Starting phenix.real_space_refine on Fri Jul 3 13:08:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fey_50345/07_2026/9fey_50345.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fey_50345/07_2026/9fey_50345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fey_50345/07_2026/9fey_50345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fey_50345/07_2026/9fey_50345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fey_50345/07_2026/9fey_50345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fey_50345/07_2026/9fey_50345.map" } resolution = 2.9 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 2620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14365 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2776 Chain: "B" Number of atoms: 2761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2776 Chain: "C" Number of atoms: 2761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2776 Chain: "D" Number of atoms: 2761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2776 Chain: "E" Number of atoms: 2761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2776 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 4.79, per 1000 atoms: 0.33 Number of scatterers: 14365 At special positions: 0 Unit cell: (99.1936, 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 2620 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=2.04 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: 1.23 Conformation dependent library (CDL) restraints added in 1.3 seconds 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3210 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 43.2% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 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: 3.521A pdb=" N LEU A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.432A pdb=" N ARG A 142 " --> pdb=" O ASP A 139 " (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: 3.957A 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: 4.502A 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: 3.661A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.424A pdb=" N ARG B 142 " --> pdb=" O ASP B 139 " (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: 3.981A 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: 4.547A 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: 3.670A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 4.358A pdb=" N ARG C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.557A pdb=" N ALA C 174 " --> pdb=" O GLY C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 226 through 239 removed outlier: 3.814A 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: 4.431A 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 Processing helix chain 'D' and resid 139 through 143 removed outlier: 4.458A pdb=" N ARG D 142 " --> pdb=" O ASP D 139 " (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: 4.007A 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: 4.550A 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 Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.324A pdb=" N ARG E 142 " --> pdb=" O ASP E 139 " (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: 4.011A 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: 4.620A 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: 4.257A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.427A 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: 6.209A pdb=" N ASP A 101 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA A 135 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 103 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.612A 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: 3.985A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.738A 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: 4.339A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.631A 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: 6.195A pdb=" N ASP B 101 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA B 135 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS B 103 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.996A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.736A 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: 4.333A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.333A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR C 60 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE C 47 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N TYR C 62 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA C 45 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLN C 64 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASP C 43 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR C 66 " --> pdb=" O AASN C 41 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N AASN C 41 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N ARG C 68 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 9.855A pdb=" N GLY C 39 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.977A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.790A 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: 4.341A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.494A 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: 6.785A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.989A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.677A 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: 4.414A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.536A 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: 6.751A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.697A 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: 7.011A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.962A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) 872 hydrogen bonds defined for protein. 