Starting phenix.real_space_refine on Thu Sep 18 07:15:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9feu_50341/09_2025/9feu_50341.cif Found real_map, /net/cci-nas-00/data/ceres_data/9feu_50341/09_2025/9feu_50341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9feu_50341/09_2025/9feu_50341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9feu_50341/09_2025/9feu_50341.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9feu_50341/09_2025/9feu_50341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9feu_50341/09_2025/9feu_50341.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 85 5.16 5 Cl 5 4.86 5 C 9625 2.51 5 N 2310 2.21 5 O 3025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15050 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2788 Chain: "B" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2788 Chain: "C" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2788 Chain: "D" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2788 Chain: "E" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2788 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Unusual residues: {' CL': 1, 'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Unusual residues: {' CL': 1, 'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Unusual residues: {' CL': 1, 'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Unusual residues: {' CL': 1, 'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Unusual residues: {' CL': 1, 'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "D" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "E" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} 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: 6.59, per 1000 atoms: 0.44 Number of scatterers: 15050 At special positions: 0 Unit cell: (99.704, 99.704, 126.896, 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 3025 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 505 " - " ASN B 8 " " NAG C 505 " - " ASN C 8 " " NAG D 506 " - " 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: 1.71 Conformation dependent library (CDL) restraints added in 989.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 42.1% alpha, 39.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 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 170 through 173 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 246 through 272 Processing helix chain 'A' and resid 279 through 306 Processing helix chain 'A' and resid 309 through 446 removed outlier: 3.963A 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 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 246 through 272 Processing helix chain 'B' and resid 279 through 306 Processing helix chain 'B' and resid 309 through 446 removed outlier: 3.963A 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 Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 237 Processing helix chain 'C' and resid 238 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: 3.963A 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 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 237 Processing helix chain 'D' and resid 238 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: 3.963A 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 237 Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 246 through 272 Processing helix chain 'E' and resid 279 through 306 Processing helix chain 'E' and resid 309 through 446 removed outlier: 3.964A 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: 4.551A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.485A 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: 6.674A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 42 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.834A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.525A 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: 4.550A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.485A 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: 6.674A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR B 176 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 42 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.835A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.525A 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: 4.551A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.672A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.555A 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: 