Starting phenix.real_space_refine on Fri Jul 3 14:18:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ff2_50349/07_2026/9ff2_50349.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ff2_50349/07_2026/9ff2_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_50349/07_2026/9ff2_50349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ff2_50349/07_2026/9ff2_50349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ff2_50349/07_2026/9ff2_50349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ff2_50349/07_2026/9ff2_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-dev-6108/lib/python3.11/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, 52 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 4, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 2, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N AASN D 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN D 41 " occ=0.50 residue: pdb=" N AASN E 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN E 41 " occ=0.50 Time building chain proxies: 5.54, per 1000 atoms: 0.38 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: 1.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.40 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: 2.77 Time building geometry restraints manager: 1.89 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.810 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 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 are 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/Z covalent geometry : bond 0.00432 / 0.20 (15070) covalent geometry : angle 0.57493 / 0.28 (20495) SS BOND : bond 0.00305 / 0.16 ( 5) SS BOND : angle 0.76023 / 0.51 ( 10) hydrogen bonds : bond 0.10621 / 7.51 ( 774) hydrogen bonds : angle 4.84606 / 3.37 ( 2428) link_ALPHA1-3 : bond 0.00175 / 0.10 ( 5) link_ALPHA1-3 : angle 1.08622 / 0.71 ( 15) link_ALPHA1-6 : bond 0.00185 / 0.10 ( 5) link_ALPHA1-6 : angle 1.02092 / 0.68 ( 15) link_BETA1-4 : bond 0.00348 / 0.22 ( 15) link_BETA1-4 : angle 1.56246 / 1.09 ( 45) link_NAG-ASN : bond 0.00248 / 0.15 ( 15) link_NAG-ASN : angle 1.31918 / 0.99 ( 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 : 0.541 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: 0.8094 time to fit residues: 228.2175 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 : 0.533 ------------------------------------------------------------------------------- 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: 5.9990 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: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2856 r_free = 0.2856 target = 0.062769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.046248 restraints weight = 155843.668| |-----------------------------------------------------------------------------| r_work (start): 0.2457 rms_B_bonded: 4.84 r_work: 0.2235 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2236 r_free = 0.2236 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 = 0.2231 r_free = 0.2231 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.2231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15115 Z= 0.183 Angle : 0.575 8.085 20625 Z= 0.296 Chirality : 0.044 0.184 2400 Planarity : 0.004 0.040 2485 Dihedral : 10.847 82.082 2896 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.17 % Allowed : 11.01 % 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 are not related in a simple way. whole: 2.24 (0.21), residues: 1715 helix: 2.62 (0.20), residues: 625 sheet: 0.69 (0.24), residues: 420 loop : 1.09 (0.28), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 68 TYR 0.026 0.002 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 D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (15070) covalent geometry : angle 0.56251 / 0.29 (20495) SS BOND : bond 0.00184 / 0.10 ( 5) SS BOND : angle 0.29670 / 0.20 ( 10) hydrogen bonds : bond 0.04349 / 2.92 ( 774) hydrogen bonds : angle 4.32045 / 3.01 ( 2428) link_ALPHA1-3 : bond 0.00772 / 0.41 ( 5) link_ALPHA1-3 : angle 1.95055 / 1.36 ( 15) link_ALPHA1-6 : bond 0.00417 / 0.22 ( 5) link_ALPHA1-6 : angle 2.01045 / 1.38 ( 15) link_BETA1-4 : bond 0.00204 / 0.11 ( 15) link_BETA1-4 : angle 1.64257 / 1.22 ( 45) link_NAG-ASN : bond 0.00065 / 0.04 ( 15) link_NAG-ASN : angle 1.44870 / 1.08 ( 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 152 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.540 Fit side-chains REVERT: B 9 MET cc_start: 0.8986 (mtp) cc_final: 0.8507 (mtm) REVERT: B 267 HIS cc_start: 0.8228 (t70) cc_final: 0.8004 (t-90) REVERT: D 307 PHE cc_start: 0.9133 (t80) cc_final: 0.8890 (t80) REVERT: E 9 MET cc_start: 0.9358 (mtp) cc_final: 0.8946 (mtm) REVERT: E 14 GLU cc_start: 0.9458 (tt0) cc_final: 0.9131 (pt0) REVERT: E 17 ASP cc_start: 0.9155 (m-30) cc_final: 0.8869 (m-30) REVERT: E 244 TYR cc_start: 0.9203 (p90) cc_final: 0.8825 (p90) outliers start: 18 outliers final: 8 residues processed: 142 average time/residue: 0.5638 time to fit residues: 87.7277 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 : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 227 MET 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 0.0370 chunk 130 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN C 309 GLN D 224 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 = 0.2890 r_free = 0.2890 target = 0.064138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.048194 restraints weight = 141348.702| |-----------------------------------------------------------------------------| r_work (start): 0.2495 rms_B_bonded: 4.59 r_work: 0.2283 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2278 r_free = 0.2278 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 = 0.2278 r_free = 0.2278 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15115 Z= 0.109 Angle : 0.530 9.116 20625 Z= 0.269 Chirality : 0.044 0.217 2400 Planarity : 0.003 0.031 2485 Dihedral : 9.579 76.365 2896 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.17 % Allowed : 11.40 % Favored : 87.43 % 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 are not related in a simple way. whole: 2.32 (0.21), residues: 1715 helix: 2.69 (0.20), residues: 625 sheet: 0.97 (0.25), residues: 400 loop : 0.94 (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 E 299 PHE 0.016 0.001 PHE D 306 TRP 0.013 0.001 TRP C 67 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (15070) covalent geometry : angle 0.51796 / 0.27 (20495) SS BOND : bond 0.00141 / 0.08 ( 5) SS BOND : angle 0.21204 / 0.15 ( 10) hydrogen bonds : bond 0.03707 / 2.46 ( 774) hydrogen bonds : angle 4.01595 / 2.80 ( 2428) link_ALPHA1-3 : bond 0.01105 / 0.58 ( 5) link_ALPHA1-3 : angle 1.94741 / 1.32 ( 15) link_ALPHA1-6 : bond 0.00722 / 0.38 ( 5) link_ALPHA1-6 : angle 2.06925 / 1.42 ( 15) link_BETA1-4 : bond 0.00280 / 0.15 ( 15) link_BETA1-4 : angle 1.41223 / 1.04 ( 45) link_NAG-ASN : bond 0.00129 / 0.08 ( 15) link_NAG-ASN : angle 1.32431 / 0.97 ( 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 161 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.516 Fit side-chains REVERT: A 244 TYR cc_start: 0.9080 (p90) cc_final: 0.8846 (p90) REVERT: B 9 MET cc_start: 0.8937 (mtp) cc_final: 0.8556 (mtt) REVERT: B 14 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: B 115 MET cc_start: 0.9470 (ttp) cc_final: 0.9024 (tmm) REVERT: B 190 GLU cc_start: 0.8996 (tt0) cc_final: 0.8625 (tt0) REVERT: B 244 TYR cc_start: 0.9239 (p90) cc_final: 0.8824 (p90) REVERT: B 267 HIS cc_start: 0.8320 (t70) cc_final: 0.7994 (t-90) REVERT: B 270 GLU cc_start: 0.8455 (pp20) cc_final: 0.8130 (pp20) REVERT: D 307 PHE cc_start: 0.9183 (t80) cc_final: 0.8970 (t80) REVERT: E 9 MET cc_start: 0.9310 (mtp) cc_final: 0.8836 (mtm) REVERT: E 14 GLU cc_start: 0.9420 (tt0) cc_final: 0.9085 (pt0) REVERT: E 224 GLN cc_start: 0.9132 (tp40) cc_final: 0.8846 (tp40) REVERT: E 244 TYR cc_start: 0.9175 (p90) cc_final: 0.8856 (p90) outliers start: 18 outliers final: 7 residues processed: 150 average time/residue: 0.6234 time to fit residues: 101.8557 Evaluate side-chains 128 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 4.