Starting phenix.real_space_refine on Thu Sep 18 05:22:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fex_50344/09_2025/9fex_50344.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fex_50344/09_2025/9fex_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fex_50344/09_2025/9fex_50344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fex_50344/09_2025/9fex_50344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fex_50344/09_2025/9fex_50344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fex_50344/09_2025/9fex_50344.map" } 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-2.0-5805/lib/python3.9/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, 23 Unusual residues: {' CL': 1, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 23 Unusual residues: {' CL': 1, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 23 Unusual residues: {' CL': 1, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 23 Unusual residues: {' CL': 1, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 23 Unusual residues: {' CL': 1, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 5.72, 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: 1.21 Conformation dependent library (CDL) restraints added in 983.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.48 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: 2.59 Time building geometry restraints manager: 1.63 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.990 Find NCS groups from input model: 0.390 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:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 aren 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 covalent geometry : bond 0.00324 (14755) covalent geometry : angle 0.53742 (20105) SS BOND : bond 0.00272 ( 5) SS BOND : angle 0.49644 ( 10) hydrogen bonds : bond 0.09138 ( 770) hydrogen bonds : angle 4.47332 ( 2490) link_ALPHA1-3 : bond 0.00130 ( 5) link_ALPHA1-3 : angle 1.31014 ( 15) link_ALPHA1-6 : bond 0.00298 ( 5) link_ALPHA1-6 : angle 0.97451 ( 15) link_BETA1-4 : bond 0.00273 ( 15) link_BETA1-4 : angle 1.54412 ( 45) link_NAG-ASN : bond 0.00062 ( 15) link_NAG-ASN : angle 1.28232 ( 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 : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8319 (t80) cc_final: 0.8012 (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: 0.7078 time to fit residues: 271.2308 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 : 0.667 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B B 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 = 0.3272 r_free = 0.3272 target = 0.085530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.059101 restraints weight = 122728.387| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 5.34 r_work: 0.2467 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 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 = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14800 Z= 0.134 Angle : 0.620 9.133 20235 Z= 0.310 Chirality : 0.045 0.177 2370 Planarity : 0.004 0.033 2440 Dihedral : 10.433 79.625 2761 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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 aren not related in a simple way. whole: 2.11 (0.22), residues: 1690 helix: 2.34 (0.21), residues: 635 sheet: 1.37 (0.26), residues: 380 loop : 0.59 (0.27), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 425 TYR 0.028 0.002 TYR E 277 PHE 0.012 0.001 PHE D 186 TRP 0.030 0.001 TRP B 241 HIS 0.003 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00293 (14755) covalent geometry : angle 0.60800 (20105) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.29515 ( 10) hydrogen bonds : bond 0.03666 ( 770) hydrogen bonds : angle 4.19824 ( 2490) link_ALPHA1-3 : bond 0.00902 ( 5) link_ALPHA1-3 : angle 2.34683 ( 15) link_ALPHA1-6 : bond 0.00561 ( 5) link_ALPHA1-6 : angle 2.05226 ( 15) link_BETA1-4 : bond 0.00304 ( 15) link_BETA1-4 : angle 1.59783 ( 45) link_NAG-ASN : bond 0.00181 ( 15) link_NAG-ASN : angle 1.41427 ( 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 317 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 272 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 55 MET cc_start: 0.9086 (mmm) cc_final: 0.8857 (mmm) REVERT: A 173 LYS cc_start: 0.9462 (mtmm) cc_final: 0.9253 (mmmm) REVERT: A 190 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8807 (tt0) REVERT: B 14 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8764 (pp20) REVERT: B 17 ASP cc_start: 0.8961 (m-30) cc_final: 0.8728 (m-30) REVERT: B 99 LEU cc_start: 0.9412 (tp) cc_final: 0.9051 (mt) REVERT: B 218 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8409 (pp) REVERT: B 224 GLN cc_start: 0.9063 (tp40) cc_final: 0.8487 (mm110) REVERT: B 244 TYR cc_start: 0.8206 (p90) cc_final: 0.7894 (p90) REVERT: B 309 GLN cc_start: 0.8334 (tp40) cc_final: 0.7938 (pm20) REVERT: C 9 MET cc_start: 0.8061 (mtp) cc_final: 0.7565 (mtp) REVERT: C 14 GLU cc_start: 0.8990 (pt0) cc_final: 0.8684 (pp20) REVERT: C 79 LEU cc_start: 0.8791 (mt) cc_final: 0.8564 (mm) REVERT: C 218 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8269 (pp) REVERT: C 244 TYR cc_start: 0.8571 (p90) cc_final: 0.8135 (p90) REVERT: C 286 MET cc_start: 0.8472 (tpp) cc_final: 0.8223 (tpt) REVERT: C 309 GLN cc_start: 0.7926 (tp40) cc_final: 0.7652 (pm20) REVERT: D 52 GLU cc_start: 0.8792 (mp0) cc_final: 0.8538 (mp0) REVERT: D 190 GLU cc_start: 0.9019 (tt0) cc_final: 0.8753 (tt0) REVERT: D 269 ARG cc_start: 0.7375 (tpm170) cc_final: 0.7158 (tpm170) REVERT: D 309 GLN cc_start: 0.8259 (tp-100) cc_final: 0.8001 (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: 0.8161 (pp) REVERT: E 282 ASP cc_start: 0.9189 (m-30) cc_final: 0.8798 (m-30) REVERT: E 309 GLN cc_start: 0.8024 (tp40) cc_final: 0.7728 (pm20) outliers start: 45 outliers final: 13 residues processed: 295 average time/residue: 0.7262 time to fit residues: 232.1147 Evaluate side-chains 270 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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: 1.9990 chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.084795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.058526 restraints weight = 123161.108| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 5.32 r_work: 0.2467 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14800 Z= 0.137 Angle : 0.598 8.861 20235 Z= 0.301 Chirality : 0.045 0.197 2370 Planarity : 0.004 0.026 2440 Dihedral : 9.712 73.247 2757 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.19 % Allowed : 14.97 % Favored : 82.85 % 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 aren not related in a simple way. whole: 1.91 (0.21), residues: 1690 helix: 2.13 (0.21), residues: 635 sheet: 1.29 (0.25), residues: 395 loop : 0.50 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 425 TYR 0.020 0.002 TYR E 277 PHE 0.011 0.001 PHE E 306 TRP 0.009 0.001 TRP B 241 HIS 0.003 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00310 (14755) covalent geometry : angle 0.58822 (20105) SS BOND : bond 0.00246 ( 5) SS BOND : angle 0.46632 ( 10) hydrogen bonds : bond 0.03493 ( 770) hydrogen bonds : angle 4.14066 ( 2490) link_ALPHA1-3 : bond 0.01007 ( 5) link_ALPHA1-3 : angle 1.65171 ( 15) link_ALPHA1-6 : bond 0.00743 ( 5) link_ALPHA1-6 : angle 2.08215 ( 15) link_BETA1-4 : bond 0.00313 ( 15) link_BETA1-4 : angle 1.42367 ( 45) link_NAG-ASN : bond 0.00097 ( 15) link_NAG-ASN : angle 1.29087 ( 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: 33 poor density : 260 time to evaluate : 0.482 Fit side-chains REVERT: A 70 LYS cc_start: 0.9398 (mtpp) cc_final: 0.9082 (mmtp) REVERT: A 79 LEU cc_start: 0.8876 (mt) cc_final: 0.8622 (mm) REVERT: A 179 GLU cc_start: 0.8824 (pp20) cc_final: 0.8389 (pp20) REVERT: A 182 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8549 (tp30) REVERT: A 190 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8963 (tt0) REVERT: A 241 TRP cc_start: 0.9140 (m100) cc_final: 0.8798 (m100) REVERT: A 309 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: A 429 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9043 (tp) REVERT: B 14 GLU cc_start: 0.9031 (pt0) cc_final: 0.8771 (pp20) REVERT: B 17 ASP cc_start: 0.9022 (m-30) cc_final: 0.8797 (m-30) REVERT: B 99 LEU cc_start: 0.9391 (tp) cc_final: 0.9039 (mt) REVERT: B 218 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8361 (pp) REVERT: B 224 GLN cc_start: 0.9094 (tp40) cc_final: 0.8506 (mm110) REVERT: B 244 TYR cc_start: 0.8381 (p90) cc_final: 0.7894 (p90) REVERT: B 306 PHE cc_start: 0.8922 (t80) cc_final: 0.8720 (t80) REVERT: B 309 GLN cc_start: 0.8242 (tp40) cc_final: 0.7918 (pm20) REVERT: C 9 MET cc_start: 0.8093 (mtp) cc_final: 0.7638 (mtp) REVERT: C 14 GLU cc_start: 0.8999 (pt0) cc_final: 0.8700 (pp20) REVERT: C 70 LYS cc_start: 0.9324 (mtpp) cc_final: 0.8971 (mmtm) REVERT: C 79 LEU cc_start: 0.8792 (mt) cc_final: 0.8551 (mm) REVERT: C 112 LYS cc_start: 0.8873 (tttm) cc_final: 0.8617 (tttm) REVERT: C 218 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8470 (pp) REVERT: C 244 TYR cc_start: 0.8610 (p90) cc_final: 0.8189 (p90) REVERT: C 425 ARG cc_start: 0.8587 (ptp-110) cc_final: 0.8081 (mtm-85) REVERT: D 14 GLU cc_start: 0.8516 (pp20) cc_final: 0.8307 (pp20) REVERT: D 52 GLU cc_start: 0.8829 (mp0) cc_final: 0.8560 (mp0) REVERT: D 103 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8256 (tmtt) REVERT: D 190 GLU cc_start: 0.9108 (tt0) cc_final: 0.8830 (tt0) REVERT: D 269 ARG cc_start: 0.7371 (tpm170) cc_final: 0.7136 (tpm170) REVERT: E 61 MET cc_start: 0.9654 (OUTLIER) cc_final: 0.9136 (pmm) REVERT: E 79 LEU cc_start: 0.8788 (mt) cc_final: 0.8569 (mm) REVERT: E 155 GLU cc_start: 0.9282 (tt0) cc_final: 0.9063 (tt0) REVERT: E 218 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8175 (pp) REVERT: E 244 TYR cc_start: 0.8325 (p90) cc_final: 0.7893 (p90) REVERT: E 269 ARG cc_start: 0.7428 (tpm170) cc_final: 0.7152 (tpm170) REVERT: E 283 MET cc_start: 0.8856 (tpp) cc_final: 0.8621 (mmm) REVERT: E 309 GLN cc_start: 0.8115 (tp40) cc_final: 0.7863 (pm20) outliers start: 33 outliers final: 5 residues processed: 270 average time/residue: 0.7472 time to fit residues: 217.7655 Evaluate side-chains 250 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 237 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 218 ILE 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 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 Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 13 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.084315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.058077 restraints weight = 119344.813| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 5.26 r_work: 0.2461 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14800 Z= 0.153 Angle : 0.617 10.178 20235 Z= 0.306 Chirality : 0.045 0.214 2370 Planarity : 0.003 0.025 2440 Dihedral : 9.094 67.574 2757 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.38 % Allowed : 15.23 % Favored : 82.38 % 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 aren not related in a simple way. whole: 1.90 (0.21), residues: 1690 helix: 2.11 (0.21), residues: 635 sheet: 0.98 (0.24), residues: 420 loop : 0.72 (0.28), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 425 TYR 0.017 0.002 TYR E 277 PHE 0.012 0.001 PHE D 293 TRP 0.009 0.001 TRP E 237 HIS 0.003 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00354 (14755) covalent geometry : angle 0.60669 (20105) SS BOND : bond 0.00293 ( 5) SS BOND : angle 0.62912 ( 10) hydrogen bonds : bond 0.03416 ( 770) hydrogen bonds : angle 4.13363 ( 2490) link_ALPHA1-3 : bond 0.01017 ( 5) link_ALPHA1-3 : angle 1.86407 ( 15) link_ALPHA1-6 : bond 0.00788 ( 5) link_ALPHA1-6 : angle 2.18738 ( 15) link_BETA1-4 : bond 0.00296 ( 15) link_BETA1-4 : angle 1.45289 ( 45) link_NAG-ASN : bond 0.00072 ( 15) link_NAG-ASN : angle 1.30318 ( 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 279 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.551 Fit side-chains REVERT: A 70 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9087 (mmtp) REVERT: A 179 GLU cc_start: 0.8852 (pp20) cc_final: 0.8422 (pp20) REVERT: A 182 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8542 (tp30) REVERT: A 190 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8954 (tt0) REVERT: A 241 TRP cc_start: 0.9158 (m100) cc_final: 0.8768 (m100) REVERT: A 309 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: B 17 ASP cc_start: 0.9037 (m-30) cc_final: 0.8786 (m-30) REVERT: B 70 LYS cc_start: 0.9419 (mtpp) cc_final: 0.9082 (mptm) REVERT: B 218 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8358 (pp) REVERT: B 224 GLN cc_start: 0.9108 (tp40) cc_final: 0.8560 (mm110) REVERT: B 244 TYR cc_start: 0.8388 (p90) cc_final: 0.7986 (p90) REVERT: B 309 GLN cc_start: 0.8235 (tp40) cc_final: 0.7925 (pm20) REVERT: C 9 MET cc_start: 0.8005 (mtp) cc_final: 0.7538 (mtp) REVERT: C 14 GLU cc_start: 0.8927 (pt0) cc_final: 0.8644 (pp20) REVERT: C 70 LYS cc_start: 0.9326 (mtpp) cc_final: 0.8963 (mmtm) REVERT: C 79 LEU cc_start: 0.8799 (mt) cc_final: 0.8558 (mm) REVERT: C 112 LYS cc_start: 0.8865 (tttm) cc_final: 0.8631 (tttm) REVERT: C 218 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8428 (pp) REVERT: C 244 TYR cc_start: 0.8635 (p90) cc_final: 0.8187 (p90) REVERT: C 309 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6704 (pm20) REVERT: C 425 ARG cc_start: 0.8570 (ptp-110) cc_final: 0.8045 (mtm-85) REVERT: D 52 GLU cc_start: 0.8852 (mp0) cc_final: 0.8556 (mp0) REVERT: D 70 LYS cc_start: 0.9483 (mtpp) cc_final: 0.9218 (mmtp) REVERT: D 190 GLU cc_start: 0.9093 (tt0) cc_final: 0.8808 (tt0) REVERT: D 244 TYR cc_start: 0.8646 (p90) cc_final: 0.8419 (p90) REVERT: D 269 ARG cc_start: 0.7419 (tpm170) cc_final: 0.7189 (tpm170) REVERT: E 17 ASP cc_start: 0.8905 (m-30) cc_final: 0.8377 (m-30) REVERT: E 61 MET cc_start: 0.9655 (OUTLIER) cc_final: 0.9122 (pmm) REVERT: E 70 LYS cc_start: 0.9365 (mtpp) cc_final: 0.9095 (mmtp) REVERT: E 79 LEU cc_start: 0.8815 (mt) cc_final: 0.8600 (mm) REVERT: E 218 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8189 (pp) REVERT: E 244 TYR cc_start: 0.8482 (p90) cc_final: 0.8024 (p90) REVERT: E 269 ARG cc_start: 0.7446 (tpm170) cc_final: 0.7044 (tpm170) REVERT: E 309 GLN cc_start: 0.8227 (tp40) cc_final: 0.8018 (pm20) outliers start: 36 outliers final: 13 residues processed: 257 average time/residue: 0.7354 time to fit residues: 204.1095 Evaluate side-chains 253 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS 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 C residue 36 VAL 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 306 PHE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 444 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 218 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 444 LEU 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: 4.9990 chunk 152 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.084105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.058060 restraints weight = 107735.502| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 5.10 r_work: 0.2471 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2465 r_free = 0.2465 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2465 r_free = 0.2465 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14800 Z= 0.147 Angle : 0.613 9.221 20235 Z= 0.304 Chirality : 0.045 0.226 2370 Planarity : 0.003 0.026 2440 Dihedral : 8.483 61.878 2757 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.25 % Allowed : 15.70 % Favored : 82.05 % 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 aren not related in a simple way. whole: 1.92 (0.21), residues: 1690 helix: 2.15 (0.21), residues: 635 sheet: 0.97 (0.24), residues: 420 loop : 0.73 (0.28), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 425 TYR 0.017 0.001 TYR A 244 PHE 0.011 0.001 PHE D 293 TRP 0.008 0.001 TRP E 426 HIS 0.003 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00337 (14755) covalent geometry : angle 0.60284 (20105) SS BOND : bond 0.00264 ( 5) SS BOND : angle 0.51391 ( 10) hydrogen bonds : bond 0.03412 ( 770) hydrogen bonds : angle 4.08885 ( 2490) link_ALPHA1-3 : bond 0.00986 ( 5) link_ALPHA1-3 : angle 1.70272 ( 15) link_ALPHA1-6 : bond 0.00878 ( 5) link_ALPHA1-6 : angle 2.19571 ( 15) link_BETA1-4 : bond 0.00307 ( 15) link_BETA1-4 : angle 1.42242 ( 45) link_NAG-ASN : bond 0.00078 ( 15) link_NAG-ASN : angle 1.35177 ( 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: 34 poor density : 243 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9476 (OUTLIER) cc_final: 0.9158 (mmtp) REVERT: A 179 GLU cc_start: 0.8878 (pp20) cc_final: 0.8397 (pp20) REVERT: A 182 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8603 (tp30) REVERT: A 190 