Starting phenix.real_space_refine on Sat Aug 23 03:15:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bla_16104/08_2025/8bla_16104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bla_16104/08_2025/8bla_16104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bla_16104/08_2025/8bla_16104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bla_16104/08_2025/8bla_16104.map" model { file = "/net/cci-nas-00/data/ceres_data/8bla_16104/08_2025/8bla_16104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bla_16104/08_2025/8bla_16104.cif" } resolution = 3.3 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= 0.001 sd= 0.051 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 6115 2.51 5 N 1515 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9400 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "D" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "E" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} 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: "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: "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: "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: "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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.92, per 1000 atoms: 0.20 Number of scatterers: 9400 At special positions: 0 Unit cell: (95.45, 95.45, 80.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1740 8.00 N 1515 7.00 C 6115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " 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 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 104 " " NAG B 501 " - " ASN B 104 " " NAG C 501 " - " ASN C 104 " " NAG D 501 " - " ASN D 104 " " NAG E 501 " - " ASN E 104 " " NAG F 1 " - " ASN A 186 " " NAG G 1 " - " ASN A 170 " " NAG H 1 " - " ASN B 186 " " NAG I 1 " - " ASN B 170 " " NAG J 1 " - " ASN C 186 " " NAG K 1 " - " ASN C 170 " " NAG L 1 " - " ASN D 186 " " NAG M 1 " - " ASN D 170 " " NAG N 1 " - " ASN E 186 " " NAG O 1 " - " ASN E 170 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 322.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 14.7% alpha, 52.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'B' and resid 32 through 43 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 163 through 166 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 163 through 166 Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'D' and resid 32 through 43 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 163 through 166 Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 192 through 198 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.952A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 154 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.952A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 72 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR A 83 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE A 70 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TRP A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR A 68 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG A 87 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE A 66 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR A 89 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP A 64 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR A 91 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N SER A 62 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.863A pdb=" N SER A 177 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA A 230 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 213 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG A 239 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU A 211 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.952A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 154 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.952A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 72 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR B 83 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE B 70 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TRP B 85 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR B 68 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG B 87 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE B 66 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR B 89 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP B 64 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR B 91 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 9.685A pdb=" N SER B 62 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.863A pdb=" N SER B 177 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 213 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG B 239 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU B 211 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.952A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL C 154 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.952A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN C 72 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR C 83 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE C 70 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TRP C 85 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR C 68 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG C 87 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE C 66 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR C 89 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP C 64 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR C 91 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 9.685A pdb=" N SER C 62 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.862A pdb=" N SER C 177 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA C 230 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 213 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG C 239 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU C 211 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.952A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL D 154 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.952A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN D 72 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR D 83 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE D 70 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TRP D 85 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR D 68 " --> pdb=" O TRP D 85 