp) REVERT: C 244 TYR cc_start: 0.8572 (p90) cc_final: 0.8137 (p90) REVERT: C 269 ARG cc_start: 0.7806 (tpm170) cc_final: 0.7602 (tpm170) REVERT: C 286 MET cc_start: 0.8481 (tpp) cc_final: 0.8240 (tpt) REVERT: C 309 GLN cc_start: 0.7871 (tp40) cc_final: 0.7553 (pm20) REVERT: D 52 GLU cc_start: 0.8791 (mp0) cc_final: 0.8538 (mp0) REVERT: D 190 GLU cc_start: 0.9008 (tt0) cc_final: 0.8745 (tt0) REVERT: D 269 ARG cc_start: 0.7377 (tpm170) cc_final: 0.7156 (tpm170) REVERT: D 309 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7997 (pm20) REVERT: E 79 LEU cc_start: 0.8792 (mt) cc_final: 0.8583 (mm) REVERT: E 218 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8162 (pp) REVERT: E 309 GLN cc_start: 0.8017 (tp40) cc_final: 0.7723 (pm20) outliers start: 45 outliers final: 13 residues processed: 296 average time/residue: 0.6347 time to fit residues: 204.0582 Evaluate side-chains 269 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 251 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 138 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 0.0000 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN B D 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.085350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.059212 restraints weight = 123634.402| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 5.31 r_work: 0.2482 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.2505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14800 Z= 0.123 Angle : 0.587 8.860 20235 Z= 0.296 Chirality : 0.044 0.197 2370 Planarity : 0.004 0.026 2440 Dihedral : 9.705 73.337 2757 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.05 % Allowed : 15.03 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.21), residues: 1690 helix: 2.14 (0.21), residues: 635 sheet: 1.34 (0.25), residues: 390 loop : 0.49 (0.27), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 425 TYR 0.020 0.001 TYR D 277 PHE 0.011 0.001 PHE E 306 TRP 0.009 0.001 TRP D 241 HIS 0.002 0.001 HIS C 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14755) covalent geometry : angle 0.57740 / 0.29 (20105) SS BOND : bond 0.00215 / 0.14 ( 5) SS BOND : angle 0.36008 / 0.26 ( 10) hydrogen bonds : bond 0.03416 / 2.23 ( 770) hydrogen bonds : angle 4.12096 / 2.88 ( 2490) link_ALPHA1-3 : bond 0.01047 / 0.67 ( 5) link_ALPHA1-3 : angle 1.59576 / 1.09 ( 15) link_ALPHA1-6 : bond 0.00774 / 0.50 ( 5) link_ALPHA1-6 : angle 2.03599 / 1.39 ( 15) link_BETA1-4 : bond 0.00335 / 0.23 ( 15) link_BETA1-4 : angle 1.38425 / 0.95 ( 45) link_NAG-ASN : bond 0.00142 / 0.10 ( 15) link_NAG-ASN : angle 1.26140 / 0.94 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.460 Fit side-chains REVERT: A 70 LYS cc_start: 0.9395 (mtpp) cc_final: 0.9075 (mmtp) REVERT: A 79 LEU cc_start: 0.8877 (mt) cc_final: 0.8623 (mm) REVERT: A 179 GLU cc_start: 0.8806 (pp20) cc_final: 0.8374 (pp20) REVERT: A 190 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8969 (tt0) REVERT: A 241 TRP cc_start: 0.9133 (m100) cc_final: 0.8802 (m100) REVERT: A 309 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: B 14 GLU cc_start: 0.9032 (pt0) cc_final: 0.8780 (pp20) REVERT: B 17 ASP cc_start: 0.9020 (m-30) cc_final: 0.8793 (m-30) REVERT: B 99 LEU cc_start: 0.9381 (tp) cc_final: 0.9036 (mt) REVERT: B 218 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8354 (pp) REVERT: B 224 GLN cc_start: 0.9091 (tp40) cc_final: 0.8516 (mm110) REVERT: B 244 TYR cc_start: 0.8366 (p90) cc_final: 0.7877 (p90) REVERT: B 306 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8702 (t80) REVERT: B 309 GLN cc_start: 0.8238 (tp40) cc_final: 0.7912 (pm20) REVERT: C 9 MET cc_start: 0.8078 (mtp) cc_final: 0.7613 (mtp) REVERT: C 14 GLU cc_start: 0.8999 (pt0) cc_final: 0.8700 (pp20) REVERT: C 70 LYS cc_start: 0.9322 (mtpp) cc_final: 0.8969 (mmtm) REVERT: C 79 LEU cc_start: 0.8792 (mt) cc_final: 0.8551 (mm) REVERT: C 112 LYS cc_start: 0.8855 (tttm) cc_final: 0.8610 (tttm) REVERT: C 218 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8256 (pp) REVERT: C 244 TYR cc_start: 0.8595 (p90) cc_final: 0.8158 (p90) REVERT: C 425 ARG cc_start: 0.8580 (ptp-110) cc_final: 0.8083 (mtm-85) REVERT: D 52 GLU cc_start: 0.8818 (mp0) cc_final: 0.8541 (mp0) REVERT: D 103 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8251 (tmtt) REVERT: D 190 GLU cc_start: 0.9089 (tt0) cc_final: 0.8805 (tt0) REVERT: D 269 ARG cc_start: 0.7374 (tpm170) cc_final: 0.7140 (tpm170) REVERT: E 61 