3.835A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.551A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.484A 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: 6.672A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR D 176 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE D 42 " --> pdb=" O THR D 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.835A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.525A 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: 4.550A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.673A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR E 176 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE E 42 " --> pdb=" O THR E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.834A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) 885 hydrogen bonds defined for protein. 2475 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: 2.95 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4370 1.34 - 1.46: 3809 1.46 - 1.58: 6741 1.58 - 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 2.57e+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 2.44e+00 bond pdb=" C1 MAN a 5 " pdb=" O5 MAN a 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C1 MAN d 5 " pdb=" O5 MAN d 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 MAN c 5 " pdb=" O5 MAN c 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.41e+00 ... (remaining 15065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 19762 1.09 - 2.19: 498 2.19 - 3.28: 184 3.28 - 4.38: 36 4.38 - 5.47: 15 Bond angle restraints: 20495 Sorted by residual: angle pdb=" C1 BMA c 3 " pdb=" O5 BMA c 3 " pdb=" C5 BMA c 3 " ideal model delta sigma weight residual 118.82 113.35 5.47 3.00e+00 1.11e-01 3.33e+00 angle pdb=" C1 BMA b 3 " pdb=" O5 BMA b 3 " pdb=" C5 BMA b 3 " ideal model delta sigma weight residual 118.82 113.39 5.43 3.00e+00 1.11e-01 3.28e+00 angle pdb=" C1 BMA d 3 " pdb=" O5 BMA d 3 " pdb=" C5 BMA d 3 " ideal model delta sigma weight residual 118.82 113.41 5.41 3.00e+00 1.11e-01 3.25e+00 angle pdb=" C1 BMA e 3 " pdb=" O5 BMA e 3 " pdb=" C5 BMA e 3 " ideal model delta sigma weight residual 118.82 113.43 5.39 3.00e+00 1.11e-01 3.23e+00 angle pdb=" C1 BMA a 3 " pdb=" O5 BMA a 3 " pdb=" C5 BMA a 3 " ideal model delta sigma weight residual 118.82 113.45 5.37 3.00e+00 1.11e-01 3.20e+00 ... (remaining 20490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 9212 21.14 - 42.28: 148 42.28 - 63.42: 15 63.42 - 84.56: 30 84.56 - 105.70: 25 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 -176.99 105.70 1 3.00e+01 1.11e-03 1.36e+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 -176.99 105.70 1 3.00e+01 1.11e-03 1.36e+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 -176.98 105.69 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 9427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1904 0.047 - 0.095: 345 0.095 - 0.142: 136 0.142 - 0.190: 10 0.190 - 0.237: 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 -2.51 0.24 2.00e-01 2.50e+01 1.40e+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 -2.51 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C5 BMA c 3 " pdb=" C4 BMA c 3 " pdb=" C6 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.51 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2397 not shown) Planarity restraints: 2500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 275 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.13e-01 pdb=" N PRO E 276 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 275 " -0.015 5.00e-02 4.00e+02 2.24e-02 8.04e-01 pdb=" N PRO A 276 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 275 " -0.015 5.00e-02 4.00e+02 2.22e-02 7.90e-01 pdb=" N PRO B 276 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " -0.012 5.00e-02 4.00e+02 ... (remaining 2497 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2717 2.77 - 3.30: 14311 3.30 - 3.84: 27722 3.84 - 4.37: 34107 4.37 - 4.90: 55199 Nonbonded interactions: 134056 Sorted by model distance: nonbonded pdb=" ND2AASN B 41 " pdb=" O ARG B 169 " model vdw 2.240 3.120 nonbonded pdb=" ND2AASN E 41 " pdb=" O ARG E 169 " model vdw 2.241 3.120 nonbonded pdb=" ND2AASN A 41 " pdb=" O ARG A 169 " model vdw 2.241 3.120 nonbonded pdb=" ND2AASN C 41 " pdb=" O ARG C 169 " model vdw 2.241 3.120 nonbonded pdb=" ND2AASN D 41 " pdb=" O ARG D 169 " model vdw 2.241 3.120 ... (remaining 