Starting phenix.real_space_refine on Fri Jul 3 15:55:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9feu_50341/07_2026/9feu_50341.cif Found real_map, /net/cci-nas-00/data/ceres_data/9feu_50341/07_2026/9feu_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_50341/07_2026/9feu_50341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9feu_50341/07_2026/9feu_50341.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9feu_50341/07_2026/9feu_50341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9feu_50341/07_2026/9feu_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 52 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 3, 'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 5.89, per 1000 atoms: 0.39 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: 1.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 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: 0.38 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: 2.68 Time building geometry restraints manager: 1.76 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: 2.830 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.930 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 are 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/Z covalent geometry : bond 0.00307 / 0.15 (15070) covalent geometry : angle 0.50195 / 0.23 (20495) SS BOND : bond 0.00135 / 0.07 ( 5) SS BOND : angle 0.54026 / 0.34 ( 10) hydrogen bonds : bond 0.24055 / 15.81 ( 780) hydrogen bonds : angle 7.12282 / 4.95 ( 2475) link_ALPHA1-3 : bond 0.00278 / 0.14 ( 5) link_ALPHA1-3 : angle 0.97746 / 0.68 ( 15) link_ALPHA1-6 : bond 0.00391 / 0.20 ( 5) link_ALPHA1-6 : angle 0.88316 / 0.61 ( 15) link_BETA1-4 : bond 0.00360 / 0.19 ( 15) link_BETA1-4 : angle 1.48875 / 1.01 ( 45) link_NAG-ASN : bond 0.00102 / 0.06 ( 15) link_NAG-ASN : angle 1.27009 / 0.81 ( 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 : 0.541 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 272 average time/residue: 0.8105 time to fit residues: 236.2196 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 : 0.520 ------------------------------------------------------------------------------- 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: 2.9990 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... 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 = 0.2838 r_free = 0.2838 target = 0.062610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.045663 restraints weight = 152044.586| |-----------------------------------------------------------------------------| r_work (start): 0.2418 rms_B_bonded: 4.69 r_work: 0.2188 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2179 r_free = 0.2179 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 = 0.2174 r_free = 0.2174 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9268 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15115 Z= 0.148 Angle : 0.570 5.319 20625 Z= 0.306 Chirality : 0.045 0.162 2400 Planarity : 0.004 0.027 2485 Dihedral : 10.238 81.889 2895 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.78 % Allowed : 12.12 % 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 are not related in a simple way. whole: 2.63 (0.21), residues: 1715 helix: 2.23 (0.21), residues: 640 sheet: 1.31 (0.22), residues: 455 loop : 1.80 (0.29), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 269 TYR 0.021 0.002 TYR C 299 PHE 0.022 0.002 PHE A 306 TRP 0.010 0.001 TRP C 67 HIS 0.002 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (15070) covalent geometry : angle 0.55558 / 0.30 (20495) SS BOND : bond 0.00156 / 0.08 ( 5) SS BOND : angle 0.36266 / 0.25 ( 10) hydrogen bonds : bond 0.06132 / 3.95 ( 780) hydrogen bonds : angle 4.96423 / 3.43 ( 2475) link_ALPHA1-3 : bond 0.00832 / 0.42 ( 5) link_ALPHA1-3 : angle 2.20930 / 1.43 ( 15) link_ALPHA1-6 : bond 0.00394 / 0.20 ( 5) link_ALPHA1-6 : angle 2.17634 / 1.47 ( 15) link_BETA1-4 : bond 0.00429 / 0.22 ( 15) link_BETA1-4 : angle 1.54361 / 1.11 ( 45) link_NAG-ASN : bond 0.00101 / 0.05 ( 15) link_NAG-ASN : angle 1.58071 / 1.09 ( 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 