MET cc_start: 0.9638 (OUTLIER) cc_final: 0.9153 (pmm) REVERT: E 79 LEU cc_start: 0.8788 (mt) cc_final: 0.8567 (mm) REVERT: E 155 GLU cc_start: 0.9276 (tt0) cc_final: 0.9067 (tt0) REVERT: E 218 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8169 (pp) REVERT: E 244 TYR cc_start: 0.8313 (p90) cc_final: 0.7941 (p90) REVERT: E 269 ARG cc_start: 0.7433 (tpm170) cc_final: 0.7153 (tpm170) REVERT: E 309 GLN cc_start: 0.8114 (tp40) cc_final: 0.7858 (pm20) outliers start: 31 outliers final: 4 residues processed: 273 average time/residue: 0.6871 time to fit residues: 203.4348 Evaluate side-chains 249 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 218 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 13 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.057652 restraints weight = 119292.757| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 5.28 r_work: 0.2452 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14800 Z= 0.175 Angle : 0.624 10.621 20235 Z= 0.310 Chirality : 0.045 0.209 2370 Planarity : 0.004 0.033 2440 Dihedral : 9.222 68.685 2757 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.32 % Allowed : 15.43 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.21), residues: 1690 helix: 2.07 (0.21), residues: 635 sheet: 1.30 (0.25), residues: 395 loop : 0.46 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 425 TYR 0.017 0.002 TYR E 277 PHE 0.012 0.001 PHE E 63 TRP 0.008 0.001 TRP E 237 HIS 0.005 0.001 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (14755) covalent geometry : angle 0.61307 / 0.31 (20105) SS BOND : bond 0.00265 / 0.17 ( 5) SS BOND : angle 0.57914 / 0.40 ( 10) hydrogen bonds : bond 0.03504 / 2.29 ( 770) hydrogen bonds : angle 4.16077 / 2.90 ( 2490) link_ALPHA1-3 : bond 0.00929 / 0.60 ( 5) link_ALPHA1-3 : angle 1.87654 / 1.27 ( 15) link_ALPHA1-6 : bond 0.00756 / 0.49 ( 5) link_ALPHA1-6 : angle 2.23099 / 1.52 ( 15) link_BETA1-4 : bond 0.00267 / 0.18 ( 15) link_BETA1-4 : angle 1.49413 / 1.03 ( 45) link_NAG-ASN : bond 0.00058 / 0.04 ( 15) link_NAG-ASN : angle 1.34040 / 0.98 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.559 Fit side-chains REVERT: A 70 LYS cc_start: 0.9413 (mtpp) cc_final: 0.9089 (mmtp) REVERT: A 179 GLU cc_start: 0.8851 (pp20) cc_final: 0.8413 (pp20) REVERT: A 190 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8979 (tt0) REVERT: A 241 TRP cc_start: 0.9169 (m100) cc_final: 0.8797 (m100) REVERT: A 309 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: B 17 ASP cc_start: 0.9044 (m-30) cc_final: 0.8792 (m-30) REVERT: B 70 LYS cc_start: 0.9421 (mtpp) cc_final: 0.9059 (mptm) REVERT: B 218 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8366 (pp) REVERT: B 224 GLN cc_start: 0.9140 (tp40) cc_final: 0.8575 (mm110) REVERT: B 244 TYR cc_start: 0.8397 (p90) cc_final: 0.7994 (p90) REVERT: B 306 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8734 (t80) REVERT: B 309 GLN cc_start: 0.8246 (tp40) cc_final: 0.7925 (pm20) REVERT: C 9 MET cc_start: 0.8064 (mtp) cc_final: 0.7561 (mtp) REVERT: C 14 GLU cc_start: 0.8960 (pt0) cc_final: 0.8693 (pp20) REVERT: C 70 LYS cc_start: 0.9330 (mtpp) cc_final: 0.8961 (mmtm) REVERT: C 79 LEU cc_start: 0.8789 (mt) cc_final: 0.8548 (mm) REVERT: C 112 LYS cc_start: 0.8849 (tttm) cc_final: 0.8615 (tttm) REVERT: C 218 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8449 (pp) REVERT: C 244 TYR cc_start: 0.8628 (p90) cc_final: 0.8180 (p90) REVERT: C 309 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6687 (pm20) REVERT: C 425 ARG cc_start: 0.8576 (ptp-110) cc_final: 0.8049 (mtm-85) REVERT: D 52 GLU cc_start: 0.8840 (mp0) cc_final: 0.8567 (mp0) REVERT: D 70 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9204 (mmtp) REVERT: D 190 GLU cc_start: 0.9088 (tt0) cc_final: 0.8795 (tt0) REVERT: D 244 TYR cc_start: 0.8675 (p90) cc_final: 0.8440 (p90) REVERT: D 269 ARG cc_start: 0.7426 (tpm170) cc_final: 0.7193 (tpm170) REVERT: E 17 ASP cc_start: 0.8919 (m-30) cc_final: 0.8391 (m-30) REVERT: E 61 MET cc_start: 0.9658 (OUTLIER) cc_final: 0.9339 (pmm) REVERT: E 70 LYS cc_start: 0.9369 (mtpp) cc_final: 0.9041 (mmtp) REVERT: E 79 LEU cc_start: 0.8816 (mt) cc_final: 0.8600 (mm) REVERT: E 218 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8204 (pp) REVERT: E 244 TYR cc_start: 0.8481 (p90) cc_final: 0.8045 (p90) REVERT: E 269 ARG cc_start: 0.7475 (tpm170) cc_final: 0.7080 (tpm170) REVERT: E 309 GLN cc_start: 0.8189 (tp40) cc_final: 0.7963 (pm20) outliers start: 35 outliers final: 14 residues processed: 253 average time/residue: 0.7164 time to fit residues: 195.9679 Evaluate side-chains 250 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.084812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.058780 restraints weight = 107908.024| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 5.12 r_work: 0.2482 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14800 Z= 0.131 Angle : 0.607 9.147 20235 Z= 0.301 Chirality : 0.044 0.225 2370 Planarity : 0.003 0.025 2440 Dihedral : 8.566 62.808 2757 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.32 % Allowed : 15.70 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.21), residues: 1690 helix: 2.13 (0.21), residues: 635 sheet: 1.30 (0.25), residues: 395 loop : 0.52 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 425 TYR 0.017 0.001 TYR A 244 PHE 0.011 0.001 PHE D 293 TRP 0.009 0.001 TRP C 67 HIS 0.002 0.001 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14755) covalent geometry : angle 0.59801 / 0.30 (20105) SS BOND : bond 0.00231 / 0.15 ( 5) SS BOND : angle 0.37503 / 0.26 ( 10) hydrogen bonds : bond 0.03352 / 2.17 ( 770) hydrogen bonds : angle 4.06220 / 2.83 ( 2490) link_ALPHA1-3 : bond 0.01037 / 0.67 ( 5) link_ALPHA1-3 : angle 1.67615 / 1.14 ( 15) link_ALPHA1-6 : bond 0.00886 / 0.57 ( 5) link_ALPHA1-6 : angle 2.18143 / 1.48 ( 15) link_BETA1-4 : bond 0.00305 / 0.21 ( 15) link_BETA1-4 : angle 1.37925 / 0.95 ( 45) link_NAG-ASN : bond 0.00108 / 0.07 ( 15) link_NAG-ASN : angle 1.30989 / 0.96 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.9157 (mmtp) REVERT: A 179 GLU cc_start: 0.8869 (pp20) cc_final: 0.8387 (pp20) REVERT: A 190 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8912 (tt0) REVERT: A 241 TRP cc_start: 0.9181 (m100) cc_final: 0.8791 (m100) REVERT: A 244 TYR cc_start: 0.8678 (p90) cc_final: 0.8359 (p90) REVERT: A 309 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: B 14 GLU cc_start: 0.8550 (pp20) cc_final: 0.8334 (pp20) REVERT: B 17 ASP cc_start: 0.9071 (m-30) cc_final: 0.8804 (m-30) REVERT: B 61 MET cc_start: 0.9559 (OUTLIER) cc_final: 0.9149 (ptp) REVERT: B 70 LYS cc_start: 0.9411 (mtpp) cc_final: 0.9066 (mptm) REVERT: B 218 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8370 (pp) REVERT: B 224 GLN cc_start: 0.9122 (tp40) cc_final: 0.8509 (mm110) REVERT: B 244 TYR cc_start: 0.8426 (p90) cc_final: 0.8010 (p90) REVERT: C 9 MET cc_start: 0.7992 (mtp) cc_final: 0.7564 (mtp) REVERT: C 61 MET cc_start: 0.9665 (OUTLIER) cc_final: 0.8548 (ptp) REVERT: C 70 LYS cc_start: 0.9327 (mtpp) cc_final: 0.8966 (mmtm) REVERT: C 79 LEU cc_start: 0.8814 (mt) cc_final: 0.8567 (mm) REVERT: C 112 LYS cc_start: 0.8872 (tttm) cc_final: 0.8643 (tttm) REVERT: C 218 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8436 (pp) REVERT: C 244 TYR cc_start: 0.8631 (p90) cc_final: 0.8207 (p90) REVERT: C 309 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: D 52 GLU cc_start: 0.8828 (mp0) cc_final: 0.8475 (mp0) REVERT: D 70 LYS cc_start: 0.9502 (mtpp) cc_final: 0.9233 (mmtp) REVERT: D 103 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8222 (tmtt) REVERT: D 190 GLU cc_start: 0.9098 (tt0) cc_final: 0.8784 (tt0) REVERT: D 269 ARG cc_start: 0.7348 (tpm170) cc_final: 0.7111 (tpm170) REVERT: D 283 MET cc_start: 0.9012 (tpp) cc_final: 0.8752 (mmm) REVERT: E 17 ASP cc_start: 0.8915 (m-30) cc_final: 0.8338 (m-30) REVERT: E 61 MET cc_start: 0.9627 (OUTLIER) cc_final: 0.9157 (pmm) REVERT: E 70 LYS cc_start: 0.9393 (mtpp) cc_final: 0.9117 (mmtp) REVERT: E 79 LEU cc_start: 0.8820 (mt) cc_final: 0.8600 (mm) REVERT: E 190 GLU cc_start: 0.9149 (tt0) cc_final: 0.8749 (tt0) REVERT: E 218 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8169 (pp) REVERT: E 244 TYR cc_start: 0.8460 (p90) cc_final: 0.8055 (p90) REVERT: E 309 GLN cc_start: 0.8215 (tp40) cc_final: 0.8014 (pm20) outliers start: 35 outliers final: 13 residues processed: 255 average time/residue: 0.7418 time to fit residues: 204.6569 Evaluate side-chains 258 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 218 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 148 optimal weight: 0.0980 chunk 155 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.059681 restraints weight = 114624.546| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 5.23 r_work: 0.2493 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14800 Z= 0.119 Angle : 0.627 10.835 20235 