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8869 (tt0) REVERT: A 241 TRP cc_start: 0.9186 (m100) cc_final: 0.8787 (m100) REVERT: A 309 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: B 14 GLU cc_start: 0.8583 (pp20) cc_final: 0.8338 (pp20) REVERT: B 17 ASP cc_start: 0.9070 (m-30) cc_final: 0.8804 (m-30) REVERT: B 70 LYS cc_start: 0.9417 (mtpp) cc_final: 0.9086 (mptm) REVERT: B 218 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8367 (pp) REVERT: B 224 GLN cc_start: 0.9130 (tp40) cc_final: 0.8543 (mm110) REVERT: B 244 TYR cc_start: 0.8361 (p90) cc_final: 0.7928 (p90) REVERT: B 306 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8688 (t80) REVERT: C 9 MET cc_start: 0.7991 (mtp) cc_final: 0.7606 (mtp) REVERT: C 70 LYS cc_start: 0.9328 (mtpp) cc_final: 0.8965 (mmtm) REVERT: C 79 LEU cc_start: 0.8843 (mt) cc_final: 0.8605 (mm) REVERT: C 112 LYS cc_start: 0.8885 (tttm) cc_final: 0.8649 (tttm) REVERT: C 218 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8435 (pp) REVERT: C 244 TYR cc_start: 0.8654 (p90) cc_final: 0.8229 (p90) REVERT: C 309 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6898 (pm20) REVERT: D 52 GLU cc_start: 0.8835 (mp0) cc_final: 0.8489 (mp0) REVERT: D 70 LYS cc_start: 0.9509 (mtpp) cc_final: 0.9244 (mmtp) REVERT: D 103 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8239 (tmtt) REVERT: D 190 GLU cc_start: 0.9099 (tt0) cc_final: 0.8767 (tt0) REVERT: D 269 ARG cc_start: 0.7337 (tpm170) cc_final: 0.7066 (tpm170) REVERT: D 283 MET cc_start: 0.9024 (tpp) cc_final: 0.8780 (mmm) REVERT: E 17 ASP cc_start: 0.8913 (m-30) cc_final: 0.8335 (m-30) REVERT: E 61 MET cc_start: 0.9634 (OUTLIER) cc_final: 0.9140 (pmm) REVERT: E 70 LYS cc_start: 0.9401 (mtpp) cc_final: 0.9079 (mmtp) REVERT: E 79 LEU cc_start: 0.8818 (mt) cc_final: 0.8597 (mm) REVERT: E 190 GLU cc_start: 0.9169 (tt0) cc_final: 0.8760 (tt0) REVERT: E 218 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8182 (pp) REVERT: E 224 GLN cc_start: 0.9056 (mm110) cc_final: 0.8651 (mm110) REVERT: E 244 TYR cc_start: 0.8484 (p90) cc_final: 0.8041 (p90) REVERT: E 269 ARG cc_start: 0.7405 (tpm170) cc_final: 0.6995 (tpm170) REVERT: E 283 MET cc_start: 0.8987 (tpp) cc_final: 0.8711 (mmm) REVERT: E 309 GLN cc_start: 0.8226 (tp40) cc_final: 0.8024 (pm20) outliers start: 34 outliers final: 12 residues processed: 254 average time/residue: 0.7832 time to fit residues: 215.1883 Evaluate side-chains 254 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 294 LEU Chi-restraints excluded: chain A residue 302 VAL 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 145 LEU Chi-restraints excluded: chain C residue 218 ILE 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 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 Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 0.0050 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.059244 restraints weight = 114353.469| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 5.24 r_work: 0.2489 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2489 ------------------------------------------------------------------------------- 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 = 0.12 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 = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14800 Z= 0.120 Angle : 0.619 10.203 20235 Z= 0.304 Chirality : 0.044 0.238 2370 Planarity : 0.003 0.025 2440 Dihedral : 7.877 56.572 2757 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.45 % Allowed : 15.96 % Favored : 81.59 % 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 aren not related in a simple way. whole: 1.97 (0.21), residues: 1690 helix: 2.18 (0.21), residues: 635 sheet: 1.32 (0.25), residues: 395 loop : 0.53 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 425 TYR 0.017 0.001 TYR A 244 PHE 0.011 0.001 PHE D 306 TRP 0.010 0.001 TRP C 67 HIS 0.002 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00270 (14755) covalent geometry : angle 0.61094 (20105) SS BOND : bond 0.00189 ( 5) SS BOND : angle 0.42422 ( 10) hydrogen bonds : bond 0.03246 ( 770) hydrogen bonds : angle 4.03364 ( 2490) link_ALPHA1-3 : bond 0.01115 ( 5) link_ALPHA1-3 : angle 1.61567 ( 15) link_ALPHA1-6 : bond 0.00984 ( 5) link_ALPHA1-6 : angle 2.09860 ( 15) link_BETA1-4 : bond 0.00363 ( 15) link_BETA1-4 : angle 1.32088 ( 45) link_NAG-ASN : bond 0.00156 ( 15) link_NAG-ASN : angle 1.28766 ( 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 282 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 70 LYS cc_start: 0.9475 (OUTLIER) cc_final: 0.9169 (mmtp) REVERT: A 79 LEU cc_start: 0.8925 (mt) cc_final: 0.8688 (mm) REVERT: A 179 GLU cc_start: 0.8855 (pp20) cc_final: 0.8359 (pp20) REVERT: A 182 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8620 (tp30) REVERT: A 190 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8941 (tt0) REVERT: A 241 TRP cc_start: 0.9214 (m100) cc_final: 0.8982 (m-90) REVERT: A 244 TYR cc_start: 0.8514 (p90) cc_final: 0.8192 (p90) REVERT: A 306 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8479 (t80) REVERT: A 309 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: B 17 ASP cc_start: 0.9117 (m-30) cc_final: 0.8858 (m-30) REVERT: B 61 MET cc_start: 0.9547 (OUTLIER) cc_final: 0.9123 (ptp) REVERT: B 70 LYS cc_start: 0.9404 (mtpp) cc_final: 0.9089 (mptm) REVERT: B 218 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8385 (pp) REVERT: B 224 GLN cc_start: 0.9131 (tp40) cc_final: 0.8614 (mm110) REVERT: B 244 TYR cc_start: 0.8416 (p90) cc_final: 0.7977 (p90) REVERT: B 309 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: C 9 MET