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 0.0170 chunk 100 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A A 224 GLN B 41 ASN A C 309 GLN D 41 ASN A D 224 GLN E 90 GLN E 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.065189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.048669 restraints weight = 142525.443| |-----------------------------------------------------------------------------| r_work (start): 0.2514 rms_B_bonded: 4.71 r_work: 0.2304 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2300 r_free = 0.2300 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2300 r_free = 0.2300 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.2300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15115 Z= 0.101 Angle : 0.519 6.636 20625 Z= 0.261 Chirality : 0.044 0.241 2400 Planarity : 0.003 0.031 2485 Dihedral : 8.722 65.631 2896 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.43 % Allowed : 11.86 % Favored : 86.71 % 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 are not related in a simple way. whole: 2.41 (0.21), residues: 1715 helix: 2.75 (0.20), residues: 625 sheet: 1.07 (0.25), residues: 400 loop : 0.97 (0.27), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 312 TYR 0.025 0.001 TYR E 299 PHE 0.017 0.001 PHE A 306 TRP 0.012 0.001 TRP C 67 HIS 0.001 0.000 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (15070) covalent geometry : angle 0.50678 / 0.26 (20495) SS BOND : bond 0.00138 / 0.07 ( 5) SS BOND : angle 0.18100 / 0.13 ( 10) hydrogen bonds : bond 0.03467 / 2.30 ( 774) hydrogen bonds : angle 3.89122 / 2.71 ( 2428) link_ALPHA1-3 : bond 0.01088 / 0.58 ( 5) link_ALPHA1-3 : angle 2.10193 / 1.39 ( 15) link_ALPHA1-6 : bond 0.00840 / 0.44 ( 5) link_ALPHA1-6 : angle 2.08851 / 1.42 ( 15) link_BETA1-4 : bond 0.00317 / 0.17 ( 15) link_BETA1-4 : angle 1.35984 / 1.00 ( 45) link_NAG-ASN : bond 0.00137 / 0.08 ( 15) link_NAG-ASN : angle 1.26996 / 0.93 ( 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 161 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.563 Fit side-chains REVERT: A 244 TYR cc_start: 0.9044 (p90) cc_final: 0.8801 (p90) REVERT: B 9 MET cc_start: 0.8921 (mtp) cc_final: 0.8600 (mtt) REVERT: B 14 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8366 (pt0) REVERT: B 115 MET cc_start: 0.9472 (ttp) cc_final: 0.9090 (tmm) REVERT: B 190 GLU cc_start: 0.8994 (tt0) cc_final: 0.8570 (tt0) REVERT: B 244 TYR cc_start: 0.9281 (p90) cc_final: 0.8895 (p90) REVERT: B 267 HIS cc_start: 0.8313 (t70) cc_final: 0.7934 (t-90) REVERT: B 270 GLU cc_start: 0.8376 (pp20) cc_final: 0.7980 (pp20) REVERT: C 9 MET cc_start: 0.8928 (mtm) cc_final: 0.8715 (mtm) REVERT: C 43 ASP cc_start: 0.8620 (t70) cc_final: 0.8316 (t0) REVERT: C 64 GLN cc_start: 0.9189 (mt0) cc_final: 0.8958 (mt0) REVERT: D 307 PHE cc_start: 0.9186 (t80) cc_final: 0.8968 (t80) REVERT: E 9 MET cc_start: 0.9304 (mtp) cc_final: 0.8900 (mtm) REVERT: E 14 GLU cc_start: 0.9417 (tt0) cc_final: 0.9095 (pt0) REVERT: E 224 GLN cc_start: 0.9115 (tp40) cc_final: 0.8849 (tp40) REVERT: E 244 TYR cc_start: 0.9159 (p90) cc_final: 0.8870 (p90) outliers start: 22 outliers final: 9 residues processed: 146 average time/residue: 0.5430 time to fit residues: 87.1669 Evaluate side-chains 137 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 132 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 97 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN D 224 GLN E 41 ASN B Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.063948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.046982 restraints weight = 163795.007| |-----------------------------------------------------------------------------| r_work (start): 0.2480 rms_B_bonded: 4.95 r_work: 0.2264 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2257 r_free = 0.2257 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2257 r_free = 0.2257 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15115 Z= 0.138 Angle : 0.540 10.040 20625 Z= 0.269 Chirality : 0.044 0.243 2400 Planarity : 0.003 0.033 2485 Dihedral : 8.412 63.108 2896 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.56 % Allowed : 12.05 % 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 are not related in a simple way. whole: 2.43 (0.21), residues: 1715 helix: 2.74 (0.20), residues: 630 sheet: 1.11 (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 C 312 TYR 0.027 0.001 TYR B 299 PHE 0.017 0.001 PHE A 306 TRP 0.009 0.001 TRP C 67 HIS 0.002 0.000 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15070) covalent geometry : angle 0.52695 / 0.27 (20495) SS BOND : bond 0.00168 / 0.09 ( 5) SS BOND : angle 0.30242 / 0.20 ( 10) hydrogen bonds : bond 0.03650 / 2.42 ( 774) hydrogen bonds : angle 3.91803 / 2.73 ( 2428) link_ALPHA1-3 : bond 0.01008 / 0.53 ( 5) link_ALPHA1-3 : angle 2.20920 / 1.48 ( 15) link_ALPHA1-6 : bond 0.00791 / 0.42 ( 5) link_ALPHA1-6 : angle 2.11857 / 1.45 ( 15) link_BETA1-4 : bond 0.00286 / 0.15 ( 15) link_BETA1-4 : angle 1.41901 / 1.03 ( 45) link_NAG-ASN : bond 0.00070 / 0.04 ( 15) link_NAG-ASN : angle 1.38028 / 1.02 ( 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 151 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.368 Fit side-chains REVERT: A 244 TYR cc_start: 0.9083 (p90) cc_final: 0.8854 (p90) REVERT: B 9 MET cc_start: 0.8916 (mtp) cc_final: 0.8651 (mtt) REVERT: B 14 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8363 (pt0) REVERT: B 190 GLU cc_start: 0.9031 (tt0) cc_final: 0.8599 (tt0) REVERT: B 244 TYR cc_start: 0.9331 (p90) cc_final: 0.8838 (p90) REVERT: B 267 HIS cc_start: 0.8355 (t70) cc_final: 0.7990 (t-90) REVERT: B 270 GLU cc_start: 0.8463 (pp20) cc_final: 0.8003 (pp20) REVERT: C 9 MET cc_start: 0.8895 (mtm) cc_final: 0.8683 (mtm) REVERT: C 43 ASP cc_start: 0.8697 (t70) cc_final: 0.8278 (t0) REVERT: D 307 PHE cc_start: 0.9218 (t80) cc_final: 0.9012 (t80) REVERT: E 9 MET cc_start: 0.9313 (mtp) cc_final: 0.8966 (mtm) REVERT: E 14 GLU cc_start: 0.9433 (tt0) cc_final: 0.9135 (pt0) REVERT: E 224 GLN cc_start: 0.9164 (tp40) cc_final: 0.8804 (tp40) REVERT: E 244 TYR cc_start: 0.9166 (p90) cc_final: 0.8877 (p90) outliers start: 24 outliers final: 9 residues processed: 134 average time/residue: 0.6195 time to fit residues: 90.5415 Evaluate side-chains 134 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR 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 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 309 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 7 optimal weight: 0.3980 chunk 99 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2904 r_free = 0.2904 target = 0.064777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.048059 restraints weight = 147094.361| |-----------------------------------------------------------------------------| r_work (start): 0.2509 rms_B_bonded: 4.79 r_work: 0.2296 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2291 r_free = 0.2291 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2291 r_free = 0.2291 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15115 Z= 0.107 Angle : 0.517 7.299 20625 Z= 0.259 Chirality : 0.044 0.247 2400 Planarity : 0.003 0.039 2485 Dihedral : 7.978 59.579 2896 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.50 % Allowed : 12.18 % Favored : 86.32 % 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 are not related in a simple way. whole: 2.45 (0.21), residues: 1715 helix: 2.75 (0.20), residues: 630 sheet: 1.13 (0.25), residues: 400 loop : 0.99 (0.27), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 312 TYR 0.025 0.001 TYR E 299 PHE 0.016 0.001 PHE D 306 TRP 0.011 0.001 TRP C 67 HIS 0.001 0.000 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (15070) covalent geometry : angle 0.50454 / 0.26 (20495) SS BOND : bond 0.00143 / 0.08 ( 5) SS BOND : angle 0.16485 / 0.11 ( 10) hydrogen bonds : bond 0.03475 / 2.30 ( 774) hydrogen bonds : angle 3.85209 / 2.69 ( 2428) link_ALPHA1-3 : bond 0.01076 / 0.57 ( 5) link_ALPHA1-3 : angle 2.16884 / 1.44 ( 15) link_ALPHA1-6 : bond 0.00900 / 0.47 ( 5) link_ALPHA1-6 : angle 2.09188 / 1.43 ( 15) link_BETA1-4 : bond 0.00325 / 0.17 ( 15) link_BETA1-4 : angle 1.32468 / 0.96 ( 45) link_NAG-ASN : bond 0.00119 / 