2456 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: 2.65 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4308 1.34 - 1.46: 3649 1.46 - 1.58: 6648 1.58 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14755 Sorted by residual: bond pdb=" C1 MAN b 5 " pdb=" O5 MAN b 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.64e+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 2.61e+00 bond pdb=" C1 MAN c 5 " pdb=" O5 MAN c 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 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 2.52e+00 bond pdb=" C1 MAN d 5 " pdb=" O5 MAN d 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.48e+00 ... (remaining 14750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 18938 1.11 - 2.22: 861 2.22 - 3.33: 250 3.33 - 4.44: 38 4.44 - 5.55: 18 Bond angle restraints: 20105 Sorted by residual: angle pdb=" CA ATYR E 66 " pdb=" CB ATYR E 66 " pdb=" CG ATYR E 66 " ideal model delta sigma weight residual 113.90 118.58 -4.68 1.80e+00 3.09e-01 6.76e+00 angle pdb=" C TYR B 66 " pdb=" N TRP B 67 " pdb=" CA TRP B 67 " ideal model delta sigma weight residual 122.39 118.72 3.67 1.64e+00 3.72e-01 5.01e+00 angle pdb=" C TYR C 66 " pdb=" N TRP C 67 " pdb=" CA TRP C 67 " ideal model delta sigma weight residual 122.53 118.96 3.57 1.61e+00 3.86e-01 4.92e+00 angle pdb=" C TYR D 66 " pdb=" N TRP D 67 " pdb=" CA TRP D 67 " ideal model delta sigma weight residual 122.39 118.77 3.62 1.64e+00 3.72e-01 4.87e+00 angle pdb=" CA ATYR D 66 " pdb=" CB ATYR D 66 " pdb=" CG ATYR D 66 " ideal model delta sigma weight residual 113.90 117.85 -3.95 1.80e+00 3.09e-01 4.82e+00 ... (remaining 20100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.11: 8874 21.11 - 42.22: 217 42.22 - 63.33: 39 63.33 - 84.45: 34 84.45 - 105.56: 21 Dihedral angle restraints: 9185 sinusoidal: 4155 harmonic: 5030 Sorted by residual: dihedral pdb=" CA PRO B 276 " pdb=" C PRO B 276 " pdb=" N TYR B 277 " pdb=" CA TYR B 277 " ideal model delta harmonic sigma weight residual 180.00 161.60 18.40 0 5.00e+00 4.00e-02 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 -176.85 105.56 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C5 BMA b 3 " pdb=" O5 BMA b 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.65 105.36 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 9182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1876 0.051 - 0.102: 379 0.102 - 0.153: 101 0.153 - 0.204: 8 0.204 - 0.255: 6 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 -2.53 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C5 BMA e 3 " pdb=" C4 BMA e 3 " pdb=" C6 BMA e 3 " pdb=" O5 BMA e 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 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 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2367 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR E 66 " 0.014 2.00e-02 2.50e+03 1.01e-02 2.03e+00 pdb=" CG ATYR E 66 " -0.024 2.00e-02 2.50e+03 pdb=" CD1ATYR E 66 " 0.003 2.00e-02 2.50e+03 pdb=" CD2ATYR E 66 " -0.000 2.00e-02 2.50e+03 pdb=" CE1ATYR E 66 " 0.001 2.00e-02 2.50e+03 pdb=" CE2ATYR E 66 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ATYR E 66 " 0.003 2.00e-02 2.50e+03 pdb=" OH ATYR E 66 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR D 66 " 0.013 2.00e-02 2.50e+03 8.64e-03 1.49e+00 pdb=" CG ATYR D 66 " -0.020 2.00e-02 2.50e+03 pdb=" CD1ATYR D 66 " 0.001 2.00e-02 2.50e+03 pdb=" CD2ATYR D 66 " -0.001 2.00e-02 2.50e+03 pdb=" CE1ATYR D 66 " 0.000 2.00e-02 2.50e+03 pdb=" CE2ATYR D 66 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ATYR D 66 " 0.004 2.00e-02 2.50e+03 pdb=" OH ATYR D 66 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR C 66 " 0.012 2.00e-02 2.50e+03 8.39e-03 1.41e+00 pdb=" CG ATYR C 66 " -0.019 2.00e-02 2.50e+03 pdb=" CD1ATYR C 66 " 0.001 2.00e-02 2.50e+03 pdb=" CD2ATYR C 66 " -0.000 2.00e-02 2.50e+03 pdb=" CE1ATYR C 66 " -0.001 2.00e-02 2.50e+03 pdb=" CE2ATYR C 66 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ATYR C 66 " 0.006 2.00e-02 2.50e+03 pdb=" OH ATYR C 66 " 0.000 2.00e-02 2.50e+03 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2706 2.77 - 3.30: 13292 3.30 - 3.84: 24656 3.84 - 4.37: 29781 4.37 - 4.90: 51001 Nonbonded interactions: 121436 Sorted by model distance: nonbonded pdb=" OH TYR B 284 " pdb=" OD1 ASN B 439 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR B 202 " pdb=" OH TYR B 205 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP D 101 " pdb=" NH2 ARG E 129 " model vdw 2.276 3.120 nonbonded pdb=" OH TYR D 23 " pdb=" OD2 ASP D 69 " model vdw 2.285 3.040 nonbonded pdb=" OD2 ASP C 95 " pdb=" N GLY C 158 " model vdw 2.296 3.120 ... (remaining 121431 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: 0.900 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.680 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14800 Z= 0.237 Angle : 0.604 5.549 20235 Z= 0.297 Chirality : 0.046 0.255 2370 Planarity : 0.003 0.026 2440 Dihedral : 12.275 105.556 5960 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.13 % Allowed : 3.84 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.22), residues: 1690 helix: 2.74 (0.22), residues: 605 sheet: 0.91 (0.25), residues: 395 loop : 0.46 (0.27), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.016 0.002 TYR B 299 PHE 0.015 0.002 PHE C 63 TRP 0.008 0.001 TRP E 67 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (14755) covalent geometry : angle 0.59520 / 0.30 (20105) SS BOND : bond 0.00330 / 0.22 ( 5) SS BOND : angle 0.85255 / 0.61 ( 10) hydrogen bonds : bond 0.10680 / 7.41 ( 781) hydrogen bonds : angle 4.80977 / 3.40 ( 2456) link_ALPHA1-3 : bond 0.00242 / 0.16 ( 5) link_ALPHA1-3 : angle 1.16102 / 0.82 ( 15) link_ALPHA1-6 : bond 0.00264 / 0.17 ( 5) link_ALPHA1-6 : angle 1.00106 / 0.70 ( 15) link_BETA1-4 : bond 0.00326 / 0.23 ( 15) link_BETA1-4 : angle 1.74253 / 1.16 ( 45) link_NAG-ASN : bond 0.00260 / 0.18 ( 15) link_NAG-ASN : angle 1.31437 / 0.83 ( 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 345 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 328 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8725 (mtp) cc_final: 0.8403 (mtm) REVERT: A 13 LYS cc_start: 0.9014 (tttt) cc_final: 0.8726 (tttm) REVERT: A 17 ASP cc_start: 0.8781 (m-30) cc_final: 0.8416 (m-30) REVERT: A 190 GLU cc_start: 0.8750 (tt0) cc_final: 0.8302 (tt0) REVERT: A 224 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8944 (mm110) REVERT: A 306 PHE cc_start: 0.9135 (t80) cc_final: 0.8682 (t80) REVERT: B 302 VAL cc_start: 0.9171 (t) cc_final: 0.8967 (p) REVERT: C 13 LYS cc_start: 0.9250 (tttt) cc_final: 0.8820 (tttm) REVERT: C 17 ASP cc_start: 0.9000 (m-30) cc_final: 0.8687 (m-30) REVERT: C 224 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8524 (mm-40) REVERT: C 251 VAL cc_start: 0.9263 (t) cc_final: 0.8869 (p) REVERT: C 424 ASP cc_start: 0.8454 (t0) cc_final: 0.8174 (t0) REVERT: D 190 GLU cc_start: 0.8727 (tt0) cc_final: 0.8496 (tt0) REVERT: D 244 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8385 (p90) REVERT: D 261 MET cc_start: 0.9064 (tpp) cc_final: 0.8795 (mmm) REVERT: D 440 LEU cc_start: 0.8987 (tp) cc_final: 0.8772 (tt) REVERT: E 52 GLU cc_start: 0.8970 (mp0) cc_final: 0.8738 (mp0) REVERT: E 79 LEU cc_start: 0.9150 (mt) cc_final: 0.8939 (mm) REVERT: E 190 GLU cc_start: 0.8738 (tt0) cc_final: 0.8402 (tt0) REVERT: E 224 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8438 (tp40) outliers start: 17 outliers final: 6 residues processed: 337 average time/residue: 0.6981 time to fit residues: 255.1529 Evaluate side-chains 221 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 212 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 244 TYR 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: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN A 148 GLN A 224 GLN A 265 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** C 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.086763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.060597 restraints weight = 115765.378| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 5.29 r_work: 0.2541 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.2545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14800 Z= 0.182 Angle : 0.655 8.997 20235 Z= 0.327 Chirality : 0.045 0.168 2370 Planarity : 0.004 0.051 2440 Dihedral : 10.879 82.615 2771 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.38 % Allowed : 14.11 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.22), residues: 1690 helix: 2.49 (0.21), residues: 635 sheet: 0.97 (0.25), residues: 395 loop : 0.46 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 68 TYR 0.026 0.002 TYR C 277 PHE 0.022 0.001 PHE A 200 TRP 0.011 0.001 TRP D 67 HIS 0.005 0.001 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (14755) covalent geometry : angle 0.64322 / 0.32 (20105) SS BOND : bond 0.00181 / 0.13 ( 5) SS BOND : angle 0.45791 / 0.31 ( 10) hydrogen bonds : bond 0.03782 / 2.49 ( 781) hydrogen bonds : angle 4.33940 / 3.04 ( 2456) link_ALPHA1-3 : bond 0.00861 / 0.58 ( 5) link_ALPHA1-3 : angle 2.23092 / 1.54 ( 15) link_ALPHA1-6 : bond 0.00524 / 0.33 ( 5) link_ALPHA1-6 : angle 2.06817 / 1.44 ( 15) link_BETA1-4 : bond 0.00286 / 0.19 ( 15) link_BETA1-4 : angle 1.73471 / 1.15 ( 45) link_NAG-ASN : bond 0.00218 / 0.15 ( 15) link_NAG-ASN : angle 1.45585 / 0.98 ( 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 290 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8495 (mtp) cc_final: 0.7959 (mtt) REVERT: A 277 TYR cc_start: 0.7460 (p90) cc_final: 0.7118 (p90) REVERT: A 306 PHE cc_start: 0.9121 (t80) cc_final: 0.8618 (t80) REVERT: B 14 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8689 (pp20) REVERT: B 55 MET cc_start: 0.9096 (mmm) cc_final: 0.8613 (mmm) REVERT: B 218 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8231 (pp) REVERT: B 269 ARG cc_start: 0.7751 (ttp-170) cc_final: 0.7340 (mtp180) REVERT: C 17 ASP cc_start: 0.9260 (m-30) cc_final: 0.9007 (m-30) REVERT: C 224 GLN cc_start: 0.8790 (tp40) cc_final: 0.8212 (tm-30) REVERT: C 424 ASP cc_start: 0.8414 (t0) cc_final: 0.8187 (t0) REVERT: C 425 ARG cc_start: 0.8255 (ptt90) cc_final: 0.7938 (mtm-85) REVERT: D 30 ASP cc_start: 0.8852 (m-30) cc_final: 0.8407 (t0) REVERT: D 141 ARG cc_start: 0.8469 (mtt90) cc_final: 0.8128 (mtp85) REVERT: D 190 GLU cc_start: 0.9002 (tt0) cc_final: 0.8661 (tt0) REVERT: D 244 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8465 (p90) REVERT: D 261 MET cc_start: 0.9076 (tpp) cc_final: 0.8781 (mmm) REVERT: D 264 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8835 (mp) REVERT: D 283 MET cc_start: 0.8822 (mmm) cc_final: 0.8578 (mmm) REVERT: D 425 ARG cc_start: 0.8584 (ppt170) cc_final: 0.8352 (ppt170) REVERT: D 440 LEU cc_start: 0.8910 (tp) cc_final: 0.8703 (tt) REVERT: E 79 LEU cc_start: 0.9234 (mt) cc_final: 0.8930 (mm) REVERT: E 190 GLU cc_start: 0.9011 (tt0) cc_final: 0.8622 (tt0) outliers start: 51 outliers final: 19 residues processed: 266 average time/residue: 0.6495 time to fit residues: 187.6047 Evaluate side-chains 238 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 302 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 136 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN B ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN B Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.061818 restraints weight = 101247.432| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 5.04 r_work: 0.2575 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14800 Z= 0.129 Angle : 0.611 8.695 20235 Z= 0.304 Chirality : 0.044 0.278 2370 Planarity : 0.004 0.077 2440 Dihedral : 9.958 76.962 2760 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.78 % Allowed : 15.50 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.21), residues: 1690 helix: 2.37 (0.21), residues: 635 sheet: 1.04 (0.25), residues: 395 loop : 0.47 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 68 TYR 0.025 0.001 TYR C 277 PHE 0.037 0.001 PHE E 307 TRP 0.012 0.001 TRP D 426 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (14755) covalent geometry : angle 0.60093 / 0.30 (20105) SS BOND : bond 0.00138 / 0.09 ( 5) SS BOND : angle 0.32491 / 0.22 ( 10) hydrogen bonds : bond 0.03460 / 2.29 ( 781) hydrogen bonds : angle 4.19227 / 2.93 ( 2456) link_ALPHA1-3 : bond 0.01001 / 0.66 ( 5) link_ALPHA1-3 : angle 1.75643 / 1.21 ( 15) link_ALPHA1-6 : bond 0.00747 / 0.47 ( 5) link_ALPHA1-6 : angle 2.02601 / 1.40 ( 15) link_BETA1-4 : bond 0.00311 / 0.21 ( 15) link_BETA1-4 : angle 1.44905 / 0.99 ( 45) link_NAG-ASN : bond 0.00155 / 0.10 ( 15) link_NAG-ASN : angle 1.33487 / 0.90 ( 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 276 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8490 (mtp) cc_final: 0.7919 (mtt) REVERT: A 14 GLU cc_start: 0.8743 (pp20) cc_final: 0.8524 (pp20) REVERT: A 277 TYR cc_start: 0.7426 (p90) cc_final: 0.7156 (p90) REVERT: A 306 PHE cc_start: 0.9115 (t80) cc_final: 0.8586 (t80) REVERT: B 14 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8700 (pp20) REVERT: B 18 LYS cc_start: 0.9351 (ttmm) cc_final: 0.9090 (tmmm) REVERT: B 55 MET cc_start: 0.9182 (mmm) cc_final: 0.8829 (mmm) REVERT: B 153 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8730 (mm-30) REVERT: B 218 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8403 (pp) REVERT: B 224 GLN cc_start: 0.9031 (tp40) cc_final: 0.8277 (tp-100) REVERT: B 269 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7267 (mtp-110) REVERT: B 306 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8387 (t80) REVERT: C 13 LYS cc_start: 0.9041 (tttt) cc_final: 0.8586 (tttm) REVERT: C 17 ASP cc_start: 0.9239 (m-30) cc_final: 0.8831 (m-30) REVERT: C 224 GLN cc_start: 0.8696 (tp40) cc_final: 0.8327 (tm-30) REVERT: C 251 VAL cc_start: 0.9277 (t) cc_final: 0.8988 (p) REVERT: C 309 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: C 424 ASP cc_start: 0.8440 (t0) cc_final: 0.8168 (t0) REVERT: C 425 ARG cc_start: 0.8230 (ptt90) cc_final: 0.7926 (mtm-85) REVERT: D 30 ASP cc_start: 0.8752 (m-30) cc_final: 0.8317 (t0) REVERT: D 141 ARG cc_start: 0.8441 (mtt90) cc_final: 0.8106 (mtp85) REVERT: D 190 GLU cc_start: 0.8964 (tt0) cc_final: 0.8617 (tt0) REVERT: D 244 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8485 (p90) REVERT: D 261 MET cc_start: 0.9044 (tpp) cc_final: 0.8794 (mmm) REVERT: D 283 MET cc_start: 0.8786 (mmm) cc_final: 0.8468 (mmm) REVERT: D 309 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7725 (mp-120) REVERT: D 425 ARG cc_start: 0.8603 (ppt170) cc_final: 0.8401 (tmm-80) REVERT: E 79 LEU cc_start: 0.9241 (mt) cc_final: 0.8919 (mm) REVERT: E 190 GLU cc_start: 0.9006 (tt0) cc_final: 0.8608 (tt0) outliers start: 42 outliers final: 15 residues processed: 255 average time/residue: 0.6523 time to fit residues: 181.1550 Evaluate side-chains 236 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain E residue 297 LEU 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 0 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 142 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.062037 restraints weight = 119650.744| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 5.39 r_work: 0.2581 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14800 Z= 0.125 Angle : 0.617 9.670 20235 Z= 0.305 Chirality : 0.044 0.241 2370 Planarity : 0.004 0.066 2440 Dihedral : 9.222 71.009 2760 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.65 % Allowed : 16.09 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.21), residues: 1690 helix: 2.29 (0.21), residues: 635 sheet: 1.09 (0.25), residues: 395 loop : 0.51 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.025 0.001 TYR C 277 PHE 0.018 0.001 PHE A 200 TRP 0.014 0.001 TRP D 241 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (14755) covalent geometry : angle 0.60832 / 0.30 (20105) SS BOND : bond 0.00108 / 0.07 ( 5) SS BOND : angle 0.24851 / 0.19 ( 10) hydrogen bonds : bond 0.03281 / 2.17 ( 781) hydrogen bonds : angle 4.11873 / 2.88 ( 2456) link_ALPHA1-3 : bond 0.01083 / 0.71 ( 5) link_ALPHA1-3 : angle 1.82745 / 1.24 ( 15) link_ALPHA1-6 : bond 0.00852 / 0.54 ( 5) link_ALPHA1-6 : angle 2.09624 / 1.45 ( 15) link_BETA1-4 : bond 0.00327 / 0.22 ( 15) link_BETA1-4 : angle 1.34952 / 0.93 ( 45) link_NAG-ASN : bond 0.00153 / 0.10 ( 15) link_NAG-ASN : angle 1.30014 / 0.87 ( 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 272 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8515 (mtp) cc_final: 0.7904 (mtt) REVERT: A 14 GLU cc_start: 0.8760 (pp20) cc_final: 0.8498 (pp20) REVERT: A 277 TYR cc_start: 0.7449 (p90) cc_final: 0.7162 (p90) REVERT: A 306 PHE cc_start: 0.9090 (t80) cc_final: 0.8538 (t80) REVERT: B 14 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8680 (pp20) REVERT: B 55 MET cc_start: 0.9171 (mmm) cc_final: 0.8887 (mmm) REVERT: B 153 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8838 (mm-30) REVERT: B 218 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8638 (pt) REVERT: B 224 GLN cc_start: 0.9083 (tp40) cc_final: 0.8284 (tp-100) REVERT: B 244 TYR cc_start: 0.8337 (p90) cc_final: 0.7465 (p90) REVERT: B 269 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.7306 (mtp-110) REVERT: B 306 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8081 (t80) REVERT: C 13 LYS cc_start: 0.9027 (tttt) cc_final: 0.8602 (tttm) REVERT: C 17 ASP cc_start: 0.9296 (m-30) cc_final: 0.8941 (m-30) REVERT: C 18 LYS cc_start: 0.9327 (ttpp) cc_final: 0.8995 (ptpp) REVERT: C 224 GLN cc_start: 0.8744 (tp40) cc_final: 0.8400 (tm-30) REVERT: C 251 VAL cc_start: 0.9290 (t) cc_final: 0.8977 (p) REVERT: C 424 ASP cc_start: 0.8444 (t0) cc_final: 0.8167 (t0) REVERT: C 425 ARG cc_start: 0.8225 (ptt90) cc_final: 0.7926 (mtm-85) REVERT: D 18 LYS cc_start: 0.9160 (ttpp) cc_final: 0.8950 (tmmm) REVERT: D 30 ASP cc_start: 0.8791 (m-30) cc_final: 0.8347 (t0) REVERT: D 141 ARG cc_start: 0.8477 (mtt90) cc_final: 0.8124 (mtp85) REVERT: D 190 GLU cc_start: 0.8977 (tt0) cc_final: 0.8609 (tt0) REVERT: D 244 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8594 (p90) REVERT: D 261 MET cc_start: 0.9100 (tpp) cc_final: 0.8821 (mmm) REVERT: D 283 MET cc_start: 0.8815 (mmm) cc_final: 0.8471 (mmm) REVERT: D 309 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: D 425 ARG cc_start: 0.8658 (ppt170) cc_final: 0.8451 (tmm-80) REVERT: E 79 LEU cc_start: 0.9270 (mt) cc_final: 0.8938 (mm) REVERT: E 172 ASP cc_start: 0.9078 (m-30) cc_final: 0.8783 (p0) REVERT: E 190 GLU cc_start: 0.9095 (tt0) cc_final: 0.8709 (tt0) outliers start: 40 outliers final: 17 residues processed: 255 average time/residue: 0.6467 time to fit residues: 180.0604 Evaluate side-chains 233 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 