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG D 87 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE D 66 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR D 89 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP D 64 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR D 91 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N SER D 62 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.863A pdb=" N SER D 177 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA D 230 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 213 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG D 239 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU D 211 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.952A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL E 154 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.952A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN E 72 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR E 83 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE E 70 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TRP E 85 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR E 68 " --> pdb=" O TRP E 85 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG E 87 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE E 66 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR E 89 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP E 64 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR E 91 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N SER E 62 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.862A pdb=" N SER E 177 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA E 230 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY E 213 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG E 239 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU E 211 " --> pdb=" O ARG E 239 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1020 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: 1.37 Time building geometry restraints manager: 0.96 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: 2855 1.34 - 1.46: 2597 1.46 - 1.58: 4173 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 9675 Sorted by residual: bond pdb=" C12 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 1.404 1.450 -0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" C12 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 1.404 1.449 -0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" C12 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 1.404 1.449 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C12 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 1.404 1.449 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C12 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 1.404 1.448 -0.044 2.00e-02 2.50e+03 4.93e+00 ... (remaining 9670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 12899 1.76 - 3.53: 260 3.53 - 5.29: 26 5.29 - 7.06: 10 7.06 - 8.82: 10 Bond angle restraints: 13205 Sorted by residual: angle pdb=" C15 VTX B 502 " pdb=" C14 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 109.33 118.15 -8.82 3.00e+00 1.11e-01 8.64e+00 angle pdb=" C15 VTX A 502 " pdb=" C14 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 109.33 118.15 -8.82 3.00e+00 1.11e-01 8.64e+00 angle pdb=" C15 VTX E 502 " pdb=" C14 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 109.33 118.14 -8.81 3.00e+00 1.11e-01 8.62e+00 angle pdb=" C15 VTX D 502 " pdb=" C14 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 109.33 118.14 -8.81 3.00e+00 1.11e-01 8.62e+00 angle pdb=" C15 VTX C 502 " pdb=" C14 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 109.33 118.13 -8.80 3.00e+00 1.11e-01 8.60e+00 ... (remaining 13200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 5724 25.07 - 50.14: 266 50.14 - 75.21: 50 75.21 - 100.28: 10 100.28 - 125.35: 5 Dihedral angle restraints: 6055 sinusoidal: 2875 harmonic: 3180 Sorted by residual: dihedral pdb=" C15 VTX D 502 " pdb=" C17 VTX D 502 " pdb=" N16 VTX D 502 " pdb=" C18 VTX D 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.03 -125.35 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C15 VTX B 502 " pdb=" C17 VTX B 502 " pdb=" N16 VTX B 502 " pdb=" C18 VTX B 502 " ideal model delta sinusoidal sigma weight residual -69.32 55.98 -125.30 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C15 VTX A 502 " pdb=" C17 VTX A 502 " pdb=" N16 VTX A 502 " pdb=" C18 VTX A 502 " ideal model delta sinusoidal sigma weight residual -69.32 55.96 -125.28 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 6052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 861 0.029 - 0.058: 380 0.058 - 0.087: 63 0.087 - 0.116: 149 0.116 - 0.145: 37 Chirality restraints: 1490 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 170 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 170 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 170 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1487 not shown) Planarity restraints: 1635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 46 " -0.127 9.50e-02 1.11e+02 5.72e-02 2.20e+00 pdb=" NE ARG A 46 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 46 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 46 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 46 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 46 " -0.127 9.50e-02 1.11e+02 5.73e-02 2.19e+00 pdb=" NE ARG C 46 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 46 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 46 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 46 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 46 " -0.127 9.50e-02 1.11e+02 5.71e-02 2.18e+00 pdb=" NE ARG B 46 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 46 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 46 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 46 " -0.002 2.00e-02 2.50e+03 ... (remaining 1632 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1417 2.77 - 3.30: 8573 3.30 - 3.83: 15086 3.83 - 4.37: 18431 4.37 - 4.90: 32574 Nonbonded interactions: 76081 Sorted by model distance: nonbonded pdb=" OD2 ASP A 167 " pdb=" NE2 GLN A 169 " model vdw 2.234 3.120 nonbonded pdb=" OD2 ASP B 167 " pdb=" NE2 GLN B 169 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP D 167 " pdb=" NE2 GLN D 169 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP E 167 " pdb=" NE2 GLN E 169 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP C 167 " pdb=" NE2 GLN C 169 " model vdw 2.235 