0.07 ( 15) link_NAG-ASN : angle 1.29881 / 0.95 ( 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 154 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.554 Fit side-chains REVERT: A 244 TYR cc_start: 0.9053 (p90) cc_final: 0.8783 (p90) REVERT: A 307 PHE cc_start: 0.9490 (t80) cc_final: 0.9230 (t80) REVERT: B 9 MET cc_start: 0.8881 (mtp) cc_final: 0.8623 (mtt) REVERT: B 14 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8422 (pt0) REVERT: B 190 GLU cc_start: 0.9017 (tt0) cc_final: 0.8591 (tt0) REVERT: B 244 TYR cc_start: 0.9330 (p90) cc_final: 0.8830 (p90) REVERT: B 267 HIS cc_start: 0.8337 (t70) cc_final: 0.7936 (t-90) REVERT: B 270 GLU cc_start: 0.8400 (pp20) cc_final: 0.7917 (pp20) REVERT: C 43 ASP cc_start: 0.8655 (t70) cc_final: 0.8328 (t0) REVERT: D 9 MET cc_start: 0.9016 (mtp) cc_final: 0.8698 (ttm) REVERT: D 61 MET cc_start: 0.9574 (OUTLIER) cc_final: 0.9137 (ptp) REVERT: D 307 PHE cc_start: 0.9200 (t80) cc_final: 0.8977 (t80) REVERT: E 9 MET cc_start: 0.9305 (mtp) cc_final: 0.8997 (mtm) REVERT: E 14 GLU cc_start: 0.9419 (tt0) cc_final: 0.9117 (pt0) REVERT: E 224 GLN cc_start: 0.9151 (tp40) cc_final: 0.8798 (tp40) REVERT: E 244 TYR cc_start: 0.9152 (p90) cc_final: 0.8868 (p90) outliers start: 23 outliers final: 7 residues processed: 142 average time/residue: 0.6204 time to fit residues: 96.5946 Evaluate side-chains 134 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 132 THR 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 61 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 0.0270 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2905 r_free = 0.2905 target = 0.064760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.048680 restraints weight = 151864.854| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 4.71 r_work: 0.2299 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2294 r_free = 0.2294 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2294 r_free = 0.2294 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15115 Z= 0.111 Angle : 0.521 9.665 20625 Z= 0.259 Chirality : 0.044 0.249 2400 Planarity : 0.003 0.038 2485 Dihedral : 7.635 56.237 2896 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.17 % Allowed : 12.51 % Favored : 86.32 % 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 are not related in a simple way. whole: 2.46 (0.21), residues: 1715 helix: 2.73 (0.20), residues: 635 sheet: 1.19 (0.25), residues: 400 loop : 0.98 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 312 TYR 0.025 0.001 TYR E 299 PHE 0.016 0.001 PHE D 306 TRP 0.011 0.001 TRP C 67 HIS 0.002 0.000 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15070) covalent geometry : angle 0.50836 / 0.26 (20495) SS BOND : bond 0.00128 / 0.07 ( 5) SS BOND : angle 0.18352 / 0.12 ( 10) hydrogen bonds : bond 0.03461 / 2.29 ( 774) hydrogen bonds : angle 3.83153 / 2.67 ( 2428) link_ALPHA1-3 : bond 0.01025 / 0.54 ( 5) link_ALPHA1-3 : angle 2.17728 / 1.45 ( 15) link_ALPHA1-6 : bond 0.00906 / 0.48 ( 5) link_ALPHA1-6 : angle 2.01100 / 1.39 ( 15) link_BETA1-4 : bond 0.00344 / 0.18 ( 15) link_BETA1-4 : angle 1.35345 / 0.98 ( 45) link_NAG-ASN : bond 0.00102 / 0.06 ( 15) link_NAG-ASN : angle 1.33347 / 0.98 ( 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 147 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.488 Fit side-chains REVERT: A 244 TYR cc_start: 0.9062 (p90) cc_final: 0.8790 (p90) REVERT: A 307 PHE cc_start: 0.9486 (t80) cc_final: 0.9233 (t80) REVERT: B 9 MET cc_start: 0.8903 (mtp) cc_final: 0.8644 (mtt) REVERT: B 14 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: B 190 GLU cc_start: 0.9021 (tt0) cc_final: 0.8601 (tt0) REVERT: B 244 TYR cc_start: 0.9327 (p90) cc_final: 0.8818 (p90) REVERT: B 267 HIS cc_start: 0.8339 (t70) cc_final: 0.8037 (t-90) REVERT: C 43 ASP cc_start: 0.8729 (t70) cc_final: 0.8409 (t0) REVERT: C 64 GLN cc_start: 0.9276 (mt0) cc_final: 0.9072 (mt0) REVERT: D 9 MET cc_start: 0.9028 (mtp) cc_final: 0.8685 (ttm) REVERT: D 307 PHE cc_start: 0.9204 (t80) cc_final: 0.8975 (t80) REVERT: E 9 MET cc_start: 0.9308 (mtp) cc_final: 