134051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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 through 504)) 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 through 504)) 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 through 504)) 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 through 504)) 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 through 504)) } 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.730 Find NCS groups from input model: 0.450 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15115 Z= 0.152 Angle : 0.510 5.472 20625 Z= 0.233 Chirality : 0.043 0.237 2400 Planarity : 0.003 0.023 2485 Dihedral : 11.405 105.701 6155 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 0.33 % Allowed : 3.19 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.21), residues: 1715 helix: 1.13 (0.21), residues: 630 sheet: 1.61 (0.23), residues: 455 loop : 1.69 (0.28), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 129 TYR 0.010 0.001 TYR B 143 PHE 0.008 0.001 PHE D 98 TRP 0.004 0.001 TRP D 67 HIS 0.001 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00307 (15070) covalent geometry : angle 0.50195 (20495) SS BOND : bond 0.00135 ( 5) SS BOND : angle 0.54026 ( 10) hydrogen bonds : bond 0.24055 ( 780) hydrogen bonds : angle 7.12282 ( 2475) link_ALPHA1-3 : bond 0.00278 ( 5) link_ALPHA1-3 : angle 0.97746 ( 15) link_ALPHA1-6 : bond 0.00391 ( 5) link_ALPHA1-6 : angle 0.88316 ( 15) link_BETA1-4 : bond 0.00360 ( 15) link_BETA1-4 : angle 1.48875 ( 45) link_NAG-ASN : bond 0.00102 ( 15) link_NAG-ASN : angle 1.27009 ( 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 272 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 267 time to evaluate : 0.617 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 272 average time/residue: 0.9222 time to fit residues: 267.7978 Evaluate side-chains 165 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN B D 41 ASN B E 41 ASN B Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.062677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.045745 restraints weight = 152903.456| |-----------------------------------------------------------------------------| r_work (start): 0.2421 rms_B_bonded: 4.69 r_work: 0.2190 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2181 r_free = 0.2181 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2177 r_free = 0.2177 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15115 Z= 0.148 Angle : 0.569 5.228 20625 Z= 0.306 Chirality : 0.045 0.164 2400 Planarity : 0.004 0.027 2485 Dihedral : 10.185 81.483 2895 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.59 % Allowed : 12.31 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.21), residues: 1715 helix: 2.20 (0.21), residues: 640 sheet: 1.30 (0.22), residues: 455 loop : 1.79 (0.29), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 269 TYR 0.020 0.002 TYR C 299 PHE 0.022 0.002 PHE A 306 TRP 0.011 0.001 TRP C 67 HIS 0.002 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00313 (15070) covalent geometry : angle 0.55585 (20495) SS BOND : bond 0.00144 ( 5) SS BOND : angle 0.33347 ( 10) hydrogen bonds : bond 0.06056 ( 780) hydrogen bonds : angle 4.93412 ( 2475) link_ALPHA1-3 : bond 0.00858 ( 5) link_ALPHA1-3 : angle 2.23020 ( 15) link_ALPHA1-6 : bond 0.00413 ( 5) link_ALPHA1-6 : angle 2.13207 ( 15) link_BETA1-4 : bond 0.00394 ( 15) link_BETA1-4 : angle 1.53000 ( 45) link_NAG-ASN : bond 0.00105 ( 15) link_NAG-ASN : angle 1.52734 ( 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 180 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.621 Fit side-chains REVERT: A 48 ASP cc_start: 0.8619 (m-30) cc_final: 0.8270 (m-30) REVERT: B 48 ASP cc_start: 0.8658 (m-30) cc_final: 0.8356 (m-30) REVERT: B 64 GLN cc_start: 0.9356 (mt0) cc_final: 0.9100 (mp10) REVERT: C 48 ASP cc_start: 0.8716 (m-30) cc_final: 0.8437 (m-30) REVERT: D 48 ASP cc_start: 0.8703 (m-30) cc_final: 0.8398 (m-30) REVERT: E 48 ASP cc_start: 0.8662 (m-30) cc_final: 0.8304 (m-30) outliers start: 9 outliers final: 0 residues processed: 175 average time/residue: 0.7313 time to fit residues: 138.5174 Evaluate side-chains 175 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.059771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.043104 restraints weight = 131271.981| |-----------------------------------------------------------------------------| r_work (start): 0.2358 rms_B_bonded: 4.42 r_work: 0.2135 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2126 