307 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 162 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.059940 restraints weight = 115528.253| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 5.26 r_work: 0.2540 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14800 Z= 0.214 Angle : 0.656 9.264 20235 Z= 0.329 Chirality : 0.046 0.257 2370 Planarity : 0.004 0.062 2440 Dihedral : 9.005 67.985 2760 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.91 % Allowed : 16.95 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.21), residues: 1690 helix: 2.17 (0.21), residues: 635 sheet: 1.10 (0.25), residues: 395 loop : 0.43 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 28 TYR 0.020 0.002 TYR B 299 PHE 0.029 0.002 PHE E 307 TRP 0.012 0.001 TRP D 426 HIS 0.003 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (14755) covalent geometry : angle 0.64587 / 0.33 (20105) SS BOND : bond 0.00184 / 0.12 ( 5) SS BOND : angle 0.51223 / 0.33 ( 10) hydrogen bonds : bond 0.03530 / 2.32 ( 781) hydrogen bonds : angle 4.20815 / 2.94 ( 2456) link_ALPHA1-3 : bond 0.00941 / 0.63 ( 5) link_ALPHA1-3 : angle 1.98747 / 1.36 ( 15) link_ALPHA1-6 : bond 0.00771 / 0.49 ( 5) link_ALPHA1-6 : angle 2.24262 / 1.54 ( 15) link_BETA1-4 : bond 0.00265 / 0.18 ( 15) link_BETA1-4 : angle 1.48380 / 1.02 ( 45) link_NAG-ASN : bond 0.00091 / 0.06 ( 15) link_NAG-ASN : angle 1.46689 / 0.98 ( 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 261 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8519 (mtp) cc_final: 0.7966 (mtt) REVERT: A 14 GLU cc_start: 0.8778 (pp20) cc_final: 0.8513 (pp20) REVERT: A 277 TYR cc_start: 0.7454 (p90) cc_final: 0.7186 (p90) REVERT: A 306 PHE cc_start: 0.9126 (t80) cc_final: 0.8597 (t80) REVERT: B 14 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8734 (pp20) REVERT: B 18 LYS cc_start: 0.9353 (ttmm) cc_final: 0.9056 (tmmm) REVERT: B 21 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8643 (mtpp) REVERT: B 55 MET cc_start: 0.9141 (mmm) cc_final: 0.8887 (mmm) REVERT: B 153 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8688 (mm-30) REVERT: B 218 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8635 (pt) REVERT: B 224 GLN cc_start: 0.9099 (tp40) cc_final: 0.8271 (tp-100) REVERT: B 244 TYR cc_start: 0.8317 (p90) cc_final: 0.7725 (p90) REVERT: B 269 ARG cc_start: 0.7702 (ttp-170) cc_final: 0.7273 (mtp-110) REVERT: C 13 LYS cc_start: 0.9054 (tttt) cc_final: 0.8606 (tttm) REVERT: C 17 ASP cc_start: 0.9269 (m-30) cc_final: 0.8890 (m-30) REVERT: C 224 GLN cc_start: 0.8806 (tp40) cc_final: 0.8437 (tm-30) REVERT: C 251 VAL cc_start: 0.9341 (t) cc_final: 0.9037 (p) REVERT: C 309 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6812 (pm20) REVERT: C 424 ASP cc_start: 0.8440 (t0) cc_final: 0.8165 (t0) REVERT: C 425 ARG cc_start: 0.8255 (ptt90) cc_final: 0.7945 (mtm-85) REVERT: D 30 ASP cc_start: 0.8789 (m-30) cc_final: 0.8340 (t0) REVERT: D 52 GLU cc_start: 0.8927 (mp0) cc_final: 0.8686 (mp0) REVERT: D 61 MET cc_start: 0.9486 (OUTLIER) cc_final: 0.8991 (ptt) REVERT: D 141 ARG cc_start: 0.8537 (mtt90) cc_final: 0.8239 (mtp85) REVERT: D 190 GLU cc_start: 0.8989 (tt0) cc_final: 0.8636 (tt0) REVERT: D 261 MET cc_start: 0.9089 (tpp) cc_final: 0.8835 (mmm) REVERT: D 264 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8870 (mp) REVERT: D 283 MET cc_start: 0.8876 (mmm) cc_final: 0.8522 (mmm) REVERT: D 309 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: D 425 ARG cc_start: 0.8622 (ppt170) cc_final: 0.8388 (tmm-80) REVERT: E 172 ASP cc_start: 0.9083 (m-30) cc_final: 0.8782 (p0) REVERT: E 190 GLU cc_start: 0.9077 (tt0) cc_final: 0.8695 (tt0) outliers start: 43 outliers final: 23 residues processed: 243 average time/residue: 0.6649 time to fit residues: 176.2021 Evaluate side-chains 242 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 302 VAL 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 128 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN B ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.087683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.062320 restraints weight = 92193.183| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 4.89 r_work: 0.2598 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14800 Z= 0.132 Angle : 0.637 10.670 20235 Z= 0.314 Chirality : 0.045 0.247 2370 Planarity : 0.004 0.059 2440 Dihedral : 8.352 62.937 2758 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.72 % Allowed : 16.95 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.21), residues: 1690 helix: 2.17 (0.21), residues: 635 sheet: 1.12 (0.25), residues: 395 loop : 0.51 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.021 0.001 TYR C 277 PHE 0.038 0.001 PHE E 307 TRP 0.011 0.001 TRP D 67 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (14755) covalent geometry : angle 0.62869 / 0.31 (20105) SS BOND : bond 0.00109 / 0.07 ( 5) SS BOND : angle 0.24773 / 0.15 ( 10) hydrogen bonds : bond 0.03268 / 2.15 ( 781) hydrogen bonds : angle 4.08272 / 2.85 ( 2456) link_ALPHA1-3 : bond 0.01093 / 0.72 ( 5) link_ALPHA1-3 : angle 1.77843 / 1.20 ( 15) link_ALPHA1-6 : bond 0.00957 / 0.61 ( 5) link_ALPHA1-6 : angle 2.15340 / 1.48 ( 15) link_BETA1-4 : bond 0.00338 / 0.23 ( 15) link_BETA1-4 : angle 1.30710 / 0.90 ( 45) link_NAG-ASN : bond 0.00133 / 0.08 ( 15) link_NAG-ASN : angle 1.33644 / 0.89 ( 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 267 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8489 (mtp) cc_final: 0.7962 (mtt) REVERT: A 14 GLU cc_start: 0.8760 (pp20) cc_final: 0.8467 (pp20) REVERT: A 306 PHE cc_start: 0.9104 (t80) cc_final: 0.8518 (t80) REVERT: B 14 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8683 (pp20) REVERT: B 21 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8594 (mtpp) REVERT: B 70 LYS cc_start: 0.9416 (mmmm) cc_final: 0.9136 (mmtm) REVERT: B 153 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8806 (mm-30) REVERT: B 218 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8627 (pt) REVERT: B 224 GLN cc_start: 0.8967 (tp40) cc_final: 0.8178 (tp-100) REVERT: B 244 TYR cc_start: 0.8272 (p90) cc_final: 0.7667 (p90) REVERT: B 269 ARG cc_start: 0.7671 (ttp-170) cc_final: 0.7414 (mtp-110) REVERT: C 13 LYS cc_start: 0.9038 (tttt) cc_final: 0.8604 (tttm) REVERT: C 17 ASP cc_start: 0.9294 (m-30) cc_final: 0.8904 (m-30) REVERT: C 18 LYS cc_start: 0.9339 (ttpp) cc_final: 0.9034 (ptpp) REVERT: C 244 TYR cc_start: 0.8686 (p90) cc_final: 0.8374 (p90) REVERT: C 251 VAL cc_start: 0.9325 (t) cc_final: 0.8872 (p) REVERT: C 309 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: C 424 ASP cc_start: 0.8442 (t0) cc_final: 0.8133 (t0) REVERT: C 425 ARG cc_start: 0.8224 (ptt90) cc_final: 0.7908 (mtm-85) REVERT: D 30 ASP cc_start: 0.8761 (m-30) cc_final: 0.8355 (t0) REVERT: D 141 ARG cc_start: 0.8454 (mtt90) cc_final: 0.8107 (mtp85) REVERT: D 190 GLU cc_start: 0.8944 (tt0) cc_final: 0.8573 (tt0) REVERT: D 261 MET cc_start: 0.9044 (tpp) cc_final: 0.8748 (mmm) REVERT: D 283 MET cc_start: 0.8861 (mmm) cc_final: 0.8463 (mmm) REVERT: D 309 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: D 425 ARG cc_start: 0.8645 (ppt170) cc_final: 0.8365 (tmm-80) REVERT: E 79 LEU cc_start: 0.9270 (mp) cc_final: 0.8976 (mm) REVERT: E 172 ASP cc_start: 0.9053 (m-30) cc_final: 0.8775 (p0) REVERT: E 190 GLU cc_start: 0.9051 (tt0) cc_final: 0.8659 (tt0) outliers start: 41 outliers final: 22 residues processed: 249 average time/residue: 0.6784 time to fit residues: 183.7976 Evaluate side-chains 237 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 132 THR 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 C residue 444 LEU Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 139 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.061656 restraints weight = 114220.586| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 5.27 r_work: 0.2574 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14800 Z= 0.141 Angle : 0.651 12.069 20235 Z= 0.321 Chirality : 0.046 0.249 2370 Planarity : 0.004 0.085 2440 Dihedral : 8.026 59.952 2758 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.52 % Allowed : 17.35 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.21), residues: 1690 helix: 2.17 (0.21), residues: 635 sheet: 1.14 (0.25), residues: 395 loop : 0.52 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.040 0.002 TYR C 299 PHE 0.017 0.001 PHE D 307 TRP 0.010 0.001 TRP D 67 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (14755) covalent geometry : angle 0.64241 / 0.32 (20105) SS BOND : bond 0.00147 / 0.10 ( 5) SS BOND : angle 0.40256 / 0.24 ( 10) hydrogen bonds : bond 0.03291 / 2.17 ( 781) hydrogen bonds : angle 4.04760 / 2.83 ( 2456) link_ALPHA1-3 : bond 0.01081 / 0.72 ( 5) link_ALPHA1-3 : angle 1.85093 / 1.26 ( 15) link_ALPHA1-6 : bond 0.00959 / 0.61 ( 5) link_ALPHA1-6 : angle 2.12328 / 1.47 ( 15) link_BETA1-4 : bond 0.00312 / 0.21 ( 15) link_BETA1-4 : angle 1.31084 / 0.91 ( 45) link_NAG-ASN : bond 0.00092 / 0.06 ( 15) link_NAG-ASN : angle 1.36564 / 0.92 ( 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 259 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8509 (mtp) cc_final: 0.7989 (mtt) REVERT: A 14 GLU cc_start: 0.8797 (pp20) cc_final: 0.8517 (pp20) REVERT: A 264 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 277 TYR cc_start: 0.7052 (p90) cc_final: 0.6829 (p90) REVERT: A 306 PHE cc_start: 0.9124 (t80) cc_final: 0.8547 (t80) REVERT: B 14 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8734 (pp20) REVERT: B 18 LYS cc_start: 0.9358 (ttmm) cc_final: 0.9052 (tmmm) REVERT: B 21 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8609 (mtpp) REVERT: B 55 MET cc_start: 0.9209 (mmm) cc_final: 0.8917 (mmm) REVERT: B 153 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8822 (mm-30) REVERT: B 218 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8630 (pt) REVERT: B 224 GLN cc_start: 0.8994 (tp40) cc_final: 0.8301 (tp-100) REVERT: B 244 TYR cc_start: 0.8201 (p90) cc_final: 0.7584 (p90) REVERT: C 13 LYS cc_start: 0.9016 (tttt) cc_final: 0.8635 (tttm) REVERT: C 17 ASP cc_start: 0.9292 (m-30) cc_final: 0.8977 (m-30) REVERT: C 18 LYS cc_start: 0.9341 (ttpp) cc_final: 0.9046 (ptpp) REVERT: C 244 TYR cc_start: 0.8636 (p90) cc_final: 0.8380 (p90) REVERT: C 251 VAL cc_start: 0.9259 (t) cc_final: 0.9024 (p) REVERT: C 309 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7332 (pm20) REVERT: C 424 ASP cc_start: 0.8461 (t0) cc_final: 0.8151 (t0) REVERT: C 425 ARG cc_start: 0.8227 (ptt90) cc_final: 0.7907 (mtm-85) REVERT: D 18 LYS cc_start: 0.9169 (tmmt) cc_final: 0.8859 (ttpp) REVERT: D 30 ASP cc_start: 0.8783 (m-30) cc_final: 0.8353 (t0) REVERT: D 141 ARG cc_start: 0.8517 (mtt90) cc_final: 0.8124 (mtp85) REVERT: D 190 GLU cc_start: 0.8970 (tt0) cc_final: 0.8601 (tt0) REVERT: D 261 MET cc_start: 0.9082 (tpp) cc_final: 0.8795 (mmm) REVERT: D 283 MET cc_start: 0.8930 (mmm) cc_final: 0.8529 (mmm) REVERT: D 425 ARG cc_start: 0.8660 (ppt170) cc_final: 0.8375 (tmm-80) REVERT: E 79 LEU cc_start: 0.9283 (mp) cc_final: 0.9002 (mm) REVERT: E 172 ASP cc_start: 0.9084 (m-30) cc_final: 0.8785 (p0) REVERT: E 190 GLU cc_start: 0.9111 (tt0) cc_final: 0.8749 (tt0) outliers start: 38 outliers final: 24 residues processed: 239 average time/residue: 0.6779 time to fit residues: 176.4478 Evaluate side-chains 240 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 297 LEU 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 70 LYS Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 102 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.061720 restraints weight = 108120.666| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 5.08 r_work: 0.2586 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 14800 Z= 0.158 Angle : 0.684 10.832 20235 Z= 0.335 Chirality : 0.046 0.252 2370 Planarity : 0.004 0.077 2440 Dihedral : 7.856 58.174 2758 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.32 % Allowed : 17.81 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.21), residues: 1690 helix: 2.09 (0.21), residues: 635 sheet: 1.15 (0.25), residues: 395 loop : 0.52 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.027 0.002 TYR C 299 PHE 0.018 0.001 PHE E 307 TRP 0.009 0.001 TRP D 67 