cc_start: 0.8060 (mtp) cc_final: 0.7695 (mtt) REVERT: C 61 MET cc_start: 0.9658 (OUTLIER) cc_final: 0.8233 (ptp) REVERT: C 70 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9009 (mmtm) REVERT: C 79 LEU cc_start: 0.8870 (mt) cc_final: 0.8625 (mm) REVERT: C 112 LYS cc_start: 0.8936 (tttm) cc_final: 0.8711 (tttm) REVERT: C 218 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8459 (pp) REVERT: C 244 TYR cc_start: 0.8605 (p90) cc_final: 0.8170 (p90) REVERT: C 309 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: D 52 GLU cc_start: 0.8837 (mp0) cc_final: 0.8457 (mp0) REVERT: D 70 LYS cc_start: 0.9504 (OUTLIER) cc_final: 0.9260 (mmtp) REVERT: D 103 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8258 (tmtt) REVERT: D 190 GLU cc_start: 0.9113 (tt0) cc_final: 0.8754 (tt0) REVERT: D 269 ARG cc_start: 0.7430 (tpm170) cc_final: 0.7211 (tpm170) REVERT: E 17 ASP cc_start: 0.8916 (m-30) cc_final: 0.8291 (m-30) REVERT: E 61 MET cc_start: 0.9604 (OUTLIER) cc_final: 0.9201 (pmm) REVERT: E 70 LYS cc_start: 0.9427 (mtpp) cc_final: 0.9020 (mmpt) REVERT: E 79 LEU cc_start: 0.8834 (mt) cc_final: 0.8611 (mm) REVERT: E 190 GLU cc_start: 0.9178 (tt0) cc_final: 0.8799 (tt0) REVERT: E 218 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8391 (pp) REVERT: E 224 GLN cc_start: 0.9059 (mm110) cc_final: 0.8679 (mm110) REVERT: E 269 ARG cc_start: 0.7454 (tpm170) cc_final: 0.7047 (tpm170) outliers start: 37 outliers final: 10 residues processed: 253 average time/residue: 0.7809 time to fit residues: 213.1409 Evaluate side-chains 256 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 306 PHE 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 309 GLN 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 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 70 LYS Chi-restraints excluded: chain D residue 103 LYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 157 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 148 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 126 optimal weight: 0.0000 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.059537 restraints weight = 110801.742| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 5.18 r_work: 0.2504 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14800 Z= 0.121 Angle : 0.622 10.455 20235 Z= 0.306 Chirality : 0.045 0.240 2370 Planarity : 0.003 0.025 2440 Dihedral : 7.430 52.449 2755 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.45 % Allowed : 16.42 % 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 aren not related in a simple way. whole: 2.01 (0.21), residues: 1690 helix: 2.19 (0.20), residues: 635 sheet: 1.36 (0.25), residues: 395 loop : 0.57 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 425 TYR 0.039 0.001 TYR E 299 PHE 0.012 0.001 PHE E 306 TRP 0.010 0.001 TRP C 67 HIS 0.002 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00271 (14755) covalent geometry : angle 0.61385 (20105) SS BOND : bond 0.00167 ( 5) SS BOND : angle 0.31492 ( 10) hydrogen bonds : bond 0.03245 ( 770) hydrogen bonds : angle 3.96665 ( 2490) link_ALPHA1-3 : bond 0.01098 ( 5) link_ALPHA1-3 : angle 1.58611 ( 15) link_ALPHA1-6 : bond 0.01003 ( 5) link_ALPHA1-6 : angle 2.02597 ( 15) link_BETA1-4 : bond 0.00379 ( 15) link_BETA1-4 : angle 1.31352 ( 45) link_NAG-ASN : bond 0.00149 ( 15) link_NAG-ASN : angle 1.30588 ( 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 275 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.9400 (ttpp) cc_final: 0.8994 (tmmm) REVERT: A 70 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.9166 (mmtp) REVERT: A 79 LEU cc_start: 0.8935 (mt) cc_final: 0.8694 (mm) REVERT: A 103 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8574 (tptp) REVERT: A 179 GLU cc_start: 0.8867 (pp20) cc_final: 0.8360 (pp20) REVERT: A 182 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8579 (tp30) REVERT: A 190 GLU cc_start: 0.9223 (tt0) cc_final: 0.8911 (tt0) REVERT: A 241 TRP cc_start: 0.9212 (m100) cc_final: 0.8984 (m-90) REVERT: A 309 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: B 17 ASP cc_start: 0.9155 (m-30) cc_final: 0.8891 (m-30) REVERT: B 61 MET cc_start: 0.9526 (OUTLIER) cc_final: 0.9096 (ptp) REVERT: B 70 LYS cc_start: 0.9405 (mtpp) cc_final: 0.9098 (mptm) REVERT: B 190 GLU cc_start: 0.9159 (tt0) cc_final: 0.8907 (pt0) REVERT: B 218 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8408 (pp) REVERT: B 224 GLN cc_start: 0.9151 (tp40) cc_final: 0.8641 (mm110) REVERT: B 244 TYR cc_start: 0.8414 (p90) cc_final: 0.7975 (p90) REVERT: B 309 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: C 9 MET cc_start: 0.8118 (mtp) cc_final: 0.7729 (mtp) REVERT: C 61 MET cc_start: 0.9629 (OUTLIER) cc_final: 0.8149 (ptp) REVERT: C 70 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9010 (mmtm) REVERT: C 79 LEU cc_start: 0.8883 (mt) cc_final: 0.8644 (mm) REVERT: C 112 LYS cc_start: 0.8951 (tttm) cc_final: 0.8725 (tttm) REVERT: C 218 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8470 (pp) REVERT: C 244 TYR cc_start: 0.8591 (p90) cc_final: 0.8155 (p90) REVERT: C 309 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7152 (pm20) REVERT: D 52 GLU cc_start: 0.8822 (mp0) cc_final: 0.8415 (mp0) REVERT: D 70 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.9215 (mmtp) REVERT: D 103 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8285 (tmtt) REVERT: D 190 GLU cc_start: 0.9115 (tt0) cc_final: 0.8711 (tt0) REVERT: D 269 ARG cc_start: 0.7474 (tpm170) cc_final: 0.7262 (tpm170) REVERT: E 17 ASP cc_start: 0.8947 (m-30) cc_final: 0.8349 (m-30) REVERT: E 61 MET cc_start: 0.9588 (OUTLIER) cc_final: 0.9224 (pmm) REVERT: E 70 LYS cc_start: 0.9427 (mtpp) cc_final: 0.9019 (mmpt) REVERT: E 79 LEU cc_start: 0.8848 (mt) cc_final: 0.8623 (mm) REVERT: E 190 GLU cc_start: 0.9115 (tt0) cc_final: 0.8706 (tt0) REVERT: E 218 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8359 (pp) REVERT: E 269 ARG cc_start: 0.7397 (tpm170) cc_final: 0.7003 (tpm170) outliers start: 37 outliers final: 12 residues processed: 252 average time/residue: 0.7727 time to fit residues: 210.4608 Evaluate side-chains 256 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 302 VAL 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 70 LYS 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 306 PHE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 103 LYS 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 302 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.084825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.058844 restraints weight = 110404.156| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 5.18 r_work: 0.2491 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2494 r_free = 0.2494 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2494 r_free = 0.2494 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14800 Z= 0.137 Angle : 0.647 12.665 20235 Z= 0.317 Chirality : 0.045 0.237 2370 Planarity : 0.003 0.032 2440 Dihedral : 7.097 48.529 2755 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.38 % Allowed : 16.49 % 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 aren not related in a simple way. whole: 1.99 (0.21), residues: 1690 helix: 2.19 (0.20), residues: 635 sheet: 1.36 (0.25), residues: 395 loop : 0.54 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 425 TYR 0.028 0.001 TYR E 299 PHE 0.018 0.001 PHE A 306 TRP 0.009 0.001 TRP C 426 HIS 0.002 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00317 (14755) covalent geometry : angle 0.63901 (20105) SS BOND : bond 0.00183 ( 5) SS BOND : angle 0.33431 ( 10) hydrogen bonds : bond 0.03308 ( 770) hydrogen bonds : angle 4.00113 ( 2490) link_ALPHA1-3 : bond 0.01086 ( 5) link_ALPHA1-3 : angle 1.57618 ( 15) link_ALPHA1-6 : bond 0.00995 ( 5) link_ALPHA1-6 : angle 1.97621 ( 15) link_BETA1-4 : bond 0.00357 ( 15) link_BETA1-4 : angle 1.34999 ( 45) link_NAG-ASN : bond 0.00090 ( 15) link_NAG-ASN : angle 1.37172 ( 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 279 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.9419 (ttpp) cc_final: 0.8990 (tmmm) REVERT: A 70 LYS cc_start: 0.9476 (OUTLIER) cc_final: 0.9160 (mmtp) REVERT: A 103 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8569 (tptp) REVERT: A 179 GLU cc_start: 0.8880 (pp20) cc_final: 0.8369 (pp20) REVERT: A 190 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8909 (tt0) REVERT: A 241 TRP cc_start: 0.9215 (m100) cc_final: 0.8977 (m-90) REVERT: A 309 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: A 425 ARG cc_start: 0.8664 (mtp-110) cc_final: 0.8271 (ptp90) REVERT: B 17 ASP cc_start: 0.9121 (m-30) cc_final: 0.8894 (m-30) REVERT: B 61 MET cc_start: 0.9548 (OUTLIER) cc_final: 0.9125 (ptp) REVERT: B 70 LYS cc_start: 0.9409 (mtpp) cc_final: 0.9136 (mptm) REVERT: B 218 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8425 (pp) REVERT: B 224 GLN cc_start: 0.9148 (tp40) cc_final: 0.8628 (mm110) REVERT: B 244 TYR cc_start: 0.8446 (p90) cc_final: 0.7988 (p90) REVERT: B 309 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: C 70 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9002 (mmtm) REVERT: C 79 LEU cc_start: 0.8879 (mt) cc_final: 0.8638 (mm) REVERT: C 112 LYS cc_start: 0.8967 (tttm) cc_final: 0.8746 (tttm) REVERT: C 137 MET cc_start: 0.8761 (mmm) cc_final: 0.8561 (mmm) REVERT: C 218 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8489 (pp) REVERT: C 244 TYR cc_start: 0.8600 (p90) cc_final: 0.8168 (p90) REVERT: C 309 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: D 52 GLU cc_start: 0.8784 (mp0) cc_final: 0.8365 (mp0) REVERT: D 70 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9258 (mmtp) REVERT: D 103 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8324 (tmtt) REVERT: D 190 GLU cc_start: 0.9108 (tt0) cc_final: 0.8699 (tt0) REVERT: D 241 TRP cc_start: 0.9285 (m100) cc_final: 0.8697 (m100) REVERT: D 269 ARG cc_start: 0.7578 (tpm170) cc_final: 0.7369 (tpm170) REVERT: E 17 ASP cc_start: 0.8952 (m-30) cc_final: 0.8340 (m-30) REVERT: E 61 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.9224 (pmm) REVERT: E 70 LYS cc_start: 0.9432 (mtpp) cc_final: 0.9024 (mmpt) REVERT: E 79 LEU cc_start: 0.8844 (mt) cc_final: 0.8616 (mm) REVERT: E 190 GLU cc_start: 0.9110 (tt0) cc_final: 0.8689 (tt0) REVERT: E 218 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8386 (pp) REVERT: E 224 GLN cc_start: 0.9043 (mm110) cc_final: 0.8670 (mm110) REVERT: E 244 TYR cc_start: 0.8646 (p90) cc_final: 0.8265 (p90) outliers start: 36 outliers final: 14 residues processed: 252 average time/residue: 0.7456 time to fit residues: 203.1593 Evaluate side-chains 262 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 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 302 VAL 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 70 LYS Chi-restraints excluded: chain C residue 87 VAL 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 70 LYS Chi-restraints excluded: chain D residue 103 LYS 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 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: 0.8980 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 139 optimal weight: 0.0040 chunk 113 