183 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.589 Fit side-chains REVERT: A 48 ASP cc_start: 0.8595 (m-30) cc_final: 0.8234 (m-30) REVERT: B 48 ASP cc_start: 0.8654 (m-30) cc_final: 0.8329 (m-30) REVERT: B 64 GLN cc_start: 0.9360 (mt0) cc_final: 0.8860 (mp10) REVERT: C 48 ASP cc_start: 0.8722 (m-30) cc_final: 0.8431 (m-30) REVERT: D 48 ASP cc_start: 0.8714 (m-30) cc_final: 0.8418 (m-30) REVERT: E 48 ASP cc_start: 0.8638 (m-30) cc_final: 0.8293 (m-30) outliers start: 12 outliers final: 0 residues processed: 176 average time/residue: 0.7199 time to fit residues: 137.4514 Evaluate side-chains 176 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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: 0.8980 chunk 5 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.059385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2378 r_free = 0.2378 target = 0.042746 restraints weight = 130373.727| |-----------------------------------------------------------------------------| r_work (start): 0.2349 rms_B_bonded: 4.42 r_work: 0.2127 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2119 r_free = 0.2119 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2119 r_free = 0.2119 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9298 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 15115 Z= 0.253 Angle : 0.610 6.099 20625 Z= 0.320 Chirality : 0.047 0.197 2400 Planarity : 0.004 0.030 2485 Dihedral : 9.811 74.701 2895 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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 are not related in a simple way. whole: 2.43 (0.21), residues: 1715 helix: 2.32 (0.20), residues: 640 sheet: 1.19 (0.23), residues: 400 loop : 1.37 (0.27), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 269 TYR 0.027 0.002 TYR E 299 PHE 0.022 0.002 PHE B 306 TRP 0.006 0.001 TRP E 426 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 (15070) covalent geometry : angle 0.59458 / 0.32 (20495) SS BOND : bond 0.00353 / 0.18 ( 5) SS BOND : angle 0.81755 / 0.55 ( 10) hydrogen bonds : bond 0.05409 / 3.48 ( 780) hydrogen bonds : angle 4.79477 / 3.31 ( 2475) link_ALPHA1-3 : bond 0.00867 / 0.44 ( 5) link_ALPHA1-3 : angle 2.23300 / 1.45 ( 15) link_ALPHA1-6 : bond 0.00475 / 0.24 ( 5) link_ALPHA1-6 : angle 2.08937 / 1.39 ( 15) link_BETA1-4 : bond 0.00311 / 0.20 ( 15) link_BETA1-4 : angle 1.79185 / 1.25 ( 45) link_NAG-ASN : bond 0.00286 / 0.15 ( 15) link_NAG-ASN : angle 1.76315 / 1.21 ( 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 151 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.612 Fit side-chains REVERT: A 48 ASP cc_start: 0.8726 (m-30) cc_final: 0.8355 (m-30) REVERT: B 48 ASP cc_start: 0.8708 (m-30) cc_final: 0.8314 (m-30) REVERT: B 64 GLN cc_start: 0.9363 (mt0) cc_final: 0.8798 (mp10) REVERT: B 68 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8888 (ttt-90) REVERT: C 48 ASP cc_start: 0.8740 (m-30) cc_final: 0.8360 (m-30) REVERT: D 48 ASP cc_start: 0.8704 (m-30) cc_final: 0.8290 (m-30) REVERT: E 48 ASP cc_start: 0.8690 (m-30) cc_final: 0.8290 (m-30) outliers start: 13 outliers final: 2 residues processed: 143 average time/residue: 0.6157 time to fit residues: 97.1148 Evaluate side-chains 131 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 0.0020 chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.060521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.043962 restraints weight = 132794.436| |-----------------------------------------------------------------------------| r_work (start): 0.2381 rms_B_bonded: 4.45 r_work: 0.2160 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2151 r_free = 0.2151 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2150 r_free = 0.2150 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9301 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15115 Z= 0.163 Angle : 0.547 6.097 20625 Z= 0.286 Chirality : 0.045 0.215 2400 Planarity : 0.003 0.030 2485 Dihedral : 9.361 69.498 2895 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.30 % Allowed : 11.79 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.21), residues: 