r_free = 0.2126 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2126 r_free = 0.2126 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15115 Z= 0.238 Angle : 0.597 6.052 20625 Z= 0.313 Chirality : 0.046 0.193 2400 Planarity : 0.004 0.029 2485 Dihedral : 9.791 75.208 2895 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.85 % Allowed : 12.18 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.21), residues: 1715 helix: 2.32 (0.20), residues: 640 sheet: 1.20 (0.23), residues: 400 loop : 1.41 (0.27), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 269 TYR 0.027 0.002 TYR D 299 PHE 0.021 0.002 PHE B 306 TRP 0.006 0.001 TRP B 67 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00547 (15070) covalent geometry : angle 0.58139 (20495) SS BOND : bond 0.00309 ( 5) SS BOND : angle 0.71120 ( 10) hydrogen bonds : bond 0.05377 ( 780) hydrogen bonds : angle 4.77164 ( 2475) link_ALPHA1-3 : bond 0.00907 ( 5) link_ALPHA1-3 : angle 2.16292 ( 15) link_ALPHA1-6 : bond 0.00484 ( 5) link_ALPHA1-6 : angle 2.12140 ( 15) link_BETA1-4 : bond 0.00303 ( 15) link_BETA1-4 : angle 1.77139 ( 45) link_NAG-ASN : bond 0.00264 ( 15) link_NAG-ASN : angle 1.70335 ( 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 150 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.604 Fit side-chains REVERT: A 48 ASP cc_start: 0.8717 (m-30) cc_final: 0.8335 (m-30) REVERT: B 48 ASP cc_start: 0.8702 (m-30) cc_final: 0.8322 (m-30) REVERT: B 64 GLN cc_start: 0.9360 (mt0) cc_final: 0.8833 (mp10) REVERT: B 68 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8890 (ttt-90) REVERT: C 48 ASP cc_start: 0.8742 (m-30) cc_final: 0.8380 (m-30) REVERT: D 48 ASP cc_start: 0.8703 (m-30) cc_final: 0.8290 (m-30) REVERT: E 48 ASP cc_start: 0.8681 (m-30) cc_final: 0.8293 (m-30) outliers start: 13 outliers final: 2 residues processed: 142 average time/residue: 0.6774 time to fit residues: 105.4396 Evaluate side-chains 136 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain E residue 115 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.061650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.044307 restraints weight = 132849.451| |-----------------------------------------------------------------------------| r_work (start): 0.2400 rms_B_bonded: 4.58 r_work: 0.2179 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2170 r_free = 0.2170 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2170 r_free = 0.2170 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15115 Z= 0.136 Angle : 0.532 5.995 20625 Z= 0.278 Chirality : 0.045 0.216 2400 Planarity : 0.003 0.030 2485 Dihedral : 9.195 68.947 2895 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.30 % Allowed : 11.66 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.21), residues: 1715 helix: 2.54 (0.20), residues: 635 sheet: 1.16 (0.23), residues: 400 loop : 1.28 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.026 0.001 TYR C 299 PHE 0.021 0.002 PHE D 306 TRP 0.009 0.001 TRP E 67 HIS 0.002 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00300 (15070) covalent geometry : angle 0.51912 (20495) SS BOND : bond 0.00180 ( 5) SS BOND : angle 0.31596 ( 10) hydrogen bonds : bond 0.04452 ( 780) hydrogen bonds : angle 4.48958 ( 2475) link_ALPHA1-3 : bond 0.01078 ( 5) link_ALPHA1-3 : angle 2.13566 ( 15) link_ALPHA1-6 : bond 0.00694 ( 5) link_ALPHA1-6 : angle 2.05493 ( 15) link_BETA1-4 : bond 0.00262 ( 15) link_BETA1-4 : angle 1.43191 ( 45) link_NAG-ASN : bond 0.00079 ( 15) link_NAG-ASN : angle 1.48468 ( 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 162 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.624 Fit side-chains REVERT: A 48 ASP cc_start: 0.8718 (m-30) cc_final: 0.8308 (m-30) REVERT: A 64 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.9015 (mp10) REVERT: B 48 ASP cc_start: 0.8688 (m-30) cc_final: 0.8238 (m-30) REVERT: B 64 GLN cc_start: 0.9341 (mt0) cc_final: 0.8801 (mp10) REVERT: B 68 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8942 (ttt-90) REVERT: C 48 ASP cc_start: 0.8734 (m-30) cc_final: 0.8344 (m-30) REVERT: D 48 ASP cc_start: 0.8723 (m-30) cc_final: 0.8271 (m-30) REVERT: D 68 ARG cc_start: 0.9249 (ttp80) cc_final: 0.9020 (ttt90) REVERT: E 48 ASP cc_start: 0.8666 (m-30) cc_final: 0.8237 (m-30) outliers start: 20 outliers final: 4 residues processed: 147 average time/residue: 0.7040 time to fit residues: 113.1892 Evaluate side-chains 137 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain E residue 115 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 45 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 0.0570 chunk 85 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 154 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 overall best weight: 1.