Starting phenix.real_space_refine on Thu Sep 18 06:02:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ff2_50349/09_2025/9ff2_50349.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ff2_50349/09_2025/9ff2_50349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ff2_50349/09_2025/9ff2_50349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ff2_50349/09_2025/9ff2_50349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ff2_50349/09_2025/9ff2_50349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ff2_50349/09_2025/9ff2_50349.map" } resolution = 2.8 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= 0.004 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 9625 2.51 5 N 2310 2.21 5 O 2655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14680 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2788 Chain: "B" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2788 Chain: "C" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2788 Chain: "D" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2788 Chain: "E" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2788 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Unusual residues: {' CL': 1, 'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 63 Unusual residues: {' CL': 1, 'D10': 4, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Unusual residues: {' CL': 1, 'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' CL': 1, 'D10': 2, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Unusual residues: {' CL': 1, 'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 5.26, per 1000 atoms: 0.36 Number of scatterers: 14680 At special positions: 0 Unit cell: (100.434, 100.434, 128.952, 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 2655 8.00 N 2310 7.00 C 9625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A 501 " - " ASN A 8 " " NAG B 506 " - " ASN B 8 " " NAG C 506 " - " ASN C 8 " " NAG D 505 " - " ASN D 8 " " NAG E 506 " - " 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: 1.51 Conformation dependent library (CDL) restraints added in 969.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 15 sheets defined 43.5% alpha, 39.2% 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 Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.586A 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 177 through 181 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 239 removed outlier: 4.072A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.503A pdb=" N LEU A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 306 Processing helix chain 'A' and resid 309 through 447 removed outlier: 3.785A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) 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: 3.712A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 239 removed outlier: 4.046A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 271 Processing helix chain 'B' and resid 279 through 306 Processing helix chain 'B' and resid 309 through 446 removed outlier: 3.756A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) 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: 3.648A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 239 removed outlier: 4.041A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 246 through 272 Processing helix chain 'C' and resid 279 through 306 Processing helix chain 'C' and resid 309 through 446 removed outlier: 3.809A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.546A pdb=" N LEU D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 4.463A 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 225 through 238 Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 246 through 272 Processing helix chain 'D' and resid 279 through 306 Processing helix chain 'D' and resid 309 through 446 removed outlier: 3.805A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) 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 170 through 173 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 239 removed outlier: 4.095A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.501A pdb=" N LEU E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 306 Processing helix chain 'E' and resid 309 through 447 removed outlier: 3.806A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.285A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.585A 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: 6.336A pdb=" N ASP A 101 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA A 135 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 103 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 4.066A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.610A 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: 4.291A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.532A 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: 6.162A pdb=" N ASP B 101 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA B 135 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 103 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.532A 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: 3.934A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.392A 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: 4.248A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR C 60 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE C 47 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N TYR C 62 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA C 45 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLN C 64 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASP C 43 