0.9037 (mtm) REVERT: E 14 GLU cc_start: 0.9424 (tt0) cc_final: 0.9137 (pt0) REVERT: E 224 GLN cc_start: 0.9162 (tp40) cc_final: 0.8823 (tp40) REVERT: E 244 TYR cc_start: 0.9143 (p90) cc_final: 0.8849 (p90) outliers start: 18 outliers final: 9 residues processed: 138 average time/residue: 0.6536 time to fit residues: 98.6709 Evaluate side-chains 135 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 132 THR 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 Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 56 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 123 optimal weight: 0.0470 chunk 102 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 309 GLN B 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 = 0.2911 r_free = 0.2911 target = 0.065127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.048622 restraints weight = 153522.409| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 4.82 r_work: 0.2308 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2303 r_free = 0.2303 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2303 r_free = 0.2303 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15115 Z= 0.105 Angle : 0.519 9.271 20625 Z= 0.258 Chirality : 0.044 0.246 2400 Planarity : 0.003 0.039 2485 Dihedral : 7.317 52.361 2896 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.04 % Allowed : 12.64 % Favored : 86.32 % 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 are not related in a simple way. whole: 2.48 (0.21), residues: 1715 helix: 2.73 (0.20), residues: 635 sheet: 1.21 (0.25), residues: 400 loop : 1.00 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 312 TYR 0.025 0.001 TYR E 299 PHE 0.015 0.001 PHE D 306 TRP 0.011 0.001 TRP C 67 HIS 0.001 0.000 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (15070) covalent geometry : angle 0.50706 / 0.26 (20495) SS BOND : bond 0.00110 / 0.06 ( 5) SS BOND : angle 0.15370 / 0.10 ( 10) hydrogen bonds : bond 0.03408 / 2.25 ( 774) hydrogen bonds : angle 3.80549 / 2.66 ( 2428) link_ALPHA1-3 : bond 0.01016 / 0.54 ( 5) link_ALPHA1-3 : angle 2.12488 / 1.42 ( 15) link_ALPHA1-6 : bond 0.00962 / 0.51 ( 5) link_ALPHA1-6 : angle 1.91770 / 1.34 ( 15) link_BETA1-4 : bond 0.00382 / 0.20 ( 15) link_BETA1-4 : angle 1.31363 / 0.95 ( 45) link_NAG-ASN : bond 0.00124 / 0.08 ( 15) link_NAG-ASN : angle 1.30431 / 0.95 ( 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: 15 poor density : 131 time to evaluate : 0.520 Fit side-chains REVERT: A 244 TYR cc_start: 0.9051 (p90) cc_final: 0.8746 (p90) REVERT: A 307 PHE cc_start: 0.9485 (t80) cc_final: 0.9238 (t80) REVERT: B 9 MET cc_start: 0.8892 (mtp) cc_final: 0.8663 (mtt) REVERT: B 14 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8415 (pt0) REVERT: B 190 GLU cc_start: 0.9044 (tt0) cc_final: 0.8617 (tt0) REVERT: B 244 TYR cc_start: 0.9346 (p90) cc_final: 0.8818 (p90) REVERT: B 267 HIS cc_start: 0.8315 (t70) cc_final: 0.7990 (t-90) REVERT: B 270 GLU cc_start: 0.8290 (pp20) cc_final: 0.7974 (pp20) REVERT: C 43 ASP cc_start: 0.8677 (t70) cc_final: 0.8353 (t0) REVERT: C 64 GLN cc_start: 0.9258 (mt0) cc_final: 0.9034 (mt0) REVERT: C 309 GLN cc_start: 0.8627 (mp10) cc_final: 0.7842 (mp10) REVERT: D 9 MET cc_start: 0.9026 (mtp) cc_final: 0.8705 (ttm) REVERT: D 307 PHE cc_start: 0.9202 (t80) cc_final: 0.8975 (t80) REVERT: E 9 MET cc_start: 0.9284 (mtp) cc_final: 0.8937 (mtm) REVERT: E 14 GLU cc_start: 0.9426 (tt0) cc_final: 0.9138 (pt0) REVERT: E 224 GLN cc_start: 0.9166 (tp40) cc_final: 0.8840 (tp40) REVERT: E 244 TYR cc_start: 0.9155 (p90) cc_final: 0.8924 (p90) outliers start: 15 outliers final: 10 residues processed: 135 average time/residue: 0.6419 time to fit residues: 94.7788 Evaluate side-chains 137 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 306 PHE 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 E residue 306 PHE Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN E 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.064212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.047437 restraints weight = 