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.060845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.044296 restraints weight = 144607.644| |-----------------------------------------------------------------------------| r_work (start): 0.2388 rms_B_bonded: 4.51 r_work: 0.2165 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2156 r_free = 0.2156 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2156 r_free = 0.2156 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 15115 Z= 0.157 Angle : 0.539 6.050 20625 Z= 0.279 Chirality : 0.045 0.227 2400 Planarity : 0.003 0.030 2485 Dihedral : 8.962 65.555 2895 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.11 % Allowed : 12.38 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.21), residues: 1715 helix: 2.62 (0.20), residues: 630 sheet: 1.11 (0.24), residues: 400 loop : 1.22 (0.27), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.027 0.002 TYR C 299 PHE 0.020 0.002 PHE B 306 TRP 0.007 0.001 TRP E 67 HIS 0.002 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00353 (15070) covalent geometry : angle 0.52457 (20495) SS BOND : bond 0.00208 ( 5) SS BOND : angle 0.46462 ( 10) hydrogen bonds : bond 0.04414 ( 780) hydrogen bonds : angle 4.41339 ( 2475) link_ALPHA1-3 : bond 0.01024 ( 5) link_ALPHA1-3 : angle 2.18104 ( 15) link_ALPHA1-6 : bond 0.00715 ( 5) link_ALPHA1-6 : angle 2.07817 ( 15) link_BETA1-4 : bond 0.00276 ( 15) link_BETA1-4 : angle 1.51460 ( 45) link_NAG-ASN : bond 0.00090 ( 15) link_NAG-ASN : angle 1.55924 ( 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: 17 poor density : 134 time to evaluate : 0.598 Fit side-chains REVERT: A 48 ASP cc_start: 0.8750 (m-30) cc_final: 0.8340 (m-30) REVERT: A 64 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.9040 (mp10) REVERT: B 48 ASP cc_start: 0.8684 (m-30) cc_final: 0.8209 (m-30) REVERT: B 64 GLN cc_start: 0.9347 (mt0) cc_final: 0.9046 (mp10) REVERT: B 68 ARG cc_start: 0.9246 (ttp80) cc_final: 0.8950 (ttt-90) REVERT: B 312 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8261 (ttt180) REVERT: C 48 ASP cc_start: 0.8704 (m-30) cc_final: 0.8294 (m-30) REVERT: D 48 ASP cc_start: 0.8721 (m-30) cc_final: 0.8225 (m-30) REVERT: D 68 ARG cc_start: 0.9235 (ttp80) cc_final: 0.9011 (ttt90) REVERT: D 224 GLN cc_start: 0.9456 (tp40) cc_final: 0.9229 (tp40) REVERT: E 48 ASP cc_start: 0.8665 (m-30) cc_final: 0.8226 (m-30) outliers start: 17 outliers final: 4 residues processed: 143 average time/residue: 0.6581 time to fit residues: 103.0089 Evaluate side-chains 138 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain E residue 115 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 109 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.061804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.044671 restraints weight = 128332.172| |-----------------------------------------------------------------------------| r_work (start): 0.2400 rms_B_bonded: 4.49 r_work: 0.2184 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2185 r_free = 0.2185 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2185 r_free = 0.2185 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15115 Z= 0.130 Angle : 0.519 6.105 20625 Z= 0.268 Chirality : 0.045 0.238 2400 Planarity : 0.003 0.030 2485 Dihedral : 8.553 61.795 2895 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 0.78 % Allowed : 12.90 % 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 aren not related in a simple way. whole: 2.51 (0.21), residues: 1715 helix: 2.67 (0.20), residues: 630 sheet: 1.08 (0.24), residues: 400 loop : 1.22 (0.27), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 269 TYR 0.026 0.001 TYR C 299 PHE 0.018 0.001 PHE A 306 TRP 0.009 0.001 TRP E 67 HIS 0.001 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00285 (15070) covalent geometry : angle 0.50517 (20495) SS BOND : bond 0.00171 ( 5) SS BOND : angle 0.32909 ( 10) hydrogen bonds : bond 0.04126 ( 780) hydrogen bonds : angle 4.27311 ( 2475) link_ALPHA1-3 : bond 0.01099 ( 5) link_ALPHA1-3 : angle 2.15901 ( 15) link_ALPHA1-6 : bond 0.00822 ( 5) link_ALPHA1-6 : angle 2.07452 ( 15) link_BETA1-4 : bond 