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N TYR C 66 " --> pdb=" O AASN C 41 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N AASN C 41 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ARG C 68 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N GLY C 39 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.823A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR C 60 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE C 47 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N TYR C 62 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA C 45 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLN C 64 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASP C 43 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N TYR C 66 " --> pdb=" O AASN C 41 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N AASN C 41 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ARG C 68 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N GLY C 39 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.932A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL C 199 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR C 205 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN C 197 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG C 207 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER C 195 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER C 209 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU C 193 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER C 211 " --> pdb=" O HIS C 191 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS C 191 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 213 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.314A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.431A 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: 6.337A pdb=" N ASP D 101 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA D 135 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS D 103 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.431A 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: 3.942A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.581A 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: 4.264A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET E 49 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR E 60 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE E 47 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N TYR E 62 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA E 45 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLN E 64 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP E 43 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TYR E 66 " --> pdb=" O AASN E 41 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N AASN E 41 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ARG E 68 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N GLY E 39 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.764A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET E 49 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR E 60 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE E 47 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N TYR E 62 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA E 45 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLN E 64 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP E 43 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TYR E 66 " --> pdb=" O AASN E 41 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N AASN E 41 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ARG E 68 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N GLY E 39 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.898A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2428 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: 2.56 Time building geometry restraints manager: 1.92 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: 4348 1.34 - 1.46: 3142 1.46 - 1.57: 7430 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 15070 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 2.50e+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 2.49e+00 bond pdb=" C1 MAN e 5 " pdb=" O5 MAN e 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 MAN a 4 " pdb=" O5 MAN a 4 " ideal model delta sigma weight residual 1.399 1.429 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C1 MAN e 4 " pdb=" O5 MAN e 4 " ideal model delta sigma weight residual 1.399 1.429 -0.030 2.00e-02 2.50e+03 2.20e+00 ... (remaining 15065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 19650 1.24 - 2.48: 614 2.48 - 3.71: 199 3.71 - 4.95: 22 4.95 - 6.19: 10 Bond angle restraints: 20495 Sorted by residual: angle pdb=" CA TYR B 299 " pdb=" CB TYR B 299 " pdb=" CG TYR B 299 " ideal model delta sigma weight residual 113.90 107.71 6.19 1.80e+00 3.09e-01 1.18e+01 angle pdb=" CA TYR E 299 " pdb=" CB TYR E 299 " pdb=" CG TYR E 299 " ideal model delta sigma weight residual 113.90 107.82 6.08 1.80e+00 3.09e-01 1.14e+01 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 108.05 5.85 1.80e+00 3.09e-01 1.05e+01 angle pdb=" CA TYR C 299 " pdb=" CB TYR C 299 " pdb=" CG TYR C 299 " ideal model delta sigma weight residual 113.90 108.12 5.78 1.80e+00 3.09e-01 1.03e+01 angle pdb=" CA TYR D 299 " pdb=" CB TYR D 299 " pdb=" CG TYR D 299 " ideal model delta sigma weight residual 113.90 108.28 5.62 1.80e+00 3.09e-01 9.75e+00 ... (remaining 20490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 9141 21.06 - 42.11: 213 42.11 - 63.17: 18 63.17 - 84.23: 36 84.23 - 105.29: 22 Dihedral angle restraints: 9430 sinusoidal: 4315 harmonic: 5115 Sorted by residual: 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 -176.58 105.29 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA c 3 " pdb=" C4 BMA c 3 " pdb=" C5 BMA c 3 " pdb=" O5 BMA c 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.30 105.01 1 3.00e+01 1.11e-03 1.34e+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 -176.19 104.90 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 9427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1887 0.050 - 0.099: 391 0.099 - 0.149: 108 0.149 - 0.199: 9 0.199 - 0.248: 5 Chirality restraints: 2400 Sorted by residual: chirality pdb=" C5 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C6 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 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 2397 not shown) Planarity restraints: 2500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 299 " 0.019 2.00e-02 2.50e+03 1.15e-02 2.64e+00 pdb=" CG TYR E 299 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR E 299 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR E 299 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 299 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 299 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 299 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 299 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 299 " -0.019 2.00e-02 2.50e+03 1.14e-02 2.59e+00 pdb=" CG TYR B 299 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 299 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 299 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 299 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 299 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 299 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 299 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " 0.018 2.00e-02 2.50e+03 1.11e-02 2.49e+00 pdb=" CG TYR A 299 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " 0.004 2.00e-02 2.50e+03 ... (remaining 2497 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 3167 2.78 - 3.31: 13465 3.31 - 3.84: 25488 3.84 - 4.37: 30702 4.37 - 4.90: 52393 Nonbonded interactions: 125215 Sorted by model distance: nonbonded pdb=" OD1 ASP D 101 " pdb=" NH2 ARG E 129 " model vdw 2.256 3.120 nonbonded pdb=" O LEU C 268 " pdb=" OG1 THR C 271 " model vdw 2.271 3.040 nonbonded pdb=" O THR E 233 " pdb=" OG SER E 236 " model vdw 2.292 3.040 nonbonded pdb=" O THR C 233 " pdb=" OG SER C 236 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR E 284 " pdb=" OD1 ASN E 439 " model vdw 2.293 3.040 ... (remaining 125210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 40 or resid 42 through 65 or resid 67 through 13 \ 7 or resid 139 through 163 or resid 165 through 242 or resid 244 through 436 or \ resid 438 through 447 or resid 503)) selection = (chain 'B' and (resid 4 through 40 or resid 42 through 65 or resid 67 through 13 \ 7 or resid 139 through 163 or resid 165 through 242 or resid 244 through 436 or \ resid 438 through 447 or resid 503)) selection = (chain 'C' and (resid 4 through 40 or resid 42 through 65 or resid 67 through 13 \ 7 or resid 139 through 163 or resid 165 through 242 or resid 244 through 436 or \ resid 438 through 447 or resid 503)) selection = (chain 'D' and (resid 4 through 40 or resid 42 through 65 or resid 67 through 13 \ 7 or resid 139 through 163 or resid 165 through 242 or resid 244 through 436 or \ resid 438 through 447 or resid 503)) selection = (chain 'E' and (resid 4 through 40 or resid 42 through 65 or resid 67 through 13 \ 7 or resid 139 through 163 or resid 165 through 242 or resid 244 through 436 or \ resid 438 through 447 or resid 503)) } 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: 0.590 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.060 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 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 : 0.004 0.032 15115 Z= 0.200 Angle : 0.583 6.191 20625 Z= 0.280 Chirality : 0.046 0.248 2400 Planarity : 0.003 0.029 2485 Dihedral : 11.892 105.286 6155 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.20 % Allowed : 2.41 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.22), residues: 1715 helix: 2.56 (0.21), residues: 640 sheet: 0.71 (0.24), residues: 425 loop : 1.21 (0.29), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 26 TYR 0.026 0.002 TYR E 299 PHE 0.011 0.001 PHE D 98 TRP 0.009 0.001 TRP C 67 HIS 0.003 0.001 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.00432 (15070) covalent geometry : angle 0.57493 (20495) SS BOND : bond 0.00305 ( 5) SS BOND : angle 0.76023 ( 10) hydrogen bonds : bond 0.10621 ( 774) hydrogen bonds : angle 4.84606 ( 2428) link_ALPHA1-3 : bond 0.00175 ( 5) link_ALPHA1-3 : angle 1.08622 ( 15) link_ALPHA1-6 : bond 0.00185 ( 5) link_ALPHA1-6 : angle 1.02092 ( 15) link_BETA1-4 : bond 0.00348 ( 15) link_BETA1-4 : angle 1.56246 ( 45) link_NAG-ASN : bond 0.00248 ( 15) link_NAG-ASN : angle 1.31918 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 261 time to evaluate : 0.603 Fit side-chains REVERT: A 307 PHE cc_start: 0.9036 (t80) cc_final: 0.8814 (t80) REVERT: B 9 MET cc_start: 0.9182 (mtp) cc_final: 0.8894 (mtm) REVERT: B 267 HIS cc_start: 0.8141 (t70) cc_final: 0.7730 (t-90) REVERT: C 52 GLU cc_start: 0.8928 (mp0) cc_final: 0.8650 (mp0) REVERT: D 267 HIS cc_start: 0.8300 (t70) cc_final: 0.8096 (t-90) REVERT: D 307 PHE cc_start: 0.8901 (t80) cc_final: 0.8661 (t80) REVERT: E 9 MET cc_start: 0.9432 (mtp) cc_final: 0.9136 (mtm) REVERT: E 13 LYS cc_start: 0.9419 (tttm) cc_final: 0.9035 (tttm) REVERT: E 14 GLU cc_start: 0.9214 (tt0) cc_final: 0.8997 (pt0) REVERT: E 17 ASP cc_start: 0.8844 (m-30) cc_final: 0.8640 (m-30) REVERT: E 190 GLU cc_start: 0.8847 (tt0) cc_final: 0.8460 (tt0) REVERT: E 244 TYR cc_start: 0.9102 (p90) cc_final: 0.8836 (p90) REVERT: E 267 HIS cc_start: 0.8323 (t70) cc_final: 0.8114 (t-90) outliers start: 3 outliers final: 1 residues processed: 264 average time/residue: 0.8770 time to fit residues: 247.2446 Evaluate side-chains 122 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 41 ASN A D 185 GLN E 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.063902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.046862 restraints weight = 155845.675| |-----------------------------------------------------------------------------| r_work (start): 0.2477 rms_B_bonded: 4.92 r_work: 0.2256 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2250 r_free = 0.2250 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2245 r_free = 0.2245 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15115 Z= 0.141 Angle : 0.561 8.615 20625 Z= 0.288 Chirality : 0.044 0.193 2400 Planarity : 0.004 0.039 2485 Dihedral : 10.670 81.866 2896 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.04 % Allowed : 11.14 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.21), residues: 1715 helix: 2.66 (0.20), residues: 625 sheet: 0.88 (0.25), residues: 400 loop : 0.96 (0.27), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 68 TYR 0.025 0.001 TYR B 299 PHE 0.016 0.001 PHE D 306 TRP 0.011 0.001 TRP C 67 HIS 0.002 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00316 (15070) covalent geometry : angle 0.54792 (20495) SS BOND : bond 0.00126 ( 5) SS BOND : angle 0.22687 ( 10) hydrogen bonds : bond 0.04093 ( 774) hydrogen bonds : angle 4.24698 ( 2428) link_ALPHA1-3 : bond 0.00826 ( 5) link_ALPHA1-3 : angle 1.98620 ( 15) link_ALPHA1-6 : bond 0.00462 ( 5) link_ALPHA1-6 : angle 2.08239 ( 15) link_BETA1-4 : bond 0.00193 ( 15) link_BETA1-4 : angle 1.59385 ( 45) link_NAG-ASN : bond 0.00075 ( 15) link_NAG-ASN : angle 1.43060 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.514 Fit side-chains REVERT: A 307 PHE cc_start: 0.9390 (t80) cc_final: 0.9154 (t80) REVERT: B 9 MET cc_start: 0.8967 (mtp) cc_final: 0.8505 (mtt) REVERT: B 244 TYR cc_start: 0.9309 (p90) cc_final: 0.9014 (p90) REVERT: B 267 HIS cc_start: 0.8234 (t70) cc_final: 0.7989 (t-90) REVERT: D 307 PHE cc_start: 0.9132 (t80) cc_final: 0.8890 (t80) REVERT: E 9 MET cc_start: 0.9348 (mtp) cc_final: 0.8927 (mtm) REVERT: E 14 GLU cc_start: 0.9457 (tt0) cc_final: 0.9134 (pt0) REVERT: E 17 ASP cc_start: 0.9160 (m-30) cc_final: 0.8872 (m-30) REVERT: E 244 TYR cc_start: 0.9202 (p90) cc_final: 0.8837 (p90) outliers start: 16 outliers final: 6 residues processed: 148 average time/residue: 0.6288 time to fit residues: 102.1599 Evaluate side-chains 125 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain D residue 306 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 140 optimal weight: 0.0980 chunk 149 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 309 GLN D 224 GLN E 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.064079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.047406 restraints weight = 141279.500| |-----------------------------------------------------------------------------| r_work (start): 0.2480 rms_B_bonded: 4.73 r_work: 0.2270 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2265 r_free = 0.2265 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2264 r_free = 0.2264 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15115 Z= 0.122 Angle : 0.532 8.989 20625 Z= 0.269 Chirality : 0.044 0.215 2400 Planarity : 0.003 0.032 2485 Dihedral : 9.633 76.184 2896 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.50 % Allowed : 11.27 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.21), residues: 1715 helix: 2.69 (0.20), residues: 625 sheet: 0.95 (0.25), residues: 400 loop : 0.93 (0.27), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 68 TYR 0.026 0.001 TYR E 299 PHE 0.017 0.001 PHE D 306 TRP 0.011 0.001 TRP C 67 HIS 0.002 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00267 (15070) covalent geometry : angle 0.51939 (20495) SS BOND : bond 0.00143 ( 5) SS BOND : angle 0.20556 ( 10) hydrogen bonds : bond 0.03797 ( 774) hydrogen bonds : angle 4.04045 ( 2428) link_ALPHA1-3 : bond 0.01072 ( 5) link_ALPHA1-3 : angle 1.96138 ( 15) link_ALPHA1-6 : bond 0.00694 ( 5) link_ALPHA1-6 : angle 2.05914 ( 15) link_BETA1-4 : bond 0.00265 ( 15) link_BETA1-4 : angle 1.45339 ( 45) link_NAG-ASN : bond 0.00103 ( 15) link_NAG-ASN : angle 1.36449 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.560 Fit side-chains REVERT: A 185 GLN cc_start: 0.8718 (tp40) cc_final: 0.8472 (tp-100) REVERT: B 9 MET cc_start: 0.8941 (mtp) cc_final: 0.8568 (mtt) REVERT: B 14 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8354 (pt0) REVERT: B 190 GLU cc_start: 0.9002 (tt0) cc_final: 0.8773 (tt0) REVERT: B 244 TYR cc_start: 0.9312 (p90) cc_final: 0.9095 (p90) REVERT: B 267 HIS cc_start: 0.8315 (t70) cc_final: 0.7998 (t-90) REVERT: B 270 GLU cc_start: 0.8417 (pp20) cc_final: 0.8098 (pp20) REVERT: D 307 PHE cc_start: 0.9171 (t80) cc_final: 0.8953 (t80) REVERT: E 9 MET cc_start: 0.9309 (mtp) cc_final: 0.8874 (mtm) REVERT: E 14 GLU cc_start: 0.9423 (tt0) cc_final: 0.9092 (pt0) REVERT: E 224 GLN cc_start: 0.9128 (tp40) cc_final: 0.8846 (tp40) REVERT: E 244 TYR cc_start: 0.9180 (p90) cc_final: 0.8847 (p90) outliers start: 23 outliers final: 9 residues processed: 150 average time/residue: 