1715 helix: 2.45 (0.20), residues: 640 sheet: 1.13 (0.23), residues: 400 loop : 1.30 (0.27), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.026 0.002 TYR C 299 PHE 0.021 0.002 PHE E 306 TRP 0.007 0.001 TRP C 67 HIS 0.002 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (15070) covalent geometry : angle 0.53315 / 0.28 (20495) SS BOND : bond 0.00214 / 0.11 ( 5) SS BOND : angle 0.41450 / 0.28 ( 10) hydrogen bonds : bond 0.04639 / 2.98 ( 780) hydrogen bonds : angle 4.55796 / 3.14 ( 2475) link_ALPHA1-3 : bond 0.01023 / 0.52 ( 5) link_ALPHA1-3 : angle 2.16962 / 1.40 ( 15) link_ALPHA1-6 : bond 0.00638 / 0.33 ( 5) link_ALPHA1-6 : angle 2.06298 / 1.37 ( 15) link_BETA1-4 : bond 0.00262 / 0.14 ( 15) link_BETA1-4 : angle 1.51275 / 1.07 ( 45) link_NAG-ASN : bond 0.00103 / 0.06 ( 15) link_NAG-ASN : angle 1.57333 / 1.07 ( 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 153 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.580 Fit side-chains REVERT: A 48 ASP cc_start: 0.8726 (m-30) cc_final: 0.8322 (m-30) REVERT: A 64 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.9038 (mp10) REVERT: B 48 ASP cc_start: 0.8674 (m-30) cc_final: 0.8227 (m-30) REVERT: B 64 GLN cc_start: 0.9361 (mt0) cc_final: 0.8850 (mp10) REVERT: B 68 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8924 (ttt-90) REVERT: B 312 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8197 (ttt180) REVERT: C 48 ASP cc_start: 0.8752 (m-30) cc_final: 0.8325 (m-30) REVERT: D 48 ASP cc_start: 0.8736 (m-30) cc_final: 0.8278 (m-30) REVERT: D 68 ARG cc_start: 0.9242 (ttp80) cc_final: 0.9003 (ttt90) REVERT: E 48 ASP cc_start: 0.8650 (m-30) cc_final: 0.8195 (m-30) outliers start: 20 outliers final: 3 residues processed: 142 average time/residue: 0.6617 time to fit residues: 103.0184 Evaluate side-chains 136 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 312 ARG 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: 2.9990 chunk 151 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 154 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.061263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.044500 restraints weight = 144053.038| |-----------------------------------------------------------------------------| r_work (start): 0.2399 rms_B_bonded: 4.56 r_work: 0.2177 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2168 r_free = 0.2168 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2168 r_free = 0.2168 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9275 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15115 Z= 0.137 Angle : 0.526 5.920 20625 Z= 0.273 Chirality : 0.045 0.230 2400 Planarity : 0.003 0.030 2485 Dihedral : 8.884 64.542 2895 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.11 % Allowed : 12.25 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.21), residues: 1715 helix: 2.62 (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 0.004 0.000 ARG A 269 TYR 0.026 0.001 TYR C 299 PHE 0.022 0.001 PHE B 306 TRP 0.009 0.001 TRP E 67 HIS 0.001 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (15070) covalent geometry : angle 0.51212 / 0.27 (20495) SS BOND : bond 0.00186 / 0.09 ( 5) SS BOND : angle 0.34106 / 0.23 ( 10) hydrogen bonds : bond 0.04275 / 2.76 ( 780) hydrogen bonds : angle 4.36743 / 3.00 ( 2475) link_ALPHA1-3 : bond 0.01080 / 0.55 ( 5) link_ALPHA1-3 : angle 2.14996 / 1.39 ( 15) link_ALPHA1-6 : bond 0.00768 / 0.39 ( 5) link_ALPHA1-6 : angle 2.06109 / 1.36 ( 15) link_BETA1-4 : bond 0.00279 / 0.14 ( 15) link_BETA1-4 : angle 1.44692 / 1.02 ( 45) link_NAG-ASN : bond 0.00075 / 0.05 ( 15) link_NAG-ASN : angle 1.51574 / 1.04 ( 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 152 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.511 Fit side-chains REVERT: A 48 ASP cc_start: 0.8749 (m-30) cc_final: 0.8332 (m-30) REVERT: A 64 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.9032 (mp10) REVERT: B 48 ASP cc_start: 0.8694 (m-30) cc_final: 0.8211 (m-30) REVERT: B 64 GLN cc_start: 0.9349 (mt0) cc_final: 0.9048 (mp10) REVERT: B 68 ARG cc_start: 0.9247 (ttp80) cc_final: 