0.00313 ( 15) link_BETA1-4 : angle 1.40252 ( 45) link_NAG-ASN : bond 0.00077 ( 15) link_NAG-ASN : angle 1.48774 ( 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 145 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.591 Fit side-chains REVERT: A 48 ASP cc_start: 0.8739 (m-30) cc_final: 0.8318 (m-30) REVERT: A 64 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.9061 (mp10) REVERT: B 48 ASP cc_start: 0.8685 (m-30) cc_final: 0.8223 (m-30) REVERT: B 64 GLN cc_start: 0.9344 (mt0) cc_final: 0.9069 (mp10) REVERT: B 312 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8245 (ttt180) REVERT: C 48 ASP cc_start: 0.8687 (m-30) cc_final: 0.8306 (m-30) REVERT: D 48 ASP cc_start: 0.8725 (m-30) cc_final: 0.8225 (m-30) REVERT: D 68 ARG cc_start: 0.9237 (ttp80) cc_final: 0.9033 (ttt90) REVERT: D 224 GLN cc_start: 0.9450 (tp40) cc_final: 0.9233 (tp40) REVERT: E 48 ASP cc_start: 0.8654 (m-30) cc_final: 0.8231 (m-30) outliers start: 12 outliers final: 6 residues processed: 139 average time/residue: 0.7096 time to fit residues: 108.0096 Evaluate side-chains 139 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain E residue 115 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 13 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 150 optimal weight: 0.0020 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.062932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.046491 restraints weight = 149489.498| |-----------------------------------------------------------------------------| r_work (start): 0.2450 rms_B_bonded: 4.61 r_work: 0.2228 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2227 r_free = 0.2227 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2227 r_free = 0.2227 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15115 Z= 0.104 Angle : 0.513 7.496 20625 Z= 0.261 Chirality : 0.044 0.241 2400 Planarity : 0.003 0.031 2485 Dihedral : 8.156 59.945 2895 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.11 % Allowed : 13.42 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.21), residues: 1715 helix: 2.72 (0.20), residues: 630 sheet: 1.06 (0.24), residues: 400 loop : 1.21 (0.27), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.025 0.001 TYR C 299 PHE 0.018 0.001 PHE A 306 TRP 0.012 0.001 TRP E 67 HIS 0.002 0.000 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00216 (15070) covalent geometry : angle 0.50039 (20495) SS BOND : bond 0.00132 ( 5) SS BOND : angle 0.17496 ( 10) hydrogen bonds : bond 0.03783 ( 780) hydrogen bonds : angle 4.09851 ( 2475) link_ALPHA1-3 : bond 0.01157 ( 5) link_ALPHA1-3 : angle 2.11964 ( 15) link_ALPHA1-6 : bond 0.00945 ( 5) link_ALPHA1-6 : angle 2.04946 ( 15) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.30227 ( 45) link_NAG-ASN : bond 0.00137 ( 15) link_NAG-ASN : angle 1.37402 ( 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 152 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.624 Fit side-chains REVERT: A 48 ASP cc_start: 0.8691 (m-30) cc_final: 0.8300 (m-30) REVERT: A 64 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.9079 (mp10) REVERT: B 48 ASP cc_start: 0.8648 (m-30) cc_final: 0.8184 (m-30) REVERT: B 64 GLN cc_start: 0.9300 (mt0) cc_final: 0.9026 (mp10) REVERT: C 48 ASP cc_start: 0.8684 (m-30) cc_final: 0.8289 (m-30) REVERT: C 224 GLN cc_start: 0.9424 (tp40) cc_final: 0.8901 (tp-100) REVERT: D 48 ASP cc_start: 0.8688 (m-30) cc_final: 0.8194 (m-30) REVERT: D 224 GLN cc_start: 0.9399 (tp40) cc_final: 0.9185 (tp40) REVERT: E 48 ASP cc_start: 0.8650 (m-30) cc_final: 0.8208 (m-30) REVERT: E 224 GLN cc_start: 0.9408 (tp40) cc_final: 0.9194 (tp40) outliers start: 17 outliers final: 4 residues processed: 145 average time/residue: 0.6909 time to fit residues: 109.8339 Evaluate side-chains 135 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain D residue 429 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 154 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.059991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.043187 restraints weight = 148503.381| |-----------------------------------------------------------------------------| r_work (start): 0.2372 rms_B_bonded: 4.60 r_work: 0.2145 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2144 r_free = 0.2144 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2144 r_free = 0.2144 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15115 Z= 0.204 Angle : 0.576 7.413 20625 Z= 0.294 Chirality : 