Z= 0.306 Chirality : 0.044 0.237 2370 Planarity : 0.003 0.029 2440 Dihedral : 7.962 57.501 2757 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.12 % Allowed : 16.36 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.21), residues: 1690 helix: 2.16 (0.21), residues: 635 sheet: 1.35 (0.25), residues: 395 loop : 0.55 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 425 TYR 0.017 0.001 TYR A 244 PHE 0.013 0.001 PHE A 306 TRP 0.010 0.001 TRP C 67 HIS 0.002 0.001 HIS C 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (14755) covalent geometry : angle 0.61887 / 0.30 (20105) SS BOND : bond 0.00199 / 0.13 ( 5) SS BOND : angle 0.39823 / 0.28 ( 10) hydrogen bonds : bond 0.03226 / 2.08 ( 770) hydrogen bonds : angle 4.00842 / 2.80 ( 2490) link_ALPHA1-3 : bond 0.01092 / 0.70 ( 5) link_ALPHA1-3 : angle 1.63610 / 1.11 ( 15) link_ALPHA1-6 : bond 0.00949 / 0.61 ( 5) link_ALPHA1-6 : angle 2.08098 / 1.41 ( 15) link_BETA1-4 : bond 0.00352 / 0.24 ( 15) link_BETA1-4 : angle 1.30848 / 0.90 ( 45) link_NAG-ASN : bond 0.00157 / 0.10 ( 15) link_NAG-ASN : angle 1.27996 / 0.94 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.660 Fit side-chains REVERT: A 70 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.9155 (mmtp) REVERT: A 79 LEU cc_start: 0.8924 (mt) cc_final: 0.8686 (mm) REVERT: A 103 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8637 (tptp) REVERT: A 179 GLU cc_start: 0.8853 (pp20) cc_final: 0.8356 (pp20) REVERT: A 190 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8922 (tt0) REVERT: A 241 TRP cc_start: 0.9214 (m100) cc_final: 0.8996 (m-90) REVERT: A 309 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: B 14 GLU cc_start: 0.8559 (pp20) cc_final: 0.8349 (pp20) REVERT: B 17 ASP cc_start: 0.9124 (m-30) cc_final: 0.8864 (m-30) REVERT: B 61 MET cc_start: 0.9546 (OUTLIER) cc_final: 0.9113 (ptp) REVERT: B 70 LYS cc_start: 0.9400 (mtpp) cc_final: 0.9084 (mptm) REVERT: B 218 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8360 (pp) REVERT: B 224 GLN cc_start: 0.9126 (tp40) cc_final: 0.8611 (mm110) REVERT: B 244 TYR cc_start: 0.8333 (p90) cc_final: 0.7899 (p90) REVERT: B 309 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: C 9 MET cc_start: 0.8022 (mtp) cc_final: 0.7660 (mtt) REVERT: C 61 MET cc_start: 0.9652 (OUTLIER) cc_final: 0.8229 (ptp) REVERT: C 70 LYS cc_start: 0.9333 (mtpp) cc_final: 0.8990 (mmtm) REVERT: C 79 LEU cc_start: 0.8871 (mt) cc_final: 0.8625 (mm) REVERT: C 112 LYS cc_start: 0.8920 (tttm) cc_final: 0.8702 (tttm) REVERT: C 218 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8446 (pp) REVERT: C 244 TYR cc_start: 0.8612 (p90) cc_final: 0.8186 (p90) REVERT: C 309 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: C 425 ARG cc_start: 0.8688 (ptp-110) cc_final: 0.8061 (mtm-85) REVERT: D 52 GLU cc_start: 0.8825 (mp0) cc_final: 0.8436 (mp0) REVERT: D 70 LYS cc_start: 0.9498 (mtpp) cc_final: 0.9206 (mmtp) REVERT: D 103 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8254 (tmtt) REVERT: D 190 GLU cc_start: 0.9108 (tt0) cc_final: 0.8745 (tt0) REVERT: E 17 ASP cc_start: 0.8931 (m-30) cc_final: 0.8310 (m-30) REVERT: E 61 MET cc_start: 0.9601 (OUTLIER) cc_final: 0.9210 (pmm) REVERT: E 70 LYS cc_start: 0.9404 (mtpp) cc_final: 0.9005 (mmpt) REVERT: E 79 LEU cc_start: 0.8845 (mt) cc_final: 0.8627 (mm) REVERT: E 190 GLU cc_start: 0.9182 (tt0) cc_final: 0.8808 (tt0) REVERT: E 218 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8392 (pp) REVERT: E 269 ARG cc_start: 0.7335 (tpm170) cc_final: 0.7086 (tpm170) outliers start: 32 outliers final: 13 residues processed: 255 average time/residue: 0.7339 time to fit residues: 202.4950 Evaluate side-chains 258 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 157 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 126 optimal weight: 0.0010 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.085846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.059882 restraints weight = 111093.964| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 5.22 r_work: 0.2503 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14800 Z= 0.120 Angle : 0.624 10.112 20235 Z= 0.308 Chirality : 0.045 0.240 2370 Planarity : 0.003 0.029 2440 Dihedral : 7.527 53.640 2755 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.25 % Allowed : 16.62 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.21), residues: 1690 helix: 2.14 (0.20), residues: 635 sheet: 1.38 (0.25), residues: 395 