158934.570| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 4.91 r_work: 0.2278 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2278 ------------------------------------------------------------------------------- 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 = 0.15 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 = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15115 Z= 0.131 Angle : 0.534 8.923 20625 Z= 0.266 Chirality : 0.044 0.239 2400 Planarity : 0.003 0.038 2485 Dihedral : 7.178 55.826 2896 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.98 % Allowed : 13.09 % 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 are not related in a simple way. whole: 2.47 (0.21), residues: 1715 helix: 2.70 (0.20), residues: 635 sheet: 0.98 (0.25), residues: 425 loop : 1.19 (0.28), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 269 TYR 0.027 0.001 TYR E 299 PHE 0.015 0.001 PHE D 306 TRP 0.013 0.001 TRP C 237 HIS 0.002 0.000 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (15070) covalent geometry : angle 0.52276 / 0.26 (20495) SS BOND : bond 0.00144 / 0.08 ( 5) SS BOND : angle 0.26897 / 0.17 ( 10) hydrogen bonds : bond 0.03572 / 2.37 ( 774) hydrogen bonds : angle 3.84584 / 2.69 ( 2428) link_ALPHA1-3 : bond 0.00951 / 0.50 ( 5) link_ALPHA1-3 : angle 2.13771 / 1.44 ( 15) link_ALPHA1-6 : bond 0.00926 / 0.49 ( 5) link_ALPHA1-6 : angle 1.72758 / 1.24 ( 15) link_BETA1-4 : bond 0.00374 / 0.20 ( 15) link_BETA1-4 : angle 1.41713 / 1.01 ( 45) link_NAG-ASN : bond 0.00080 / 0.05 ( 15) link_NAG-ASN : angle 1.38562 / 1.02 ( 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 : 0.546 Fit side-chains REVERT: A 244 TYR cc_start: 0.9064 (p90) cc_final: 0.8777 (p90) REVERT: A 307 PHE cc_start: 0.9510 (t80) cc_final: 0.9265 (t80) REVERT: B 9 MET cc_start: 0.8876 (mtp) cc_final: 0.8654 (mtt) REVERT: B 14 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: B 190 GLU cc_start: 0.9029 (tt0) cc_final: 0.8611 (tt0) REVERT: B 244 TYR cc_start: 0.9334 (p90) cc_final: 0.8864 (p90) REVERT: B 267 HIS cc_start: 0.8295 (t70) cc_final: 0.7962 (t-90) REVERT: B 270 GLU cc_start: 0.8324 (pp20) cc_final: 0.7916 (pp20) REVERT: B 309 GLN cc_start: 0.8685 (mt0) cc_final: 0.8420 (mp10) REVERT: C 309 GLN cc_start: 0.8717 (mp10) cc_final: 0.7909 (mp10) REVERT: D 307 PHE cc_start: 0.9202 (t80) cc_final: 0.8978 (t80) REVERT: E 9 MET cc_start: 0.9300 (mtp) cc_final: 0.8967 (mtm) REVERT: E 14 GLU cc_start: 0.9424 (tt0) cc_final: 0.9129 (pt0) REVERT: E 224 GLN cc_start: 0.9207 (tp40) cc_final: 0.8888 (tp40) REVERT: E 244 TYR cc_start: 0.9177 (p90) cc_final: 0.8904 (p90) outliers start: 14 outliers final: 11 residues processed: 131 average time/residue: 0.6422 time to fit residues: 91.6591 Evaluate side-chains 137 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 306 PHE Chi-restraints excluded: chain B residue 14 GLU 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 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 Chi-restraints excluded: chain E residue 309 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2894 r_free = 0.2894 target = 0.064224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.047643 restraints weight = 156910.387| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 4.88 r_work: 0.2284 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2288 r_free = 0.2288 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2288 r_free = 0.2288 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15115 Z= 0.123 Angle : 0.531 9.059 20625 Z= 0.265 Chirality : 0.044 0.233 2400 Planarity : 0.003 0.038 2485 Dihedral : 6.910 58.253 2896 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.91 % Allowed : 13.16 % 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 are not related in a simple way. whole: 2.50 (0.21), residues: 1715 helix: 2.76 (0.20), residues: 630 sheet: 0.98 (0.25), residues: 425 loop : 1.20 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 269 TYR 0.026 0.001 TYR B 299 PHE 0.016 0.001 PHE D 306 TRP 0.010 0.001 TRP C 237 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (15070) covalent