0.046 0.240 2400 Planarity : 0.004 0.031 2485 Dihedral : 8.348 59.819 2895 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Rotamer: Outliers : 0.52 % Allowed : 14.33 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.21), residues: 1715 helix: 2.71 (0.20), residues: 635 sheet: 1.08 (0.24), residues: 400 loop : 1.13 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.028 0.002 TYR E 299 PHE 0.020 0.002 PHE C 306 TRP 0.006 0.001 TRP C 426 HIS 0.002 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00464 (15070) covalent geometry : angle 0.56146 (20495) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.75157 ( 10) hydrogen bonds : bond 0.04456 ( 780) hydrogen bonds : angle 4.34915 ( 2475) link_ALPHA1-3 : bond 0.00899 ( 5) link_ALPHA1-3 : angle 2.27053 ( 15) link_ALPHA1-6 : bond 0.00740 ( 5) link_ALPHA1-6 : angle 2.12369 ( 15) link_BETA1-4 : bond 0.00289 ( 15) link_BETA1-4 : angle 1.58528 ( 45) link_NAG-ASN : bond 0.00151 ( 15) link_NAG-ASN : angle 1.67036 ( 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 134 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.612 Fit side-chains REVERT: A 48 ASP cc_start: 0.8717 (m-30) cc_final: 0.8310 (m-30) REVERT: A 64 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.9068 (mp10) REVERT: B 48 ASP cc_start: 0.8688 (m-30) cc_final: 0.8217 (m-30) REVERT: B 64 GLN cc_start: 0.9358 (mt0) cc_final: 0.9063 (mp10) REVERT: C 48 ASP cc_start: 0.8670 (m-30) cc_final: 0.8214 (m-30) REVERT: D 48 ASP cc_start: 0.8745 (m-30) cc_final: 0.8224 (m-30) REVERT: D 224 GLN cc_start: 0.9488 (tp40) cc_final: 0.9255 (tp40) REVERT: E 48 ASP cc_start: 0.8666 (m-30) cc_final: 0.8225 (m-30) outliers start: 8 outliers final: 3 residues processed: 129 average time/residue: 0.6869 time to fit residues: 97.4346 Evaluate side-chains 130 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 306 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.061591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.045041 restraints weight = 160917.122| |-----------------------------------------------------------------------------| r_work (start): 0.2416 rms_B_bonded: 4.72 r_work: 0.2188 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2180 r_free = 0.2180 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2180 r_free = 0.2180 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15115 Z= 0.120 Angle : 0.533 8.431 20625 Z= 0.270 Chirality : 0.044 0.241 2400 Planarity : 0.003 0.030 2485 Dihedral : 8.015 58.109 2895 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.33 % Allowed : 14.53 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.21), residues: 1715 helix: 2.74 (0.20), residues: 630 sheet: 1.04 (0.24), residues: 400 loop : 1.10 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.025 0.001 TYR C 299 PHE 0.018 0.001 PHE A 306 TRP 0.009 0.001 TRP D 67 HIS 0.001 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00262 (15070) covalent geometry : angle 0.52077 (20495) SS BOND : bond 0.00145 ( 5) SS BOND : angle 0.24935 ( 10) hydrogen bonds : bond 0.03998 ( 780) hydrogen bonds : angle 4.16040 ( 2475) link_ALPHA1-3 : bond 0.01068 ( 5) link_ALPHA1-3 : angle 2.09981 ( 15) link_ALPHA1-6 : bond 0.00920 ( 5) link_ALPHA1-6 : angle 2.09068 ( 15) link_BETA1-4 : bond 0.00321 ( 15) link_BETA1-4 : angle 1.34850 ( 45) link_NAG-ASN : bond 0.00078 ( 15) link_NAG-ASN : angle 1.44401 ( 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 131 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.576 Fit side-chains REVERT: A 48 ASP cc_start: 0.8722 (m-30) cc_final: 0.8316 (m-30) REVERT: A 64 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.9067 (mp10) REVERT: B 48 ASP cc_start: 0.8673 (m-30) cc_final: 0.8199 (m-30) REVERT: B 64 GLN cc_start: 0.9350 (mt0) cc_final: 0.9066 (mp10) REVERT: C 48 ASP cc_start: 0.8631 (m-30) cc_final: 0.8215 (m-30) REVERT: D 48 ASP cc_start: 0.8717 (m-30) cc_final: 0.8183 (m-30) REVERT: D 68 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8798 (tpp80) REVERT: D 224 GLN cc_start: 0.9445 (tp40) cc_final: 0.9228 (tp40) REVERT: E 48 ASP cc_start: 0.8648 (m-30) cc_final: 0.8192 (m-30) REVERT: E 244 TYR cc_start: 0.9103 (p90) cc_final: 0.8814 (p90) outliers start: 5 outliers final: 1 residues processed: 128 average time/residue: 0.7081 time to fit residues: 99.0731 Evaluate side-chains 129 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain D residue 68 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 