0.6881 time to fit residues: 112.5658 Evaluate side-chains 130 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 306 PHE 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 11 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 100 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A A 224 GLN D 41 ASN A D 224 GLN E 41 ASN B E 90 GLN E 185 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.048012 restraints weight = 141654.813| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 4.58 r_work: 0.2280 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2276 r_free = 0.2276 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2276 r_free = 0.2276 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15115 Z= 0.117 Angle : 0.528 6.942 20625 Z= 0.266 Chirality : 0.044 0.231 2400 Planarity : 0.003 0.031 2485 Dihedral : 9.099 68.335 2896 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.30 % Allowed : 12.05 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.21), residues: 1715 helix: 2.72 (0.20), residues: 625 sheet: 1.01 (0.25), residues: 400 loop : 0.93 (0.27), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 312 TYR 0.026 0.001 TYR E 299 PHE 0.017 0.001 PHE A 306 TRP 0.010 0.001 TRP C 67 HIS 0.001 0.000 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.00257 (15070) covalent geometry : angle 0.51530 (20495) SS BOND : bond 0.00136 ( 5) SS BOND : angle 0.18423 ( 10) hydrogen bonds : bond 0.03656 ( 774) hydrogen bonds : angle 3.96535 ( 2428) link_ALPHA1-3 : bond 0.01068 ( 5) link_ALPHA1-3 : angle 2.10695 ( 15) link_ALPHA1-6 : bond 0.00757 ( 5) link_ALPHA1-6 : angle 2.09564 ( 15) link_BETA1-4 : bond 0.00276 ( 15) link_BETA1-4 : angle 1.41519 ( 45) link_NAG-ASN : bond 0.00092 ( 15) link_NAG-ASN : angle 1.33172 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.574 Fit side-chains REVERT: A 185 GLN cc_start: 0.8744 (tp40) cc_final: 0.8497 (tp-100) REVERT: A 244 TYR cc_start: 0.8948 (p90) cc_final: 0.8688 (p90) REVERT: B 9 MET cc_start: 0.8933 (mtp) cc_final: 0.8600 (mtt) REVERT: B 14 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: B 190 GLU cc_start: 0.8994 (tt0) cc_final: 0.8618 (tt0) REVERT: B 244 TYR cc_start: 0.9322 (p90) cc_final: 0.9077 (p90) REVERT: B 267 HIS cc_start: 0.8329 (t70) cc_final: 0.7961 (t-90) REVERT: B 270 GLU cc_start: 0.8392 (pp20) cc_final: 0.8066 (pp20) REVERT: C 43 ASP cc_start: 0.8711 (t70) cc_final: 0.8393 (t0) REVERT: D 307 PHE cc_start: 0.9205 (t80) cc_final: 0.8990 (t80) REVERT: E 9 MET cc_start: 0.9316 (mtp) cc_final: 0.8888 (mtm) REVERT: E 14 GLU cc_start: 0.9419 (tt0) cc_final: 0.9106 (pt0) REVERT: E 224 GLN cc_start: 0.9137 (tp40) cc_final: 0.8862 (tp40) REVERT: E 244 TYR cc_start: 0.9173 (p90) cc_final: 0.8879 (p90) outliers start: 20 outliers final: 11 residues processed: 140 average time/residue: 0.6619 time to fit residues: 101.3597 Evaluate side-chains 131 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 97 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 41 ASN A D 224 GLN D 309 GLN E 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.063798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.047656 restraints weight = 163884.195| |-----------------------------------------------------------------------------| r_work (start): 0.2483 rms_B_bonded: 4.78 r_work: 0.2266 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2262 r_free = 0.2262 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2262 r_free = 0.2262 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15115 Z= 0.129 Angle : 0.534 10.288 20625 Z= 0.267 Chirality : 0.044 0.239 2400 Planarity : 0.003 0.034 2485 Dihedral : 8.634 64.761 2896 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.43 % Allowed : 12.18 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.21), residues: 1715 helix: 2.71 (0.20), residues: 630 sheet: 1.02 (0.25), residues: 400 loop : 0.97 (0.27), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 269 TYR 0.026 0.001 TYR E 299 PHE 0.018 0.001 PHE A 306 TRP 0.010 0.001 TRP C 67 HIS 0.001 0.000 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.00287 (15070) covalent geometry : angle 0.52154 (20495) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.23159 ( 10) hydrogen bonds : bond 0.03666 ( 774) hydrogen bonds : angle 3.94610 ( 2428) link_ALPHA1-3 : bond 0.01035 ( 5) link_ALPHA1-3 : angle 2.17376 ( 15) link_ALPHA1-6 : bond 0.00789 ( 5) link_ALPHA1-6 : angle 2.11607 ( 15) link_BETA1-4 : bond 0.00275 ( 15) link_BETA1-4 : angle 1.41165 ( 45) link_NAG-ASN : bond 0.00077 ( 15) link_NAG-ASN : angle 1.36669 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.612 Fit side-chains REVERT: A 185 GLN cc_start: 0.8749 (tp40) cc_final: 0.8501 (tp-100) REVERT: A 244 TYR cc_start: 0.9030 (p90) cc_final: 0.8763 (p90) REVERT: B 9 MET cc_start: 0.8926 (mtp) cc_final: 0.8649 (mtt) REVERT: B 14 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: B 190 GLU cc_start: 0.9017 (tt0) cc_final: 0.8640 (tt0) REVERT: B 244 TYR cc_start: 0.9345 (p90) cc_final: 0.8929 (p90) REVERT: B 267 HIS cc_start: 0.8340 (t70) cc_final: 0.7902 (t-90) REVERT: D 9 MET cc_start: 0.9086 (mtp) cc_final: 0.8777 (ttm) REVERT: D 307 PHE cc_start: 0.9202 (t80) cc_final: 0.8956 (t80) REVERT: E 9 MET cc_start: 0.9319 (mtp) cc_final: 0.8949 (mtm) REVERT: E 14 GLU cc_start: 0.9423 (tt0) cc_final: 0.9114 (pt0) REVERT: E 172 ASP cc_start: 0.8969 (p0) cc_final: 0.8729 (p0) REVERT: E 224 GLN cc_start: 0.9175 (tp40) cc_final: 0.8906 (tp40) REVERT: E 244 TYR cc_start: 0.9181 (p90) cc_final: 0.8862 (p90) outliers start: 22 outliers final: 13 residues processed: 137 average