loop : 0.60 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 425 TYR 0.040 0.001 TYR E 299 PHE 0.015 0.001 PHE A 306 TRP 0.010 0.001 TRP C 67 HIS 0.002 0.001 HIS C 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14755) covalent geometry : angle 0.61625 / 0.31 (20105) SS BOND : bond 0.00163 / 0.11 ( 5) SS BOND : angle 0.36012 / 0.25 ( 10) hydrogen bonds : bond 0.03224 / 2.09 ( 770) hydrogen bonds : angle 3.95700 / 2.76 ( 2490) link_ALPHA1-3 : bond 0.01131 / 0.73 ( 5) link_ALPHA1-3 : angle 1.61967 / 1.11 ( 15) link_ALPHA1-6 : bond 0.00982 / 0.64 ( 5) link_ALPHA1-6 : angle 2.03025 / 1.38 ( 15) link_BETA1-4 : bond 0.00345 / 0.23 ( 15) link_BETA1-4 : angle 1.28699 / 0.88 ( 45) link_NAG-ASN : bond 0.00157 / 0.10 ( 15) link_NAG-ASN : angle 1.28896 / 0.94 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.9409 (ttpp) cc_final: 0.8993 (tmmm) REVERT: A 70 LYS cc_start: 0.9475 (OUTLIER) cc_final: 0.9162 (mmtp) REVERT: A 79 LEU cc_start: 0.8930 (mt) cc_final: 0.8691 (mm) REVERT: A 103 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8609 (tptp) REVERT: A 179 GLU cc_start: 0.8864 (pp20) cc_final: 0.8362 (pp20) REVERT: A 190 GLU cc_start: 0.9233 (tt0) cc_final: 0.8927 (tt0) REVERT: A 241 TRP cc_start: 0.9215 (m100) cc_final: 0.8985 (m-90) REVERT: A 309 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: B 14 GLU cc_start: 0.8581 (pp20) cc_final: 0.8362 (pp20) REVERT: B 17 ASP cc_start: 0.9162 (m-30) cc_final: 0.8898 (m-30) REVERT: B 61 MET cc_start: 0.9526 (OUTLIER) cc_final: 0.9097 (ptp) REVERT: B 70 LYS cc_start: 0.9401 (mtpp) cc_final: 0.9093 (mptm) REVERT: B 218 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8386 (pp) REVERT: B 224 GLN cc_start: 0.9140 (tp40) cc_final: 0.8617 (mm110) REVERT: B 244 TYR cc_start: 0.8358 (p90) cc_final: 0.7921 (p90) REVERT: B 309 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: C 9 MET cc_start: 0.8137 (mtp) cc_final: 0.7732 (mtp) REVERT: C 61 MET cc_start: 0.9622 (OUTLIER) cc_final: 0.8154 (ptp) REVERT: C 70 LYS cc_start: 0.9335 (mtpp) cc_final: 0.9002 (mmtm) REVERT: C 79 LEU cc_start: 0.8872 (mt) cc_final: 0.8626 (mm) REVERT: C 112 LYS cc_start: 0.8920 (tttm) cc_final: 0.8704 (tttm) REVERT: C 218 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8461 (pp) REVERT: C 244 TYR cc_start: 0.8604 (p90) cc_final: 0.8193 (p90) REVERT: C 309 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.7146 (pm20) REVERT: D 52 GLU cc_start: 0.8810 (mp0) cc_final: 0.8413 (mp0) REVERT: D 70 LYS cc_start: 0.9498 (mtpp) cc_final: 0.9213 (mmtp) REVERT: D 103 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8256 (tmtt) REVERT: D 190 GLU cc_start: 0.9114 (tt0) cc_final: 0.8722 (tt0) REVERT: D 283 MET cc_start: 0.9023 (tpp) cc_final: 0.8556 (mmm) REVERT: E 17 ASP cc_start: 0.8943 (m-30) cc_final: 0.8339 (m-30) REVERT: E 61 MET cc_start: 0.9575 (OUTLIER) cc_final: 0.9235 (pmm) REVERT: E 70 LYS cc_start: 0.9430 (mtpp) cc_final: 0.8970 (mmpt) REVERT: E 79 LEU cc_start: 0.8847 (mt) cc_final: 0.8623 (mm) REVERT: E 190 GLU cc_start: 0.9133 (tt0) cc_final: 0.8742 (tt0) REVERT: E 218 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8397 (pp) REVERT: E 269 ARG cc_start: 0.7413 (tpm170) cc_final: 0.7170 (tpm170) outliers start: 34 outliers final: 13 residues processed: 253 average time/residue: 0.6557 time to fit residues: 179.4322 Evaluate side-chains 260 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 302 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.059063 restraints weight = 110573.274| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 5.17 r_work: 0.2488 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14800 Z= 0.136 Angle : 0.647 12.228 20235 Z= 0.318 Chirality : 0.045 0.240 2370 Planarity : 0.003 0.036 2440 Dihedral : 7.167 49.347 2755 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.25 % Allowed : 16.82 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.21), residues: 1690 helix: 2.13 (0.20), residues: 635 sheet: 1.39 (0.25), residues: 395 loop : 0.55 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 425 TYR 0.030 0.001 TYR E 299 PHE 0.020 0.001 PHE A 306 TRP 0.008 0.001 TRP A 426 HIS 0.003 0.001 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (14755) covalent geometry : angle 0.63911 / 0.32 (20105) SS BOND : bond 0.00194 / 0.13 ( 5) SS BOND : angle 0.38238 / 0.27 ( 10) hydrogen bonds : bond 0.03303 / 2.15 ( 770) hydrogen bonds : angle 4.00371 / 2.79 ( 2490) link_ALPHA1-3 : bond 0.01075 / 0.69 ( 5) link_ALPHA1-3 : angle 1.59227 / 1.08 ( 15) link_ALPHA1-6 : bond 0.00983 / 0.64 ( 5) link_ALPHA1-6 : angle 1.98045 / 1.35 ( 15) link_BETA1-4 : bond 0.00343 / 0.23 ( 15) link_BETA1-4 : angle 1.34843 / 0.92 ( 45) link_NAG-ASN : bond 0.00091 / 0.06 ( 15) link_NAG-ASN : angle 1.37446 / 1.01 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.9424 (ttpp) cc_final: 0.8990 (tmmm) REVERT: A 70 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9153 (mmtp) REVERT: A 179 GLU cc_start: 0.8875 (pp20) cc_final: 0.8364 (pp20) REVERT: A 190 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8922 (tt0) REVERT: A 241 TRP cc_start: 0.9219 (m100) cc_final: 0.8982 (m-90) REVERT: A 309 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: B 17 ASP cc_start: 0.9128 (m-30) cc_final: 0.8872 (m-30) REVERT: B 18 LYS cc_start: 0.9447 (ttmm) cc_final: 0.9055 (tmmm) REVERT: B 61 MET cc_start: 0.9555 (OUTLIER) cc_final: 0.9135 (ptp) REVERT: B 70 LYS cc_start: 0.9409 (mtpp) cc_final: 0.9101 (mptm) REVERT: B 218 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 224 GLN cc_start: 0.9130 (tp40) cc_final: 0.8614 (mm110) REVERT: B 244 TYR cc_start: 0.8426 (p90) cc_final: 0.7984 (p90) REVERT: C 61 MET cc_start: 0.9607 (OUTLIER) cc_final: 0.8077 (ptp) REVERT: C 70 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9002 (mmtm) REVERT: C 79 LEU cc_start: 0.8877 (mt) cc_final: 0.8638 (mm) REVERT: C 112 LYS cc_start: 0.8944 (tttm) cc_final: 0.8734 (tttm) REVERT: C 137 MET cc_start: 0.8718 (mmm) cc_final: 0.8476 (mmm) REVERT: C 218 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8477 (pp) REVERT: C 244 TYR cc_start: 0.8596 (p90) cc_final: 0.8168 (p90) REVERT: C 309 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: D 52 GLU cc_start: 0.8773 (mp0) cc_final: 0.8357 (mp0) REVERT: D 70 LYS cc_start: 0.9508 (mtpp) cc_final: 0.9225 (mmtp) REVERT: D 103 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8314 (tmtt) REVERT: D 190 GLU cc_start: 0.9112 (tt0) cc_final: 0.8724 (tt0) REVERT: D 241 TRP cc_start: 0.9293 (m100) cc_final: 0.8763 (m100) REVERT: E 17 ASP cc_start: 0.8953 (m-30) cc_final: 0.8346 (m-30) REVERT: E 61 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.9216 (pmm) REVERT: E 70 LYS cc_start: 0.9432 (mtpp) cc_final: 0.9022 (mmpt) REVERT: E 79 LEU cc_start: 0.8844 (mt) cc_final: 0.8617 (mm) REVERT: E 190 GLU cc_start: 0.9118 (tt0) cc_final: 0.8698 (tt0) REVERT: E 218 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8361 (pp) REVERT: E 244 TYR cc_start: 0.8641 (p90) cc_final: 0.8269 (p90) REVERT: E 269 ARG cc_start: 0.7445 (tpm170) cc_final: 0.7171 (tpm170) outliers start: 34 outliers final: 14 residues processed: 252 average time/residue: 0.6109 time to fit residues: 166.4574 Evaluate side-chains 259 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 157 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 chunk 98 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.085729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.059680 restraints weight = 121612.584| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 5.40 r_work: 0.2510 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14800 Z= 0.123 Angle : 0.656 10.968 20235 Z= 0.322 Chirality : 0.045 0.235 2370 Planarity : 0.003 0.024 2440 Dihedral : 6.792 45.275 2755 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.79 % Allowed : 17.68 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.21), residues: 1690 helix: 2.10 (0.20), residues: 635 sheet: 1.40 (0.25), residues: 395 loop : 0.56 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 425 TYR 0.025 0.001 TYR E 299 PHE 0.024 0.001 PHE A 306 TRP 0.010 0.001 TRP E 67 HIS 0.002 0.001 HIS C 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (14755) covalent geometry : angle 0.64904 / 0.32 (20105) SS BOND : bond 0.00143 / 0.09 ( 5) SS BOND : angle 0.31205 / 0.21 ( 10) hydrogen bonds : bond 0.03264 / 2.11 ( 770) hydrogen bonds : angle 3.97168 / 2.77 ( 2490) link_ALPHA1-3 : bond 0.01136 / 0.73 ( 5) link_ALPHA1-3 : angle 1.42889 / 0.98 ( 15) link_ALPHA1-6 : bond 0.01057 / 0.68 ( 5) link_ALPHA1-6 : angle 1.86552 / 1.27 ( 15) link_BETA1-4 : bond 0.00407 / 0.28 ( 15) link_BETA1-4 : angle 1.28926 / 0.88 ( 45) link_NAG-ASN : bond 0.00164 / 0.10 ( 15) link_NAG-ASN : angle 1.33404 / 0.98 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 250 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9164 (mmtp) REVERT: A 