124 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 118 optimal weight: 0.0020 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.062635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.046267 restraints weight = 141617.957| |-----------------------------------------------------------------------------| r_work (start): 0.2447 rms_B_bonded: 4.54 r_work: 0.2226 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2218 r_free = 0.2218 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2218 r_free = 0.2218 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15115 Z= 0.107 Angle : 0.525 8.495 20625 Z= 0.263 Chirality : 0.044 0.245 2400 Planarity : 0.003 0.031 2485 Dihedral : 7.580 53.482 2895 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.26 % Allowed : 14.66 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.21), residues: 1715 helix: 2.78 (0.20), residues: 630 sheet: 1.05 (0.24), residues: 400 loop : 1.12 (0.27), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.025 0.001 TYR C 299 PHE 0.019 0.001 PHE A 306 TRP 0.011 0.001 TRP E 67 HIS 0.001 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00225 (15070) covalent geometry : angle 0.51250 (20495) SS BOND : bond 0.00130 ( 5) SS BOND : angle 0.19250 ( 10) hydrogen bonds : bond 0.03773 ( 780) hydrogen bonds : angle 4.05170 ( 2475) link_ALPHA1-3 : bond 0.01093 ( 5) link_ALPHA1-3 : angle 2.08275 ( 15) link_ALPHA1-6 : bond 0.00983 ( 5) link_ALPHA1-6 : angle 2.07979 ( 15) link_BETA1-4 : bond 0.00357 ( 15) link_BETA1-4 : angle 1.31090 ( 45) link_NAG-ASN : bond 0.00116 ( 15) link_NAG-ASN : angle 1.40022 ( 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 131 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.592 Fit side-chains REVERT: A 48 ASP cc_start: 0.8688 (m-30) cc_final: 0.8287 (m-30) REVERT: A 64 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.9073 (mp10) REVERT: B 48 ASP cc_start: 0.8629 (m-30) cc_final: 0.8157 (m-30) REVERT: C 48 ASP cc_start: 0.8562 (m-30) cc_final: 0.8215 (m-30) REVERT: C 224 GLN cc_start: 0.9428 (tp40) cc_final: 0.8844 (tp40) REVERT: D 48 ASP cc_start: 0.8673 (m-30) cc_final: 0.8165 (m-30) REVERT: D 224 GLN cc_start: 0.9411 (tp40) cc_final: 0.9204 (tp40) REVERT: E 48 ASP cc_start: 0.8633 (m-30) cc_final: 0.8174 (m-30) REVERT: E 224 GLN cc_start: 0.9416 (tp40) cc_final: 0.9206 (tp40) REVERT: E 244 TYR cc_start: 0.9103 (p90) cc_final: 0.8831 (p90) REVERT: E 274 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8866 (mtmm) outliers start: 4 outliers final: 2 residues processed: 128 average time/residue: 0.6928 time to fit residues: 97.2626 Evaluate side-chains 131 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 274 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 3.9990 chunk 133 optimal weight: 0.0970 chunk 116 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.059790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.042959 restraints weight = 155306.083| |-----------------------------------------------------------------------------| r_work (start): 0.2365 rms_B_bonded: 4.66 r_work: 0.2139 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2130 r_free = 0.2130 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2130 r_free = 0.2130 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 15115 Z= 0.208 Angle : 0.585 8.939 20625 Z= 0.296 Chirality : 0.046 0.245 2400 Planarity : 0.004 0.031 2485 Dihedral : 7.825 55.091 2895 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 0.39 % Allowed : 14.46 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.21), residues: 1715 helix: 2.73 (0.21), residues: 630 sheet: 1.05 (0.24), residues: 400 loop : 1.05 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.029 0.002 TYR A 299 PHE 0.020 0.002 PHE A 306 TRP 0.008 0.001 TRP C 426 HIS 0.002 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00473 (15070) covalent geometry : angle 0.57032 (20495) SS BOND : bond 0.00216 ( 5) SS BOND : angle 0.79197 ( 10) hydrogen bonds : bond 0.04446 ( 780) hydrogen bonds : angle 4.32072 ( 2475) link_ALPHA1-3 : bond 0.00855 ( 5) link_ALPHA1-3 : angle 2.25047 ( 15) link_ALPHA1-6 : bond 0.00785 ( 5) link_ALPHA1-6 : angle 2.11104 ( 15) link_BETA1-4 : bond 0.00309 ( 15) link_BETA1-4 : angle 1.58999 ( 45) link_NAG-ASN : bond 0.00175 ( 15) link_NAG-ASN : angle 1.69481 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5370.52 seconds wall clock time: 92 minutes 27.01 seconds (5547.01 seconds total)