0.8956 (ttt-90) REVERT: C 48 ASP cc_start: 0.8702 (m-30) cc_final: 0.8278 (m-30) REVERT: C 64 GLN cc_start: 0.9315 (mt0) cc_final: 0.9077 (mm-40) REVERT: D 48 ASP cc_start: 0.8721 (m-30) cc_final: 0.8244 (m-30) REVERT: D 68 ARG cc_start: 0.9232 (ttp80) cc_final: 0.9009 (ttt90) REVERT: D 224 GLN cc_start: 0.9450 (tp40) cc_final: 0.9228 (tp40) REVERT: E 48 ASP cc_start: 0.8680 (m-30) cc_final: 0.8257 (m-30) REVERT: E 68 ARG cc_start: 0.9258 (ttp80) cc_final: 0.8966 (ttt-90) outliers start: 17 outliers final: 6 residues processed: 145 average time/residue: 0.6432 time to fit residues: 102.0235 Evaluate side-chains 140 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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: 0.0570 chunk 111 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.062081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.044926 restraints weight = 128143.031| |-----------------------------------------------------------------------------| r_work (start): 0.2408 rms_B_bonded: 4.51 r_work: 0.2192 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2192 r_free = 0.2192 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2192 r_free = 0.2192 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9293 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15115 Z= 0.123 Angle : 0.524 7.079 20625 Z= 0.269 Chirality : 0.045 0.240 2400 Planarity : 0.003 0.030 2485 Dihedral : 8.476 60.839 2895 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.85 % Allowed : 13.03 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.21), residues: 1715 helix: 2.65 (0.20), residues: 630 sheet: 1.06 (0.24), residues: 400 loop : 1.24 (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/Z covalent geometry : bond 0.00269 / 0.12 (15070) covalent geometry : angle 0.51096 / 0.27 (20495) SS BOND : bond 0.00181 / 0.09 ( 5) SS BOND : angle 0.29178 / 0.20 ( 10) hydrogen bonds : bond 0.04060 / 2.62 ( 780) hydrogen bonds : angle 4.23826 / 2.91 ( 2475) link_ALPHA1-3 : bond 0.01123 / 0.57 ( 5) link_ALPHA1-3 : angle 2.18399 / 1.42 ( 15) link_ALPHA1-6 : bond 0.00853 / 0.43 ( 5) link_ALPHA1-6 : angle 2.06361 / 1.35 ( 15) link_BETA1-4 : bond 0.00312 / 0.16 ( 15) link_BETA1-4 : angle 1.38420 / 0.98 ( 45) link_NAG-ASN : bond 0.00081 / 0.05 ( 15) link_NAG-ASN : angle 1.46903 / 1.00 ( 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 148 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.605 Fit side-chains REVERT: A 48 ASP cc_start: 0.8740 (m-30) cc_final: 0.8317 (m-30) REVERT: A 64 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.9064 (mp10) REVERT: B 48 ASP cc_start: 0.8674 (m-30) cc_final: 0.8191 (m-30) REVERT: C 48 ASP cc_start: 0.8688 (m-30) cc_final: 0.8287 (m-30) REVERT: D 48 ASP cc_start: 0.8744 (m-30) cc_final: 0.8223 (m-30) REVERT: D 68 ARG cc_start: 0.9224 (ttp80) cc_final: 0.9021 (ttt90) REVERT: D 224 GLN cc_start: 0.9454 (tp40) cc_final: 0.9245 (tp40) REVERT: E 48 ASP cc_start: 0.8659 (m-30) cc_final: 0.8230 (m-30) REVERT: E 68 ARG cc_start: 0.9264 (ttp80) cc_final: 0.8998 (ttt-90) outliers start: 13 outliers final: 3 residues processed: 141 average time/residue: 0.6676 time to fit residues: 102.9721 Evaluate side-chains 136 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 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 B residue 309 GLN 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: 0.6980 chunk 13 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.062385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.044980 restraints weight = 147944.754| |-----------------------------------------------------------------------------| r_work (start): 0.2421 rms_B_bonded: 4.73 r_work: 0.2197 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2190 r_free = 0.2190 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2190 r_free = 0.2190 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9267 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15115 Z= 0.118 Angle : 0.524 7.525 20625 Z= 0.268 Chirality : 0.045 0.264 2400 Planarity : 0.003 0.032 2485 Dihedral : 8.283 58.644 2895 