79 LEU cc_start: 0.8914 (mt) cc_final: 0.8668 (mm) REVERT: A 103 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8579 (tptp) REVERT: A 179 GLU cc_start: 0.8884 (pp20) cc_final: 0.8369 (pp20) REVERT: A 190 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8935 (tt0) REVERT: A 241 TRP cc_start: 0.9252 (m100) cc_final: 0.8945 (m-90) REVERT: A 306 PHE cc_start: 0.8890 (t80) cc_final: 0.8314 (t80) REVERT: A 309 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: B 17 ASP cc_start: 0.9166 (m-30) cc_final: 0.8902 (m-30) REVERT: B 61 MET cc_start: 0.9514 (OUTLIER) cc_final: 0.9087 (ptp) REVERT: B 70 LYS cc_start: 0.9393 (mtpp) cc_final: 0.9141 (mptm) REVERT: B 190 GLU cc_start: 0.9156 (tt0) cc_final: 0.8889 (pt0) REVERT: B 218 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8384 (pp) REVERT: B 224 GLN cc_start: 0.9119 (tp40) cc_final: 0.8613 (mm110) REVERT: B 244 TYR cc_start: 0.8453 (p90) cc_final: 0.8017 (p90) REVERT: C 61 MET cc_start: 0.9573 (OUTLIER) cc_final: 0.8044 (ptp) REVERT: C 70 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9056 (mmtm) REVERT: C 79 LEU cc_start: 0.8861 (mt) cc_final: 0.8618 (mm) REVERT: C 112 LYS cc_start: 0.8915 (tttm) cc_final: 0.8684 (tttm) REVERT: C 137 MET cc_start: 0.8747 (mmm) cc_final: 0.8537 (mmm) REVERT: C 218 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8466 (pp) REVERT: C 244 TYR cc_start: 0.8592 (p90) cc_final: 0.8163 (p90) REVERT: C 309 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7138 (pm20) REVERT: D 52 GLU cc_start: 0.8748 (mp0) cc_final: 0.8324 (mp0) REVERT: D 70 LYS cc_start: 0.9492 (mtpp) cc_final: 0.9223 (mmtp) REVERT: D 103 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8258 (tmtt) REVERT: D 190 GLU cc_start: 0.9123 (tt0) cc_final: 0.8715 (tt0) REVERT: D 241 TRP cc_start: 0.9296 (m100) cc_final: 0.8705 (m100) REVERT: D 283 MET cc_start: 0.8957 (tpp) cc_final: 0.8664 (mmm) REVERT: E 17 ASP cc_start: 0.8957 (m-30) cc_final: 0.8374 (m-30) REVERT: E 61 MET cc_start: 0.9555 (OUTLIER) cc_final: 0.9233 (pmm) REVERT: E 70 LYS cc_start: 0.9427 (mtpp) cc_final: 0.8941 (mmpt) REVERT: E 79 LEU cc_start: 0.8848 (mt) cc_final: 0.8626 (mm) REVERT: E 190 GLU cc_start: 0.9121 (tt0) cc_final: 0.8714 (tt0) REVERT: E 218 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8511 (pt) REVERT: E 224 GLN cc_start: 0.9061 (mm110) cc_final: 0.8686 (mm110) REVERT: E 244 TYR cc_start: 0.8686 (p90) cc_final: 0.8336 (p90) outliers start: 27 outliers final: 10 residues processed: 255 average time/residue: 0.5873 time to fit residues: 162.3967 Evaluate side-chains 262 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 2 optimal weight: 0.0020 chunk 84 optimal weight: 8.9990 chunk 85 optimal weight: 0.0570 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 82 optimal weight: 0.0770 chunk 126 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 79 optimal weight: 0.1980 overall best weight: 0.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN B C 41 ASN B D 41 ASN B E 41 ASN B Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.061477 restraints weight = 122098.000| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 5.52 r_work: 0.2550 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14800 Z= 0.117 Angle : 0.651 10.725 20235 Z= 0.321 Chirality : 0.044 0.225 2370 Planarity : 0.003 0.029 2440 Dihedral : 6.323 42.058 2755 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.39 % Allowed : 18.21 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.22), residues: 1690 helix: 2.14 (0.21), residues: 635 sheet: 1.46 (0.25), residues: 395 loop : 0.62 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 425 TYR 0.023 0.001 TYR E 299 PHE 0.025 0.001 PHE A 306 TRP 0.013 0.001 TRP E 67 HIS 0.001 0.000 HIS C 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (14755) covalent geometry : angle 0.64581 / 0.32 (20105) SS BOND : bond 0.00102 / 0.07 ( 5) SS BOND : angle 0.19265 / 0.14 ( 10) hydrogen bonds : bond 0.03143 / 2.03 ( 770) hydrogen bonds : angle 3.94614 / 2.76 ( 2490) link_ALPHA1-3 : bond 0.01174 / 0.76 ( 5) link_ALPHA1-3 : angle 1.26983 / 0.89 ( 15) link_ALPHA1-6 : bond 0.01109 / 0.72 ( 5) link_ALPHA1-6 : angle 1.66308 / 1.14 ( 15) link_BETA1-4 : bond 0.00482 / 0.33 ( 15) link_BETA1-4 : angle 1.21756 / 0.84 ( 45) link_NAG-ASN : bond 0.00239 / 0.16 ( 15) link_NAG-ASN : angle 1.25030 / 0.93 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.9450 (ttmm) cc_final: 0.8949 (tmmm) REVERT: A 54 ASN cc_start: 0.8418 (m-40) cc_final: 0.8027 (m-40) REVERT: A 70 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.9168 (mmtp) REVERT: A 103 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8640 (tptp) REVERT: A 179 GLU cc_start: 0.8881 (pp20) cc_final: 0.8358 (pp20) REVERT: A 190 GLU cc_start: 0.9257 (tt0) cc_final: 0.8928 (tt0) REVERT: A 241 TRP cc_start: 0.9267 (m100) cc_final: 0.8930 (m-90) REVERT: A 306 PHE cc_start: 0.8876 (t80) cc_final: 0.8344 (t80) REVERT: A 309 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: B 17 ASP cc_start: 0.9153 (m-30) cc_final: 0.8886 (m-30) REVERT: B 70 LYS cc_start: 0.9388 (mtpp) cc_final: 0.9095 (mptm) REVERT: B 79 LEU cc_start: 0.8959 (mt) cc_final: 0.8753 (mm) REVERT: B 190 GLU cc_start: 0.9212 (tt0) cc_final: 0.8971 (pt0) REVERT: B 218 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8368 (pp) REVERT: B 224 GLN cc_start: 0.9121 (tp40) cc_final: 0.8567 (mm110) REVERT: B 244 TYR cc_start: 0.8424 (p90) cc_final: 0.7985 (p90) REVERT: C 14 GLU cc_start: 0.8604 (pp20) cc_final: 0.8196 (pm20) REVERT: C 61 MET cc_start: 0.9499 (OUTLIER) cc_final: 0.7978 (ptp) REVERT: C 70 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9067 (mmtm) REVERT: C 79 LEU cc_start: 0.8856 (mt) cc_final: 0.8619 (mm) REVERT: C 112 LYS cc_start: 0.8903 (tttm) cc_final: 0.8690 (tttm) REVERT: C 218 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8468 (pp) REVERT: C 244 TYR cc_start: 0.8587 (p90) cc_final: 0.8175 (p90) REVERT: C 309 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: D 52 GLU cc_start: 0.8685 (mp0) cc_final: 0.8424 (mp0) REVERT: D 70 LYS cc_start: 0.9486 (mtpp) cc_final: 0.9227 (mmtp) REVERT: D 99 LEU cc_start: 0.9375 (tp) cc_final: 0.9065 (mm) REVERT: D 103 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8240 (tmtt) REVERT: D 190 GLU cc_start: 0.9159 (tt0) cc_final: 0.8723 (tt0) REVERT: D 241 TRP cc_start: 0.9304 (m100) cc_final: 0.8735 (m100) REVERT: D 279 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8212 (mtmp) REVERT: D 283 MET cc_start: 0.8955 (tpp) cc_final: 0.8687 (mmm) REVERT: D 306 PHE cc_start: 0.8838 (t80) cc_final: 0.8393 (t80) REVERT: E 17 ASP cc_start: 0.9013 (m-30) cc_final: 0.8394 (m-30) REVERT: E 61 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.9155 (pmm) REVERT: E 70 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9098 (mmpt) REVERT: E 79 LEU cc_start: 0.8859 (mt) cc_final: 0.8639 (mm) REVERT: E 190 GLU cc_start: 0.9135 (tt0) cc_final: 0.8695 (tt0) REVERT: E 218 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8506 (pt) REVERT: E 244 TYR cc_start: 0.8583 (p90) cc_final: 0.8266 (p90) outliers start: 21 outliers final: 9 residues processed: 264 average time/residue: 0.6098 time to fit residues: 174.8886 Evaluate side-chains 264 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 115 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 28 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.085974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.059727 restraints weight = 117997.047| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 5.40 r_work: 0.2515 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14800 Z= 0.149 Angle : 0.840 43.509 20235 Z= 0.396 Chirality : 0.046 0.220 2370 Planarity : 0.004 0.068 2440 Dihedral : 6.300 39.623 2755 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.79 % Allowed : 18.48 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.21), residues: 1690 helix: 2.01 (0.20), residues: 635 sheet: 1.51 (0.25), residues: 395 loop : 0.56 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 425 TYR 0.044 0.002 TYR B 299 PHE 0.027 0.001 PHE A 306 TRP 0.009 0.001 TRP E 67 HIS 0.003 0.001 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (14755) covalent geometry : angle 0.83602 / 0.40 (20105) SS BOND : bond 0.00193 / 0.13 ( 5) SS BOND : angle 0.34967 / 0.26 ( 10) hydrogen bonds : bond 0.03287 / 2.13 ( 770) hydrogen bonds : angle 3.96410 / 2.77 ( 2490) link_ALPHA1-3 : bond 0.01059 / 0.68 ( 5) link_ALPHA1-3 : angle 1.41214 / 0.97 ( 15) link_ALPHA1-6 : bond 0.01023 / 0.67 ( 5) link_ALPHA1-6 : angle 1.73685 / 1.19 ( 15) link_BETA1-4 : bond 0.00386 / 0.26 ( 15) link_BETA1-4 : angle 1.33720 / 0.92 ( 45) link_NAG-ASN : bond 0.00081 / 0.06 ( 15) link_NAG-ASN : angle 1.37600 / 1.00 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5914.96 seconds wall clock time: 101 minutes 37.82 seconds (6097.82 seconds total)