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (14755) covalent geometry : angle 0.67569 / 0.33 (20105) SS BOND : bond 0.00110 / 0.07 ( 5) SS BOND : angle 0.36493 / 0.22 ( 10) hydrogen bonds : bond 0.03312 / 2.18 ( 781) hydrogen bonds : angle 4.05423 / 2.84 ( 2456) link_ALPHA1-3 : bond 0.01037 / 0.68 ( 5) link_ALPHA1-3 : angle 1.82884 / 1.25 ( 15) link_ALPHA1-6 : bond 0.00965 / 0.62 ( 5) link_ALPHA1-6 : angle 2.12711 / 1.48 ( 15) link_BETA1-4 : bond 0.00308 / 0.21 ( 15) link_BETA1-4 : angle 1.32202 / 0.92 ( 45) link_NAG-ASN : bond 0.00075 / 0.05 ( 15) link_NAG-ASN : angle 1.39563 / 0.94 ( 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 252 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8519 (mtp) cc_final: 0.8015 (mtt) REVERT: A 14 GLU cc_start: 0.8794 (pp20) cc_final: 0.8571 (pp20) REVERT: A 277 TYR cc_start: 0.7021 (p90) cc_final: 0.6797 (p90) REVERT: A 306 PHE cc_start: 0.9121 (t80) cc_final: 0.8544 (t80) REVERT: B 14 GLU cc_start: 0.9069 (pt0) cc_final: 0.8739 (pp20) REVERT: B 18 LYS cc_start: 0.9352 (ttmm) cc_final: 0.9052 (tmmm) REVERT: B 21 LYS cc_start: 0.8896 (ttmt) cc_final: 0.8609 (mtpp) REVERT: B 153 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8494 (mm-30) REVERT: B 218 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8620 (pt) REVERT: B 224 GLN cc_start: 0.9036 (tp40) cc_final: 0.8329 (tp-100) REVERT: B 244 TYR cc_start: 0.8178 (p90) cc_final: 0.7565 (p90) REVERT: B 269 ARG cc_start: 0.6767 (mtp180) cc_final: 0.6564 (mtp-110) REVERT: C 13 LYS cc_start: 0.9013 (tttt) cc_final: 0.8628 (tttm) REVERT: C 17 ASP cc_start: 0.9295 (m-30) cc_final: 0.8960 (m-30) REVERT: C 18 LYS cc_start: 0.9345 (ttpp) cc_final: 0.9055 (ptpp) REVERT: C 70 LYS cc_start: 0.9485 (mmtm) cc_final: 0.9210 (mmpt) REVERT: C 244 TYR cc_start: 0.8628 (p90) cc_final: 0.8379 (p90) REVERT: C 251 VAL cc_start: 0.9263 (t) cc_final: 0.9055 (p) REVERT: C 309 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: C 424 ASP cc_start: 0.8454 (t0) cc_final: 0.8139 (t0) REVERT: C 425 ARG cc_start: 0.8234 (ptt90) cc_final: 0.7915 (mtm-85) REVERT: D 18 LYS cc_start: 0.9172 (tmmt) cc_final: 0.8859 (ttpp) REVERT: D 30 ASP cc_start: 0.8772 (m-30) cc_final: 0.8348 (t0) REVERT: D 141 ARG cc_start: 0.8517 (mtt90) cc_final: 0.8126 (mtp85) REVERT: D 190 GLU cc_start: 0.8952 (tt0) cc_final: 0.8586 (tt0) REVERT: D 261 MET cc_start: 0.9091 (tpp) cc_final: 0.8805 (mmm) REVERT: D 283 MET cc_start: 0.8930 (mmm) cc_final: 0.8523 (mmm) REVERT: D 425 ARG cc_start: 0.8629 (ppt170) cc_final: 0.8359 (tmm-80) REVERT: E 79 LEU cc_start: 0.9242 (mp) cc_final: 0.8972 (mm) REVERT: E 172 ASP cc_start: 0.9068 (m-30) cc_final: 0.8776 (p0) REVERT: E 190 GLU cc_start: 0.9074 (tt0) cc_final: 0.8713 (tt0) outliers start: 35 outliers final: 24 residues processed: 233 average time/residue: 0.6641 time to fit residues: 168.7200 Evaluate side-chains 234 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 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 70 LYS Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 49 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 142 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.087200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.061669 restraints weight = 100306.260| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 5.03 r_work: 0.2579 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 14800 Z= 0.159 Angle : 0.687 10.688 20235 Z= 0.339 Chirality : 0.046 0.253 2370 Planarity : 0.004 0.075 2440 Dihedral : 7.686 56.442 2758 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.05 % Allowed : 18.01 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.21), residues: 1690 helix: 2.04 (0.20), residues: 635 sheet: 1.16 (0.25), residues: 395 loop : 0.53 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.024 0.001 TYR C 299 PHE 0.019 0.001 PHE E 307 TRP 0.012 0.001 TRP D 426 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (14755) covalent geometry : angle 0.67910 / 0.34 (20105) SS BOND : bond 0.00106 / 0.07 ( 5) SS BOND : angle 0.35567 / 0.22 ( 10) hydrogen bonds : bond 0.03307 / 2.18 ( 781) hydrogen bonds : angle 4.06215 / 2.85 ( 2456) link_ALPHA1-3 : bond 0.01041 / 0.68 ( 5) link_ALPHA1-3 : angle 1.81095 / 1.24 ( 15) link_ALPHA1-6 : bond 0.00981 / 0.63 ( 5) link_ALPHA1-6 : angle 2.09812 / 1.47 ( 15) link_BETA1-4 : bond 0.00322 / 0.22 ( 15) link_BETA1-4 : angle 1.33163 / 0.92 ( 45) link_NAG-ASN : bond 0.00104 / 0.06 ( 15) link_NAG-ASN : angle 1.41676 / 0.95 ( 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 244 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8535 (mtp) cc_final: 0.7999 (mtt) REVERT: A 14 GLU cc_start: 0.8805 (pp20) cc_final: 0.8559 (pp20) REVERT: A 277 TYR cc_start: 0.7028 (p90) cc_final: 0.6798 (p90) REVERT: A 306 PHE cc_start: 0.9124 (t80) cc_final: 0.8556 (t80) REVERT: B 14 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8738 (pp20) REVERT: B 18 LYS cc_start: 0.9357 (ttmm) cc_final: 0.9049 (tmmm) REVERT: B 21 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8624 (mtpp) REVERT: B 54 ASN cc_start: 0.9244 (m-40) cc_final: 0.9010 (m110) REVERT: B 55 MET cc_start: 0.9103 (mmm) cc_final: 0.8824 (mmm) REVERT: B 218 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8430 (pp) REVERT: B 224 GLN cc_start: 0.9029 (tp40) cc_final: 0.8319 (tp-100) REVERT: B 244 TYR cc_start: 0.8177 (p90) cc_final: 0.7557 (p90) REVERT: C 13 LYS cc_start: 0.9037 (tttt) cc_final: 0.8614 (tttm) REVERT: C 17 ASP cc_start: 0.9290 (m-30) cc_final: 0.8957 (m-30) REVERT: C 18 LYS cc_start: 0.9338 (ttpp) cc_final: 0.9048 (ptpp) REVERT: C 244 TYR cc_start: 0.8683 (p90) cc_final: 0.8420 (p90) REVERT: C 251 VAL cc_start: 0.9258 (t) cc_final: 0.9054 (p) REVERT: C 309 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: C 424 ASP cc_start: 0.8458 (t0) cc_final: 0.8141 (t0) REVERT: C 425 ARG cc_start: 0.8224 (ptt90) cc_final: 0.7903 (mtm-85) REVERT: D 18 LYS cc_start: 0.9172 (tmmt) cc_final: 0.8849 (ttpp) REVERT: D 30 ASP cc_start: 0.8777 (m-30) cc_final: 0.8347 (t0) REVERT: D 141 ARG cc_start: 0.8516 (mtt90) cc_final: 0.8124 (mtp85) REVERT: D 190 GLU cc_start: 0.8955 (tt0) cc_final: 0.8570 (tt0) REVERT: D 261 MET cc_start: 0.9069 (tpp) cc_final: 0.8786 (mmm) REVERT: D 283 MET cc_start: 0.8959 (mmm) cc_final: 0.8555 (mmm) REVERT: D 425 ARG cc_start: 0.8682 (ppt170) cc_final: 0.8393 (tmm-80) REVERT: E 79 LEU cc_start: 0.9240 (mp) cc_final: 0.8967 (mm) REVERT: E 172 ASP cc_start: 0.9087 (m-30) cc_final: 0.8782 (p0) REVERT: E 190 GLU cc_start: 0.9095 (tt0) cc_final: 0.8730 (tt0) outliers start: 30 outliers final: 22 residues processed: 228 average time/residue: 0.6846 time to fit residues: 169.9529 Evaluate side-chains 235 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 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 70 LYS Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 143 optimal weight: 0.2980 chunk 88 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN B Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.088124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.062516 restraints weight = 105168.279| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 5.13 r_work: 0.2605 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14800 Z= 0.137 Angle : 0.710 13.863 20235 Z= 0.345 Chirality : 0.046 0.253 2370 Planarity : 0.004 0.073 2440 Dihedral : 7.420 54.268 2758 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.92 % Allowed : 18.34 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.21), residues: 1690 helix: 2.05 (0.20), residues: 635 sheet: 1.19 (0.26), residues: 395 loop : 0.52 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 68 TYR 0.023 0.001 TYR C 299 PHE 0.084 0.001 PHE E 307 TRP 0.012 0.001 TRP D 426 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (14755) covalent geometry : angle 0.70348 / 0.34 (20105) SS BOND : bond 0.00076 / 0.05 ( 5) SS BOND : angle 0.26593 / 0.15 ( 10) hydrogen bonds : bond 0.03237 / 2.13 ( 781) hydrogen bonds : angle 4.02486 / 2.82 ( 2456) link_ALPHA1-3 : bond 0.01087 / 0.72 ( 5) link_ALPHA1-3 : angle 1.71732 / 1.17 ( 15) link_ALPHA1-6 : bond 0.01036 / 0.66 ( 5) link_ALPHA1-6 : angle 2.01515 / 1.42 ( 15) link_BETA1-4 : bond 0.00361 / 0.24 ( 15) link_BETA1-4 : angle 1.27070 / 0.88 ( 45) link_NAG-ASN : bond 0.00159 / 0.09 ( 15) link_NAG-ASN : angle 1.36235 / 0.92 ( 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 250 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8495 (mtp) cc_final: 0.7985 (mtt) REVERT: A 14 GLU cc_start: 0.8810 (pp20) cc_final: 0.8545 (pp20) REVERT: A 55 MET cc_start: 0.8982 (tpt) cc_final: 0.8731 (tpt) REVERT: B 14 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8718 (pp20) REVERT: B 18 LYS cc_start: 0.9356 (ttmm) cc_final: 0.9043 (tmmm) REVERT: B 21 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8588 (mtpp) REVERT: B 54 ASN cc_start: 0.9232 (m-40) cc_final: 0.9008 (m-40) REVERT: B 153 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8747 (mm-30) REVERT: B 218 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8401 (pp) REVERT: B 224 GLN cc_start: 0.9029 (tp40) cc_final: 0.8329 (tp-100) REVERT: B 244 TYR cc_start: 0.8227 (p90) cc_final: 0.7558 (p90) REVERT: C 13 LYS cc_start: 0.9066 (tttt) cc_final: 0.8649 (tttm) REVERT: C 17 ASP cc_start: 0.9286 (m-30) cc_final: 0.8901 (m-30) REVERT: C 18 LYS cc_start: 0.9346 (ttpp) cc_final: 0.9054 (ptpp) REVERT: C 244 TYR cc_start: 0.8676 (p90) cc_final: 0.8423 (p90) REVERT: C 286 MET cc_start: 0.8542 (tpp) cc_final: 0.8277 (mmm) REVERT: C 309 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7360 (pm20) REVERT: C 424 ASP cc_start: 0.8443 (t0) cc_final: 0.8125 (t0) REVERT: C 425 ARG cc_start: 0.8195 (ptt90) cc_final: 0.7860 (mtm-85) REVERT: D 18 LYS cc_start: 0.9166 (tmmt) cc_final: 0.8856 (ttpp) REVERT: D 30 ASP cc_start: 0.8773 (m-30) cc_final: 0.8333 (t0) REVERT: D 55 MET cc_start: 0.9480 (tpt) cc_final: 0.9214 (tpt) REVERT: D 141 ARG cc_start: 0.8488 (mtt90) cc_final: 0.8092 (mtp85) REVERT: D 155 GLU cc_start: 0.9071 (tt0) cc_final: 0.8560 (tt0) REVERT: D 190 GLU cc_start: 0.8961 (tt0) cc_final: 0.8573 (tt0) REVERT: D 261 MET cc_start: 0.9040 (tpp) cc_final: 0.8789 (mmm) REVERT: D 283 MET cc_start: 0.8940 (mmm) cc_final: 0.8533 (mmm) REVERT: D 425 ARG cc_start: 0.8680 (ppt170) cc_final: 0.8380 (tmm-80) REVERT: E 79 LEU cc_start: 0.9231 (mp) cc_final: 0.8950 (mm) REVERT: E 172 ASP cc_start: 0.9102 (m-30) cc_final: 0.8791 (p0) REVERT: E 190 GLU cc_start: 0.9104 (tt0) cc_final: 0.8721 (tt0) outliers start: 28 outliers final: 20 residues processed: 237 average time/residue: 0.6825 time to fit residues: 175.9178 Evaluate side-chains 236 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 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 70 LYS Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 141 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.062464 restraints weight = 134061.568| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 5.59 r_work: 0.2589 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14800 Z= 0.133 Angle : 0.691 11.899 20235 Z= 0.336 Chirality : 0.045 0.255 2370 Planarity : 0.004 0.072 2440 Dihedral : 7.087 51.324 2758 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.72 % Allowed : 18.54 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.21), residues: 1690 helix: 2.07 (0.20), residues: 635 sheet: 1.19 (0.26), residues: 395 loop : 0.53 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 68 TYR 0.025 0.001 TYR C 299 PHE 0.025 0.001 PHE E 307 TRP 0.012 0.001 TRP D 426 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (14755) covalent geometry : angle 0.68414 / 0.34 (20105) SS BOND : bond 0.00102 / 0.07 ( 5) SS BOND : angle 0.19931 / 0.14 ( 10) hydrogen bonds : bond 0.03158 / 2.09 ( 781) hydrogen bonds : angle 3.96208 / 2.78 ( 2456) link_ALPHA1-3 : bond 0.01117 / 0.73 ( 5) link_ALPHA1-3 : angle 1.67888 / 1.15 ( 15) link_ALPHA1-6 : bond 0.01059 / 0.68 ( 5) link_ALPHA1-6 : angle 1.94830 / 1.39 ( 15) link_BETA1-4 : bond 0.00383 / 0.26 ( 15) link_BETA1-4 : angle 1.24673 / 0.87 ( 45) link_NAG-ASN : bond 0.00129 / 0.08 ( 15) link_NAG-ASN : angle 1.33219 / 0.90 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5356.21 seconds wall clock time: 92 minutes 16.29 seconds (5536.29 seconds total)