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.59 % Allowed : 13.68 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.21), residues: 1715 helix: 2.70 (0.20), residues: 630 sheet: 1.05 (0.24), residues: 400 loop : 1.21 (0.27), 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 0.017 0.001 PHE A 306 TRP 0.009 0.001 TRP E 67 HIS 0.002 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (15070) covalent geometry : angle 0.51084 / 0.27 (20495) SS BOND : bond 0.00157 / 0.08 ( 5) SS BOND : angle 0.28322 / 0.19 ( 10) hydrogen bonds : bond 0.03957 / 2.55 ( 780) hydrogen bonds : angle 4.15352 / 2.85 ( 2475) link_ALPHA1-3 : bond 0.01097 / 0.56 ( 5) link_ALPHA1-3 : angle 2.15904 / 1.40 ( 15) link_ALPHA1-6 : bond 0.00895 / 0.46 ( 5) link_ALPHA1-6 : angle 2.06294 / 1.35 ( 15) link_BETA1-4 : bond 0.00334 / 0.17 ( 15) link_BETA1-4 : angle 1.36894 / 0.96 ( 45) link_NAG-ASN : bond 0.00090 / 0.06 ( 15) link_NAG-ASN : angle 1.45309 / 0.99 ( 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 141 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.566 Fit side-chains REVERT: A 48 ASP cc_start: 0.8705 (m-30) cc_final: 0.8306 (m-30) REVERT: A 64 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.9049 (mp10) REVERT: B 48 ASP cc_start: 0.8674 (m-30) cc_final: 0.8193 (m-30) REVERT: B 64 GLN cc_start: 0.9334 (mt0) cc_final: 0.9095 (mp10) REVERT: C 48 ASP cc_start: 0.8694 (m-30) cc_final: 0.8280 (m-30) REVERT: D 48 ASP cc_start: 0.8743 (m-30) cc_final: 0.8219 (m-30) REVERT: D 68 ARG cc_start: 0.9231 (ttp80) cc_final: 0.9028 (ttt90) REVERT: D 224 GLN cc_start: 0.9430 (tp40) cc_final: 0.9210 (tp40) REVERT: E 48 ASP cc_start: 0.8678 (m-30) cc_final: 0.8229 (m-30) REVERT: E 68 ARG cc_start: 0.9275 (ttp80) cc_final: 0.9010 (ttt-90) outliers start: 9 outliers final: 5 residues processed: 135 average time/residue: 0.6734 time to fit residues: 99.4168 Evaluate side-chains 136 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 1.984 ------------------------------------------------------------------------------- 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 C residue 115 MET Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain E residue 115 MET 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: 1.9990 chunk 90 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 151 optimal weight: 0.3980 chunk 134 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.062704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.046333 restraints weight = 148813.972| |-----------------------------------------------------------------------------| r_work (start): 0.2450 rms_B_bonded: 4.59 r_work: 0.2227 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2220 r_free = 0.2220 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2220 r_free = 0.2220 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9254 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15115 Z= 0.108 Angle : 0.522 8.228 20625 Z= 0.263 Chirality : 0.044 0.244 2400 Planarity : 0.003 0.030 2485 Dihedral : 7.892 58.796 2895 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.65 % Allowed : 13.88 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.21), residues: 1715 helix: 2.71 (0.20), residues: 630 sheet: 1.06 (0.24), residues: 400 loop : 1.20 (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 0.018 0.001 PHE D 306 TRP 0.010 0.001 TRP E 67 HIS 0.001 0.000 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (15070) covalent geometry : angle 0.51018 / 0.26 (20495) SS BOND : bond 0.00142 / 0.07 ( 5) SS BOND : angle 0.21667 / 0.15 ( 10) hydrogen bonds : bond 0.03790 / 2.45 ( 780) hydrogen bonds : angle 4.05545 / 2.78 ( 2475) link_ALPHA1-3 : bond 0.01105 / 0.56 ( 5) link_ALPHA1-3 : angle 2.11723 / 1.37 ( 15) link_ALPHA1-6 : bond 0.00966 / 0.49 ( 5) link_ALPHA1-6 : angle 2.06510 / 1.35 ( 15) link_BETA1-4 : bond 0.00340 / 0.17 ( 15) link_BETA1-4 : angle 1.30513 / 0.92 ( 45) link_NAG-ASN : bond 0.00121 / 0.08 ( 15) link_NAG-ASN : angle 1.38665 / 0.94 ( 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 143 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.493 