time/residue: 0.6995 time to fit residues: 104.4287 Evaluate side-chains 143 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 306 PHE 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 7 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 132 optimal weight: 0.0170 chunk 47 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 chunk 155 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN B 185 GLN D 224 GLN E 41 ASN A Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.064650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.048029 restraints weight = 147550.450| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 4.77 r_work: 0.2289 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2283 r_free = 0.2283 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2283 r_free = 0.2283 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15115 Z= 0.110 Angle : 0.525 7.491 20625 Z= 0.263 Chirality : 0.044 0.246 2400 Planarity : 0.003 0.037 2485 Dihedral : 8.153 61.001 2896 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.43 % Allowed : 12.44 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.21), residues: 1715 helix: 2.73 (0.20), residues: 630 sheet: 1.08 (0.25), residues: 400 loop : 0.98 (0.27), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 269 TYR 0.025 0.001 TYR E 299 PHE 0.017 0.001 PHE A 306 TRP 0.011 0.001 TRP C 67 HIS 0.001 0.000 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.00239 (15070) covalent geometry : angle 0.51325 (20495) SS BOND : bond 0.00140 ( 5) SS BOND : angle 0.17872 ( 10) hydrogen bonds : bond 0.03513 ( 774) hydrogen bonds : angle 3.87122 ( 2428) link_ALPHA1-3 : bond 0.01074 ( 5) link_ALPHA1-3 : angle 2.17128 ( 15) link_ALPHA1-6 : bond 0.00864 ( 5) link_ALPHA1-6 : angle 2.09106 ( 15) link_BETA1-4 : bond 0.00314 ( 15) link_BETA1-4 : angle 1.34206 ( 45) link_NAG-ASN : bond 0.00110 ( 15) link_NAG-ASN : angle 1.31403 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.530 Fit side-chains REVERT: A 185 GLN cc_start: 0.8758 (tp40) cc_final: 0.8527 (tp-100) REVERT: A 244 TYR cc_start: 0.9023 (p90) cc_final: 0.8703 (p90) REVERT: A 307 PHE cc_start: 0.9481 (t80) cc_final: 0.9225 (t80) REVERT: B 9 MET cc_start: 0.8909 (mtp) cc_final: 0.8640 (mtt) REVERT: B 14 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8423 (pt0) REVERT: B 115 MET cc_start: 0.9428 (ttp) cc_final: 0.9211 (tmm) REVERT: B 190 GLU cc_start: 0.9012 (tt0) cc_final: 0.8577 (tt0) REVERT: B 244 TYR cc_start: 0.9341 (p90) cc_final: 0.8907 (p90) REVERT: B 267 HIS cc_start: 0.8238 (t70) cc_final: 0.7926 (t-90) REVERT: B 270 GLU cc_start: 0.8303 (pp20) cc_final: 0.7997 (pp20) REVERT: C 43 ASP cc_start: 0.8633 (t70) cc_final: 0.8304 (t0) REVERT: D 307 PHE cc_start: 0.9200 (t80) cc_final: 0.8980 (t80) REVERT: D 309 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: E 9 MET cc_start: 0.9307 (mtp) cc_final: 0.8984 (mtm) REVERT: E 14 GLU cc_start: 0.9425 (tt0) cc_final: 0.9125 (pt0) REVERT: E 172 ASP cc_start: 0.8976 (p0) cc_final: 0.8734 (p0) REVERT: E 224 GLN cc_start: 0.9145 (tp40) cc_final: 0.8783 (tp40) REVERT: E 244 TYR cc_start: 0.9164 (p90) cc_final: 0.8880 (p90) outliers start: 22 outliers final: 11 residues processed: 147 average time/residue: 0.6615 time to fit residues: 105.8335 Evaluate side-chains 140 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 306 PHE 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: 5.9990 chunk 27 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 0.0060 chunk 15 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.064870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.048905 restraints weight = 151755.211| |-----------------------------------------------------------------------------| r_work (start): 0.2517 rms_B_bonded: 4.70 r_work: 0.2304 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2305 r_free = 0.2305 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2305 r_free = 0.2305 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15115 Z= 0.106 Angle : 0.525 9.195 20625 Z= 0.261 Chirality : 0.044 0.249 2400 Planarity : 0.003 0.038 2485 Dihedral : 7.765 57.636 2896 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.17 % Allowed : 12.90 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.21), residues: 1715 helix: 2.69 (0.20), residues: 635 sheet: 1.16 (0.25), residues: 400 loop : 0.98 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 269 TYR 0.025 0.001 TYR E 299 PHE 0.018 0.001 PHE A 306 TRP 0.011 0.001 TRP C 67 HIS 0.001 0.000 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.00231 (15070) covalent geometry : angle 0.51333 (20495) SS BOND : bond 0.00140 ( 5) SS BOND : angle 0.14780 ( 10) hydrogen bonds : bond 0.03427 ( 774) hydrogen bonds : angle 3.83075 ( 2428) link_ALPHA1-3 : bond 0.01059 ( 5) link_ALPHA1-3 : angle 2.16835 ( 15) link_ALPHA1-6 : bond 0.00915 ( 5) link_ALPHA1-6 : angle 2.04866 ( 15) link_BETA1-4 : bond 0.00343 ( 15) link_BETA1-4 : angle 1.32905 ( 45) link_NAG-ASN : bond 0.00117 ( 15) link_NAG-ASN : angle 1.32266 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.571 Fit side-chains REVERT: A 185 GLN cc_start: 0.8743 (tp40) cc_final: 0.8476 (tp40) REVERT: A 244 TYR cc_start: 0.9034 (p90) cc_final: 0.8700 (p90) REVERT: A 307 PHE cc_start: 0.9475 (t80) cc_final: 0.9228 (t80) REVERT: B 9 MET cc_start: 0.8911 (mtp) cc_final: 0.8641 (mtt) REVERT: B 14 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: B 190 GLU cc_start: 0.9018 (tt0) cc_final: 0.8597 (tt0) REVERT: B 244 TYR cc_start: 0.9356 (p90) cc_final: 0.9110 (p90) REVERT: B 267 HIS cc_start: 0.8227 (t70) cc_final: 0.7891 (t-90) REVERT: B 270 GLU cc_start: 0.8295 (pp20) cc_final: 0.7989 (pp20) REVERT: C 43 ASP cc_start: 0.8620 (t70) cc_final: 0.8291 (t0) REVERT: D 9 MET cc_start: 0.9040 (mtp) cc_final: 0.8729 (ttm) REVERT: D 307 PHE cc_start: 0.9186 (t80) cc_final: 0.8970 (t80) REVERT: D 309 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8164 (mp10) REVERT: E 9 MET cc_start: 0.9304 (mtp) cc_final: 0.9023 (mtm) REVERT: E 14 GLU cc_start: 0.9424 (tt0) cc_final: 0.9134 (pt0) REVERT: E 172 ASP cc_start: 0.8960 (p0) cc_final: 0.8725 (p0) REVERT: E 224 GLN cc_start: 0.9140 (tp40) cc_final: 0.8785 (tp40) REVERT: E 244 TYR cc_start: 0.9150 (p90) cc_final: 0.8866 (p90) outliers start: 18 outliers final: 8 residues processed: 146 average time/residue: 0.7023 time to fit residues: 111.8922 Evaluate side-chains 138 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 56 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.064611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.047971 restraints weight = 152549.377| |-----------------------------------------------------------------------------| r_work (start): 0.2506 rms_B_bonded: 4.85 r_work: 0.2294 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2289 r_free = 0.2289 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2289 r_free = 0.2289 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15115 Z= 0.113 Angle : 0.529 8.975 20625 Z= 0.263 Chirality : 0.044 0.249 2400 Planarity : 0.003 0.038 2485 Dihedral : 7.547 55.087 2896 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.91 % Allowed : 13.49 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.21), residues: 1715 helix: 2.68 (0.20), residues: 635 sheet: 1.18 (0.25), residues: 400 loop : 0.98 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 269 TYR 0.025 0.001 TYR E 299 PHE 0.018 0.001 PHE A 306 TRP 0.010 0.001 TRP C 67 HIS 0.001 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00250 (15070) covalent geometry : angle 0.51670 (20495) SS BOND : bond 0.00125 ( 5) SS BOND : angle 0.17227 ( 10) hydrogen bonds : bond 0.03450 ( 774) hydrogen bonds : angle 3.83203 ( 2428) link_ALPHA1-3 : bond 0.01022 ( 5) link_ALPHA1-3 : angle 2.17699 ( 15) link_ALPHA1-6 : bond 0.00913 ( 5) link_ALPHA1-6 : angle 1.99479 ( 15) link_BETA1-4 : bond 0.00353 ( 15) link_BETA1-4 : angle 1.34204 ( 45) link_NAG-ASN : bond 0.00107 ( 15) link_NAG-ASN : angle 1.33145 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.591 Fit side-chains REVERT: A 185 GLN cc_start: 0.8748 (tp40) cc_final: 0.8480 (tp40) REVERT: A 244 TYR cc_start: 0.9061 (p90) cc_final: 0.8733 (p90) REVERT: A 307 PHE cc_start: 0.9482 (t80) cc_final: 0.9235 (t80) REVERT: B 9 MET cc_start: 0.8901 (mtp) cc_final: 0.8648 (mtt) REVERT: B 14 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: B 190 GLU cc_start: 0.9020 (tt0) cc_final: 0.8598 (tt0) REVERT: B 244 TYR cc_start: 0.9354 (p90) cc_final: 0.9079 (p90) REVERT: B 267 HIS cc_start: 0.8250 (t70) cc_final: 0.7899 (t-90) REVERT: B 270 GLU cc_start: 0.8227 (pp20) cc_final: 0.7921 (pp20) REVERT: C 43 ASP cc_start: 0.8621 (t70) cc_final: 0.8288 (t0) REVERT: D 9 MET cc_start: 0.9039 (mtp) cc_final: 0.8689 (ttm) REVERT: D 55 MET cc_start: 0.9447 (mmt) cc_final: 0.9227 (mmt) REVERT: D 307 PHE cc_start: 0.9176 (t80) cc_final: 0.8949 (t80) REVERT: D 309 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: E 9 MET cc_start: 0.9305 (mtp) cc_final: 0.9057 (mtm) REVERT: E 14 GLU cc_start: 0.9427 (tt0) cc_final: 0.9138 (pt0) REVERT: E 172 ASP cc_start: 0.8976 (p0) cc_final: 0.8739 (p0) REVERT: E 224 GLN cc_start: 0.9149 (tp40) cc_final: 0.8803 (tp40) REVERT: E 244 TYR cc_start: 0.9150 (p90) cc_final: 0.8891 (p90) outliers start: 14 outliers final: 8 residues processed: 139 average time/residue: 0.6891 time to fit residues: 104.7180 Evaluate side-chains 140 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 309 GLN B 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.062184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.045966 restraints weight = 159230.918| |-----------------------------------------------------------------------------| r_work (start): 0.2451 rms_B_bonded: 4.75 r_work: 0.2234 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2238 r_free = 0.2238 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2238 r_free = 0.2238 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15115 Z= 0.205 Angle : 0.581 8.884 20625 Z= 0.291 Chirality : 0.045 0.244 2400 Planarity : 0.004 0.038 2485 Dihedral : 7.669 54.234 2896 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.98 % Allowed : 13.36 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.21), residues: 1715 helix: 2.65 (0.20), residues: 630 sheet: 1.09 (0.25), residues: 400 loop : 0.92 (0.27), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 269 TYR 0.029 0.002 TYR B 299 PHE 0.016 0.001 PHE D 306 TRP 0.013 0.001 TRP C 237 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00471 (15070) covalent geometry : angle 0.56840 (20495) SS BOND : bond 0.00228 ( 5) SS BOND : angle 0.50869 ( 10) hydrogen bonds : bond 0.03958 ( 774) hydrogen bonds : angle 3.99727 ( 2428) link_ALPHA1-3 : bond 0.00841 ( 5) link_ALPHA1-3 : angle 2.25871 ( 15) link_ALPHA1-6 : bond 0.00794 ( 5) link_ALPHA1-6 : angle 1.84758 ( 15) link_BETA1-4 : bond 0.00313 ( 15) link_BETA1-4 : angle 1.56494 ( 45) link_NAG-ASN : bond 0.00102 ( 15) link_NAG-ASN : angle 1.49779 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.469 Fit side-chains REVERT: A 185 GLN cc_start: 0.8760 (tp40) cc_final: 0.8494 (tp40) REVERT: A 244 TYR cc_start: 0.9095 (p90) cc_final: 0.8833 (p90) REVERT: A 307 PHE cc_start: 0.9523 (t80) cc_final: 0.9274 (t80) REVERT: B 14 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: B 190 GLU cc_start: 0.9036 (tt0) cc_final: 0.8655 (tt0) REVERT: B 244 TYR cc_start: 0.9379 (p90) cc_final: 0.8898 (p90) REVERT: B 267 HIS cc_start: 0.8268 (t70) cc_final: 0.7944 (t-90) REVERT: B 270 GLU cc_start: 0.8244 (pp20) cc_final: 0.7908 (pp20) REVERT: D 9 MET cc_start: 0.9113 (mtp) cc_final: 0.8837 (ttm) REVERT: D 55 MET cc_start: 0.9456 (mmt) cc_final: 0.9227 (mmt) REVERT: D 307 PHE cc_start: 0.9214 (t80) cc_final: 0.8964 (t80) REVERT: E 9 MET cc_start: 0.9303 (mtp) cc_final: 0.9019 (mtm) REVERT: E 14 GLU cc_start: 0.9435 (tt0) cc_final: 0.9142 (pt0) REVERT: E 17 ASP cc_start: 0.9216 (m-30) cc_final: 0.8847 (m-30) REVERT: E 61 MET cc_start: 0.9577 (ptt) cc_final: 0.9152 (ptt) REVERT: E 224 GLN cc_start: 0.9219 (tp40) cc_final: 0.8864 (tp40) REVERT: E 244 TYR cc_start: 0.9207 (p90) cc_final: 0.8897 (p90) outliers start: 14 outliers final: 9 residues processed: 132 average time/residue: 0.6997 time to fit residues: 100.4531 Evaluate side-chains 133 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.061839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.044986 restraints weight = 153738.313| |-----------------------------------------------------------------------------| r_work (start): 0.2433 rms_B_bonded: 4.86 r_work: 0.2218 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2212 r_free = 0.2212 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2212 r_free = 0.2212 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15115 Z= 0.204 Angle : 0.584 8.676 20625 Z= 0.293 Chirality : 0.045 0.236 2400 Planarity : 0.004 0.038 2485 Dihedral : 7.655 58.739 2896 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.65 % Allowed : 13.88 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.21), residues: 1715 helix: 2.59 (0.20), residues: 630 sheet: 0.99 (0.25), residues: 400 loop : 0.89 (0.27), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 269 TYR 0.029 0.002 TYR B 299 PHE 0.017 0.001 PHE D 306 TRP 0.012 0.001 TRP C 237 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00468 (15070) covalent geometry : angle 0.57192 (20495) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.48261 ( 10) hydrogen bonds : bond 0.04127 ( 774) hydrogen bonds : angle 4.07451 ( 2428) link_ALPHA1-3 : bond 0.00853 ( 5) link_ALPHA1-3 : angle 2.14308 ( 15) link_ALPHA1-6 : bond 0.00884 ( 5) link_ALPHA1-6 : angle 1.56400 ( 15) link_BETA1-4 : bond 0.00345 ( 15) link_BETA1-4 : angle 1.57927 ( 45) link_NAG-ASN : bond 0.00124 ( 15) link_NAG-ASN : angle 1.51362 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.422 Fit side-chains REVERT: A 185 GLN cc_start: 0.8772 (tp40) cc_final: 0.8527 (tp40) REVERT: A 244 TYR cc_start: 0.9105 (p90) cc_final: 0.8893 (p90) REVERT: B 14 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8290 (pt0) REVERT: B 190 GLU cc_start: 0.9045 (tt0) cc_final: 0.8671 (tt0) REVERT: B 244 TYR cc_start: 0.9395 (p90) cc_final: 0.9084 (p90) REVERT: B 267 HIS cc_start: 0.8270 (t70) cc_final: 0.7954 (t-90) REVERT: B 270 GLU cc_start: 0.8263 (pp20) cc_final: 0.7946 (pp20) REVERT: D 307 PHE cc_start: 0.9231 (t80) cc_final: 0.8987 (t80) REVERT: E 9 MET cc_start: 0.9305 (mtp) cc_final: 0.9018 (mtm) REVERT: E 14 GLU cc_start: 0.9425 (tt0) cc_final: 0.9116 (pt0) REVERT: E 17 ASP cc_start: 0.9214 (m-30) cc_final: 0.8894 (m-30) REVERT: E 61 MET cc_start: 0.9582 (ptt) cc_final: 0.9181 (ptt) REVERT: E 224 GLN cc_start: 0.9237 (tp40) cc_final: 0.8860 (tp40) REVERT: E 227 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8504 (mmt) REVERT: E 244 TYR cc_start: 0.9214 (p90) cc_final: 0.8882 (p90) outliers start: 9 outliers final: 6 residues processed: 124 average time/residue: 0.7611 time to fit residues: 102.3749 Evaluate side-chains 125 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 306 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 84 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.062462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.045578 restraints weight = 156687.832| |-----------------------------------------------------------------------------| r_work (start): 0.2449 rms_B_bonded: 4.89 r_work: 0.2232 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2227 r_free = 0.2227 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2227 r_free = 0.2227 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15115 Z= 0.163 Angle : 0.561 8.591 20625 Z= 0.282 Chirality : 0.044 0.235 2400 Planarity : 0.003 0.038 2485 Dihedral : 7.222 59.995 2896 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.72 % Allowed : 13.94 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.21), residues: 1715 helix: 2.65 (0.20), residues: 630 sheet: 0.78 (0.24), residues: 425 loop : 1.11 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 269 TYR 0.028 0.002 TYR B 299 PHE 0.017 0.001 PHE A 306 TRP 0.010 0.001 TRP E 426 HIS 0.002 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00371 (15070) covalent geometry : angle 0.54995 (20495) SS BOND : bond 0.00159 ( 5) SS BOND : angle 0.30296 ( 10) hydrogen bonds : bond 0.03900 ( 774) hydrogen bonds : angle 3.98874 ( 2428) link_ALPHA1-3 : bond 0.00899 ( 5) link_ALPHA1-3 : angle 2.00806 ( 15) link_ALPHA1-6 : bond 0.00999 ( 5) link_ALPHA1-6 : angle 1.43553 ( 15) link_BETA1-4 : bond 0.00375 ( 15) link_BETA1-4 : angle 1.53575 ( 45) link_NAG-ASN : bond 0.00079 ( 15) link_NAG-ASN : angle 1.47821 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4469.94 seconds wall clock time: 77 minutes 9.24 seconds (4629.24 seconds total)