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.085393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.059382 restraints weight = 120178.632| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 5.33 r_work: 0.2494 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2502 r_free = 0.2502 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2502 r_free = 0.2502 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2774 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= 0.125 Angle : 0.647 11.727 20235 Z= 0.317 Chirality : 0.045 0.235 2370 Planarity : 0.003 0.030 2440 Dihedral : 6.738 44.515 2755 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.99 % Allowed : 17.35 % Favored : 80.66 % 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 aren not related in a simple way. whole: 1.99 (0.21), residues: 1690 helix: 2.17 (0.20), residues: 635 sheet: 1.37 (0.25), residues: 395 loop : 0.54 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 425 TYR 0.026 0.001 TYR E 299 PHE 0.023 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 covalent geometry : bond 0.00285 (14755) covalent geometry : angle 0.64026 (20105) SS BOND : bond 0.00156 ( 5) SS BOND : angle 0.27762 ( 10) hydrogen bonds : bond 0.03270 ( 770) hydrogen bonds : angle 3.96426 ( 2490) link_ALPHA1-3 : bond 0.01117 ( 5) link_ALPHA1-3 : angle 1.42574 ( 15) link_ALPHA1-6 : bond 0.00995 ( 5) link_ALPHA1-6 : angle 1.82452 ( 15) link_BETA1-4 : bond 0.00395 ( 15) link_BETA1-4 : angle 1.31088 ( 45) link_NAG-ASN : bond 0.00136 ( 15) link_NAG-ASN : angle 1.34680 ( 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 275 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.9434 (ttpp) cc_final: 0.8998 (tmmm) REVERT: A 70 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9168 (mmtp) REVERT: A 103 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8573 (tptp) REVERT: A 179 GLU cc_start: 0.8902 (pp20) cc_final: 0.8381 (pp20) REVERT: A 190 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8922 (tt0) REVERT: A 215 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8496 (ttmm) REVERT: A 241 TRP cc_start: 0.9261 (m100) cc_final: 0.9020 (m-90) REVERT: A 306 PHE cc_start: 0.8896 (t80) cc_final: 0.8295 (t80) REVERT: A 309 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7400 (pm20) REVERT: B 17 ASP cc_start: 0.9161 (m-30) cc_final: 0.8689 (m-30) REVERT: B 61 MET cc_start: 0.9534 (OUTLIER) cc_final: 0.9115 (ptp) REVERT: B 70 LYS cc_start: 0.9399 (mtpp) cc_final: 0.9146 (mptm) REVERT: B 190 GLU cc_start: 0.9187 (tt0) cc_final: 0.8970 (pt0) REVERT: B 218 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8419 (pp) REVERT: B 224 GLN cc_start: 0.9118 (tp40) cc_final: 0.8625 (mm110) REVERT: B 244 TYR cc_start: 0.8449 (p90) cc_final: 0.8013 (p90) REVERT: C 61 MET cc_start: 0.9584 (OUTLIER) cc_final: 0.8040 (ptp) REVERT: C 70 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9021 (mmtm) REVERT: C 79 LEU cc_start: 0.8880 (mt) cc_final: 0.8635 (mm) REVERT: C 112 LYS cc_start: 0.8971 (tttm) cc_final: 0.8738 (tttm) REVERT: C 218 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8499 (pp) REVERT: C 244 TYR cc_start: 0.8606 (p90) cc_final: 0.8172 (p90) REVERT: C 309 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7228 (pm20) REVERT: D 52 GLU cc_start: 0.8780 (mp0) cc_final: 0.8354 (mp0) REVERT: D 70 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.9232 (mmtp) REVERT: D 103 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8295 (tmtt) REVERT: D 190 GLU cc_start: 0.9127 (tt0) cc_final: 0.8708 (tt0) REVERT: D 241 TRP cc_start: 0.9336 (m100) cc_final: 0.8722 (m100) REVERT: D 244 TYR cc_start: 0.8320 (p90) cc_final: 0.8039 (p90) REVERT: D 269 ARG cc_start: 0.7482 (tpm170) cc_final: 0.7238 (tpm170) REVERT: D 279 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8438 (mtmp) REVERT: D 283 MET cc_start: 0.8931 (tpp) cc_final: 0.8706 (mmm) REVERT: E 17 ASP cc_start: 0.8957 (m-30) cc_final: 0.8359 (m-30) REVERT: E 61 MET cc_start: 0.9574 (OUTLIER) cc_final: 0.9232 (pmm) REVERT: E 70 LYS cc_start: 0.9416 (mtpp) cc_final: 0.8936 (mmpt) REVERT: E 79 LEU cc_start: 0.8865 (mt) cc_final: 0.8640 (mm) REVERT: E 190 GLU cc_start: 0.9112 (tt0) cc_final: 0.8713 (tt0) REVERT: E 218 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8537 (pt) REVERT: E 224 GLN cc_start: 0.9061 (mm110) cc_final: 0.8684 (mm110) REVERT: E 244 TYR cc_start: 0.8688 (p90) cc_final: 0.8332 (p90) outliers start: 30 outliers final: 13 residues processed: 255 average time/residue: 0.7490 time to fit residues: 206.4303 Evaluate side-chains 265 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 309 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 232 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 179 GLU 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 70 LYS Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 294 LEU 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: 0.0770 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.085254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.059151 restraints weight = 117954.554| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 5.32 r_work: 0.2497 rms_B_bonded: 5.06 restraints_weight: 2.0000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14800 Z= 0.135 Angle : 0.661 12.841 20235 Z= 0.327 Chirality : 0.045 0.230 2370 Planarity : 0.003 0.030 2440 Dihedral : 6.587 42.347 2755 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.79 % Allowed : 17.55 % Favored : 80.66 % 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 aren not related in a simple way. whole: 1.95 (0.21), residues: 