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: 0.9294 (OUTLIER) cc_final: 0.9073 (mp10) REVERT: B 48 ASP cc_start: 0.8645 (m-30) cc_final: 0.8177 (m-30) REVERT: B 64 GLN cc_start: 0.9327 (mt0) cc_final: 0.9095 (mp10) REVERT: C 48 ASP cc_start: 0.8685 (m-30) cc_final: 0.8288 (m-30) REVERT: D 48 ASP cc_start: 0.8683 (m-30) cc_final: 0.8200 (m-30) REVERT: D 224 GLN cc_start: 0.9417 (tp40) cc_final: 0.9205 (tp40) REVERT: E 48 ASP cc_start: 0.8653 (m-30) cc_final: 0.8211 (m-30) REVERT: E 68 ARG cc_start: 0.9264 (ttp80) cc_final: 0.9011 (ttt-90) REVERT: E 224 GLN cc_start: 0.9412 (tp40) cc_final: 0.9200 (tp40) outliers start: 10 outliers final: 5 residues processed: 137 average time/residue: 0.6554 time to fit residues: 98.2533 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 : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain E residue 115 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 95 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.062609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.046125 restraints weight = 160616.920| |-----------------------------------------------------------------------------| r_work (start): 0.2445 rms_B_bonded: 4.70 r_work: 0.2218 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2210 r_free = 0.2210 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 = 0.2210 r_free = 0.2210 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9260 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15115 Z= 0.115 Angle : 0.525 9.527 20625 Z= 0.264 Chirality : 0.044 0.245 2400 Planarity : 0.003 0.030 2485 Dihedral : 7.672 54.355 2895 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 0.52 % Allowed : 14.14 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.21), residues: 1715 helix: 2.74 (0.20), residues: 630 sheet: 1.08 (0.24), residues: 400 loop : 1.17 (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 C 306 TRP 0.009 0.001 TRP E 67 HIS 0.002 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15070) covalent geometry : angle 0.51291 / 0.26 (20495) SS BOND : bond 0.00154 / 0.08 ( 5) SS BOND : angle 0.29521 / 0.20 ( 10) hydrogen bonds : bond 0.03808 / 2.46 ( 780) hydrogen bonds : angle 4.03985 / 2.77 ( 2475) link_ALPHA1-3 : bond 0.01064 / 0.54 ( 5) link_ALPHA1-3 : angle 2.13363 / 1.38 ( 15) link_ALPHA1-6 : bond 0.00964 / 0.49 ( 5) link_ALPHA1-6 : angle 2.07606 / 1.35 ( 15) link_BETA1-4 : bond 0.00337 / 0.17 ( 15) link_BETA1-4 : angle 1.33214 / 0.94 ( 45) link_NAG-ASN : bond 0.00099 / 0.07 ( 15) link_NAG-ASN : angle 1.41191 / 0.96 ( 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 139 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.562 Fit side-chains REVERT: A 48 ASP cc_start: 0.8683 (m-30) cc_final: 0.8285 (m-30) REVERT: A 64 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.9081 (mp10) REVERT: B 48 ASP cc_start: 0.8643 (m-30) cc_final: 0.8176 (m-30) REVERT: B 64 GLN cc_start: 0.9334 (mt0) cc_final: 0.9106 (mp10) REVERT: C 48 ASP cc_start: 0.8664 (m-30) cc_final: 0.8272 (m-30) REVERT: D 48 ASP cc_start: 0.8679 (m-30) cc_final: 0.8143 (m-30) REVERT: E 48 ASP cc_start: 0.8654 (m-30) cc_final: 0.8213 (m-30) REVERT: E 68 ARG cc_start: 0.9274 (ttp80) cc_final: 0.9024 (ttt-90) REVERT: E 224 GLN cc_start: 0.9411 (tp40) cc_final: 0.9199 (tp40) outliers start: 8 outliers final: 4 residues processed: 132 average time/residue: 0.6337 time to fit residues: 91.4871 Evaluate side-chains 133 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 C residue 115 MET Chi-restraints excluded: chain E residue 115 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 124 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 154 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.062939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.046322 restraints weight = 141095.893| |-----------------------------------------------------------------------------| r_work (start): 0.2456 rms_B_bonded: 4.59 r_work: 0.2235 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2228 r_free = 0.2228 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2228 