geometry : angle 0.52019 / 0.26 (20495) SS BOND : bond 0.00129 / 0.07 ( 5) SS BOND : angle 0.19364 / 0.13 ( 10) hydrogen bonds : bond 0.03506 / 2.32 ( 774) hydrogen bonds : angle 3.82619 / 2.67 ( 2428) link_ALPHA1-3 : bond 0.00968 / 0.51 ( 5) link_ALPHA1-3 : angle 2.03187 / 1.38 ( 15) link_ALPHA1-6 : bond 0.00991 / 0.52 ( 5) link_ALPHA1-6 : angle 1.46454 / 1.01 ( 15) link_BETA1-4 : bond 0.00417 / 0.22 ( 15) link_BETA1-4 : angle 1.40275 / 1.01 ( 45) link_NAG-ASN : bond 0.00095 / 0.06 ( 15) link_NAG-ASN : angle 1.36257 / 1.00 ( 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 144 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.473 Fit side-chains REVERT: A 244 TYR cc_start: 0.9037 (p90) cc_final: 0.8760 (p90) REVERT: A 307 PHE cc_start: 0.9480 (t80) cc_final: 0.9234 (t80) REVERT: B 9 MET cc_start: 0.8883 (mtp) cc_final: 0.8668 (mtt) REVERT: B 14 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: B 190 GLU cc_start: 0.9044 (tt0) cc_final: 0.8614 (tt0) REVERT: B 244 TYR cc_start: 0.9335 (p90) cc_final: 0.8969 (p90) REVERT: B 267 HIS cc_start: 0.8293 (t70) cc_final: 0.7954 (t-90) REVERT: B 270 GLU cc_start: 0.8259 (pp20) cc_final: 0.7882 (pp20) REVERT: B 309 GLN cc_start: 0.8630 (mt0) cc_final: 0.8338 (mp10) REVERT: C 309 GLN cc_start: 0.8697 (mp10) cc_final: 0.7847 (mp10) REVERT: D 9 MET cc_start: 0.9022 (mtp) cc_final: 0.8641 (ttm) REVERT: D 307 PHE cc_start: 0.9198 (t80) cc_final: 0.8973 (t80) REVERT: E 9 MET cc_start: 0.9282 (mtp) cc_final: 0.8972 (mtm) REVERT: E 14 GLU cc_start: 0.9432 (tt0) cc_final: 0.9144 (pt0) REVERT: E 224 GLN cc_start: 0.9210 (tp40) cc_final: 0.8897 (tp40) REVERT: E 227 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8429 (mmt) REVERT: E 244 TYR cc_start: 0.9186 (p90) cc_final: 0.8942 (p90) outliers start: 13 outliers final: 10 residues processed: 138 average time/residue: 0.6156 time to fit residues: 92.8718 Evaluate side-chains 138 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain B residue 14 GLU 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 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 Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 97 optimal weight: 5.9990 chunk 98 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.0020 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.065852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.049269 restraints weight = 156641.607| |-----------------------------------------------------------------------------| r_work (start): 0.2533 rms_B_bonded: 4.90 r_work: 0.2319 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2315 r_free = 0.2315 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2315 r_free = 0.2315 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15115 Z= 0.099 Angle : 0.515 8.988 20625 Z= 0.257 Chirality : 0.043 0.222 2400 Planarity : 0.003 0.038 2485 Dihedral : 6.305 58.823 2896 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.85 % Allowed : 13.36 % Favored : 85.80 % 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 are not related in a simple way. whole: 2.52 (0.21), residues: 1715 helix: 2.70 (0.20), residues: 635 sheet: 1.05 (0.25), residues: 420 loop : 1.22 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 269 TYR 0.024 0.001 TYR E 299 PHE 0.015 0.001 PHE D 306 TRP 0.014 0.001 TRP C 67 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (15070) covalent geometry : angle 0.50543 / 0.26 (20495) SS BOND : bond 0.00123 / 0.07 ( 5) SS BOND : angle 0.14281 / 0.10 ( 10) hydrogen bonds : bond 0.03279 / 2.16 ( 774) hydrogen bonds : angle 3.75604 / 2.62 ( 2428) link_ALPHA1-3 : bond 0.00989 / 0.52 ( 5) link_ALPHA1-3 : angle 1.80722 / 1.26 ( 15) link_ALPHA1-6 : bond 0.01116 / 0.59 ( 5) link_ALPHA1-6 : angle 1.39731 / 1.04 ( 15) link_BETA1-4 : bond 0.00487 / 0.26 ( 15) link_BETA1-4 : angle 1.29311 / 0.94 ( 45) link_NAG-ASN : bond 0.00165 / 0.10 ( 15) link_NAG-ASN : angle 1.29353 / 0.94 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4138.77 seconds wall clock time: 71 minutes 43.28 seconds (4303.28 seconds total)