1690 helix: 2.12 (0.20), residues: 635 sheet: 1.37 (0.25), residues: 395 loop : 0.53 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 425 TYR 0.024 0.001 TYR E 299 PHE 0.025 0.001 PHE A 306 TRP 0.010 0.001 TRP E 67 HIS 0.002 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00308 (14755) covalent geometry : angle 0.65425 (20105) SS BOND : bond 0.00150 ( 5) SS BOND : angle 0.37583 ( 10) hydrogen bonds : bond 0.03328 ( 770) hydrogen bonds : angle 3.99807 ( 2490) link_ALPHA1-3 : bond 0.01120 ( 5) link_ALPHA1-3 : angle 1.43130 ( 15) link_ALPHA1-6 : bond 0.00942 ( 5) link_ALPHA1-6 : angle 1.73569 ( 15) link_BETA1-4 : bond 0.00392 ( 15) link_BETA1-4 : angle 1.33305 ( 45) link_NAG-ASN : bond 0.00129 ( 15) link_NAG-ASN : angle 1.36380 ( 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 273 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.9436 (ttpp) cc_final: 0.8996 (tmmm) REVERT: A 70 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.9156 (mmtp) REVERT: A 103 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8524 (tptp) REVERT: A 179 GLU cc_start: 0.8903 (pp20) cc_final: 0.8380 (pp20) REVERT: A 190 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8911 (tt0) REVERT: A 241 TRP cc_start: 0.9258 (m100) cc_final: 0.8977 (m-90) REVERT: A 306 PHE cc_start: 0.8886 (t80) cc_final: 0.8270 (t80) REVERT: A 309 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7398 (pm20) REVERT: B 17 ASP cc_start: 0.9158 (m-30) cc_final: 0.8682 (m-30) REVERT: B 61 MET cc_start: 0.9527 (OUTLIER) cc_final: 0.9115 (ptp) REVERT: B 70 LYS cc_start: 0.9397 (mtpp) cc_final: 0.9139 (mptm) REVERT: B 190 GLU cc_start: 0.9204 (tt0) cc_final: 0.8983 (pt0) REVERT: B 218 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8386 (pp) REVERT: B 224 GLN cc_start: 0.9132 (tp40) cc_final: 0.8606 (mm110) REVERT: B 244 TYR cc_start: 0.8452 (p90) cc_final: 0.8019 (p90) REVERT: C 14 GLU cc_start: 0.8644 (pp20) cc_final: 0.8275 (pm20) REVERT: C 61 MET cc_start: 0.9576 (OUTLIER) cc_final: 0.8048 (ptp) REVERT: C 70 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9007 (mmtm) REVERT: C 79 LEU cc_start: 0.8861 (mt) cc_final: 0.8617 (mm) REVERT: C 112 LYS cc_start: 0.8942 (tttm) cc_final: 0.8727 (tttm) REVERT: C 218 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8485 (pp) REVERT: C 244 TYR cc_start: 0.8612 (p90) cc_final: 0.8174 (p90) REVERT: C 309 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: D 52 GLU cc_start: 0.8766 (mp0) cc_final: 0.8347 (mp0) REVERT: D 70 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.9230 (mmtp) REVERT: D 103 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8258 (tmtt) REVERT: D 190 GLU cc_start: 0.9126 (tt0) cc_final: 0.8702 (tt0) REVERT: D 241 TRP cc_start: 0.9334 (m100) cc_final: 0.8719 (m100) REVERT: D 279 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8460 (mtmp) REVERT: E 17 ASP cc_start: 0.8985 (m-30) cc_final: 0.8371 (m-30) REVERT: E 61 MET cc_start: 0.9574 (OUTLIER) cc_final: 0.9222 (pmm) REVERT: E 70 LYS cc_start: 0.9417 (mtpp) cc_final: 0.8930 (mmpt) REVERT: E 79 LEU cc_start: 0.8844 (mt) cc_final: 0.8619 (mm) REVERT: E 190 GLU cc_start: 0.9107 (tt0) cc_final: 0.8677 (tt0) REVERT: E 218 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8519 (pt) REVERT: E 244 TYR cc_start: 0.8695 (p90) cc_final: 0.8353 (p90) outliers start: 27 outliers final: 13 residues processed: 253 average time/residue: 0.7427 time to fit residues: 203.7535 Evaluate side-chains 267 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 309 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 232 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 218 ILE Chi-restraints excluded: chain C residue 238 VAL 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 103 LYS Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 294 LEU 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 115 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 106 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 102 optimal weight: 0.1980 chunk 158 optimal weight: 0.0000 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B D 41 ASN B E 41 ASN B Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.060309 restraints weight = 121544.651| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 5.39 r_work: 0.2526 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 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 = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14800 Z= 0.120 Angle : 0.660 10.324 20235 Z= 0.325 Chirality : 0.044 0.222 2370 Planarity : 0.003 0.027 2440 Dihedral : 6.287 39.113 2755 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.52 % Allowed : 17.95 % 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 aren 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 : 0.55 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 425 TYR 0.023 0.001 TYR E 299 PHE 0.024 0.001 PHE A 306 TRP 0.012 0.001 TRP E 67 HIS 0.002 0.000 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00268 (14755) covalent geometry : angle 0.65405 (20105) SS BOND : bond 0.00124 ( 5) SS BOND : angle 0.34685 ( 10) hydrogen bonds : bond 0.03251 ( 770) hydrogen bonds : angle 3.98363 ( 2490) link_ALPHA1-3 : bond 0.01147 ( 5) link_ALPHA1-3 : angle 1.26903 ( 15) link_ALPHA1-6 : bond 0.01074 ( 5) link_ALPHA1-6 : angle 1.64644 ( 15) link_BETA1-4 : bond 0.00444 ( 15) link_BETA1-4 : angle 1.26271 ( 45) link_NAG-ASN : bond 0.00202 ( 15) link_NAG-ASN : angle 1.32489 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6638.90 seconds wall clock time: 113 minutes 40.84 seconds (6820.84 seconds total)