r_free = 0.2228 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9270 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15115 Z= 0.110 Angle : 0.525 9.730 20625 Z= 0.263 Chirality : 0.044 0.247 2400 Planarity : 0.003 0.031 2485 Dihedral : 7.322 52.139 2895 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.46 % Allowed : 14.14 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.21), residues: 1715 helix: 2.74 (0.20), residues: 630 sheet: 0.89 (0.24), residues: 425 loop : 1.37 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.025 0.001 TYR A 299 PHE 0.019 0.001 PHE A 306 TRP 0.010 0.001 TRP E 67 HIS 0.001 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (15070) covalent geometry : angle 0.51323 / 0.26 (20495) SS BOND : bond 0.00143 / 0.07 ( 5) SS BOND : angle 0.23991 / 0.16 ( 10) hydrogen bonds : bond 0.03717 / 2.41 ( 780) hydrogen bonds : angle 3.99038 / 2.74 ( 2475) link_ALPHA1-3 : bond 0.01062 / 0.54 ( 5) link_ALPHA1-3 : angle 2.08483 / 1.35 ( 15) link_ALPHA1-6 : bond 0.01000 / 0.51 ( 5) link_ALPHA1-6 : angle 2.06724 / 1.35 ( 15) link_BETA1-4 : bond 0.00363 / 0.18 ( 15) link_BETA1-4 : angle 1.29979 / 0.91 ( 45) link_NAG-ASN : bond 0.00113 / 0.07 ( 15) link_NAG-ASN : angle 1.37864 / 0.93 ( 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 140 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.611 Fit side-chains REVERT: A 48 ASP cc_start: 0.8656 (m-30) cc_final: 0.8268 (m-30) REVERT: B 48 ASP cc_start: 0.8620 (m-30) cc_final: 0.8152 (m-30) REVERT: B 64 GLN cc_start: 0.9325 (mt0) cc_final: 0.9111 (mp10) REVERT: C 48 ASP cc_start: 0.8617 (m-30) cc_final: 0.8223 (m-30) REVERT: C 224 GLN cc_start: 0.9427 (tp40) cc_final: 0.8857 (tp40) REVERT: D 48 ASP cc_start: 0.8649 (m-30) cc_final: 0.8159 (m-30) REVERT: E 48 ASP cc_start: 0.8642 (m-30) cc_final: 0.8195 (m-30) REVERT: E 68 ARG cc_start: 0.9276 (ttp80) cc_final: 0.9060 (ttt-90) REVERT: E 224 GLN cc_start: 0.9417 (tp40) cc_final: 0.9217 (tp40) REVERT: E 244 TYR cc_start: 0.9118 (p90) cc_final: 0.8848 (p90) outliers start: 7 outliers final: 2 residues processed: 133 average time/residue: 0.6460 time to fit residues: 94.4027 Evaluate side-chains 132 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain B residue 115 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.061013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.044223 restraints weight = 156418.901| |-----------------------------------------------------------------------------| r_work (start): 0.2401 rms_B_bonded: 4.69 r_work: 0.2173 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2165 r_free = 0.2165 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2165 r_free = 0.2165 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9302 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15115 Z= 0.164 Angle : 0.558 9.809 20625 Z= 0.282 Chirality : 0.045 0.247 2400 Planarity : 0.003 0.030 2485 Dihedral : 7.412 52.555 2895 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 0.13 % Allowed : 14.40 % 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 are not related in a simple way. whole: 2.50 (0.21), residues: 1715 helix: 2.71 (0.20), residues: 635 sheet: 1.08 (0.24), residues: 400 loop : 1.16 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.029 0.002 TYR E 299 PHE 0.016 0.001 PHE A 306 TRP 0.009 0.001 TRP C 426 HIS 0.002 0.001 HIS E 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (15070) covalent geometry : angle 0.54463 / 0.28 (20495) SS BOND : bond 0.00184 / 0.09 ( 5) SS BOND : angle 0.58942 / 0.40 ( 10) hydrogen bonds : bond 0.04146 / 2.68 ( 780) hydrogen bonds : angle 4.15495 / 2.86 ( 2475) link_ALPHA1-3 : bond 0.00906 / 0.46 ( 5) link_ALPHA1-3 : angle 2.19078 / 1.43 ( 15) link_ALPHA1-6 : bond 0.00878 / 0.45 ( 5) link_ALPHA1-6 : angle 2.06604 / 1.35 ( 15) link_BETA1-4 : bond 0.00309 / 0.16 ( 15) link_BETA1-4 : angle 1.47296 / 1.02 ( 45) link_NAG-ASN : bond 0.00104 / 0.06 ( 15) link_NAG-ASN : angle 1.57046 / 1.07 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5005.15 seconds wall clock time: 86 minutes 11.12 seconds (5171.12 seconds total)