3.120 ... (remaining 76076 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=1.00 max=1.00 mean=1.00 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: 1.480 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.600 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9705 Z= 0.213 Angle : 0.651 8.821 13290 Z= 0.288 Chirality : 0.047 0.145 1490 Planarity : 0.005 0.057 1620 Dihedral : 15.400 125.353 3980 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.26), residues: 1045 helix: -0.41 (0.57), residues: 95 sheet: -0.75 (0.24), residues: 395 loop : -0.89 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 46 TYR 0.009 0.001 TYR C 89 PHE 0.007 0.001 PHE C 221 TRP 0.004 0.001 TRP B 190 HIS 0.001 0.000 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9675) covalent geometry : angle 0.64791 (13205) SS BOND : bond 0.00146 ( 5) SS BOND : angle 0.29140 ( 10) hydrogen bonds : bond 0.21399 ( 290) hydrogen bonds : angle 9.04104 ( 1020) link_BETA1-4 : bond 0.00109 ( 10) link_BETA1-4 : angle 1.09335 ( 30) link_NAG-ASN : bond 0.00085 ( 15) link_NAG-ASN : angle 1.04548 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.330 Fit side-chains REVERT: A 149 LYS cc_start: 0.8488 (ptmt) cc_final: 0.7907 (pttt) REVERT: B 46 ARG cc_start: 0.7125 (ptp90) cc_final: 0.6801 (ptm-80) REVERT: B 223 MET cc_start: 0.8159 (mmm) cc_final: 0.7760 (mmt) REVERT: C 46 ARG cc_start: 0.6980 (ptp90) cc_final: 0.6627 (ptm-80) REVERT: C 94 PHE cc_start: 0.8588 (m-10) cc_final: 0.8290 (m-10) REVERT: C 101 ASP cc_start: 0.8807 (t0) cc_final: 0.8588 (t70) REVERT: D 46 ARG cc_start: 0.6991 (ptp90) cc_final: 0.6605 (ptm-80) REVERT: E 46 ARG cc_start: 0.7041 (ptp90) cc_final: 0.6638 (ptm-80) REVERT: E 149 LYS cc_start: 0.8322 (ptmt) cc_final: 0.8025 (pttt) REVERT: E 197 LYS cc_start: 0.7380 (ttpp) cc_final: 0.6816 (ttpt) REVERT: E 232 MET cc_start: 0.8574 (tpp) cc_final: 0.8177 (ttm) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1084 time to fit residues: 14.2251 Evaluate side-chains 88 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN C 123 ASN C 152 GLN D 123 ASN D 152 GLN E 152 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.116180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.100742 restraints weight = 12194.915| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.97 r_work: 0.2931 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9705 Z= 0.129 Angle : 0.593 5.928 13290 Z= 0.310 Chirality : 0.049 0.143 1490 Planarity : 0.004 0.033 1620 Dihedral : 11.085 117.592 1795 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.19 % Allowed : 12.48 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.26), residues: 1045 helix: 0.03 (0.57), residues: 95 sheet: -0.99 (0.23), residues: 395 loop : -0.75 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 140 TYR 0.014 0.001 TYR B 89 PHE 0.014 0.001 PHE D 221 TRP 0.005 0.001 TRP E 190 HIS 0.001 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9675) covalent geometry : angle 0.58646 (13205) SS BOND : bond 0.00370 ( 5) SS BOND : angle 0.37869 ( 10) hydrogen bonds : bond 0.04481 ( 290) hydrogen bonds : angle 6.01244 ( 1020) link_BETA1-4 : bond 0.00056 ( 10) link_BETA1-4 : angle 1.19302 ( 30) link_NAG-ASN : bond 0.00231 ( 15) link_NAG-ASN : angle 1.37360 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.257 Fit side-chains REVERT: A 149 LYS cc_start: 0.8111 (ptmt) cc_final: 0.7507 (pttt) REVERT: B 232 MET cc_start: 0.8549 (tpp) cc_final: 0.8301 (ttm) REVERT: C 46 ARG cc_start: 0.7075 (ptp90) cc_final: 0.6534 (ptm160) REVERT: C 94 PHE cc_start: 0.8494 (m-10) cc_final: 0.8289 (m-10) REVERT: D 100 GLU cc_start: 0.8097 (pm20) cc_final: 0.7861 (pm20) REVERT: E 232 MET cc_start: 0.8581 (tpp) cc_final: 0.8253 (ttm) outliers start: 12 outliers final: 12 residues processed: 100 average time/residue: 0.0954 time to fit residues: 13.0949 Evaluate side-chains 95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.114816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.099289 restraints weight = 12303.816| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.98 r_work: 0.2905 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9705 Z= 0.149 Angle : 0.567 6.390 13290 Z= 0.292 Chirality : 0.048 0.154 1490 Planarity : 0.004 0.032 1620 Dihedral : 11.066 119.428 1795 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.67 % Allowed : 11.39 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.26), residues: 1045 helix: 0.39 (0.57), residues: 95 sheet: -0.89 (0.21), residues: 485 loop : -0.73 (0.32), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 219 TYR 0.013 0.001 TYR D 89 PHE 0.015 0.001 PHE E 221 TRP 0.008 0.001 TRP B 178 HIS 0.001 0.000 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9675) covalent geometry : angle 0.55903 (13205) SS BOND : bond 0.00257 ( 5) SS BOND : angle 0.68776 ( 10) hydrogen bonds : bond 0.03997 ( 290) hydrogen bonds : angle 5.55922 ( 1020) link_BETA1-4 : bond 0.00139 ( 10) link_BETA1-4 : angle 1.26177 ( 30) link_NAG-ASN : bond 0.00155 ( 15) link_NAG-ASN : angle 1.42693 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.269 Fit side-chains REVERT: A 56 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8719 (ttm110) REVERT: B 232 MET cc_start: 0.8550 (tpp) cc_final: 0.8294 (ttm) REVERT: C 46 ARG cc_start: 0.7146 (ptp90) cc_final: 0.6464 (ptm160) REVERT: C 56 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8713 (ttm110) REVERT: C 130 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8374 (mttp) REVERT: D 56 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7754 (mtm110) REVERT: E 46 ARG cc_start: 0.7301 (ptp90) cc_final: 0.7032 (ptp90) REVERT: E 56 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.7470 (mtm110) REVERT: E 232 MET cc_start: 0.8483 (tpp) cc_final: 0.8190 (ttm) outliers start: 27 outliers final: 21 residues processed: 116 average time/residue: 0.1097 time to fit residues: 16.7824 Evaluate side-chains 109 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 76 optimal weight: 0.0030 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN E 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.116192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.099857 restraints weight = 12321.583| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.08 r_work: 0.2908 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9705 Z= 0.121 Angle : 0.543 5.777 13290 Z= 0.278 Chirality : 0.047 0.145 1490 Planarity : 0.004 0.030 1620 Dihedral : 10.868 118.357 1795 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.37 % Allowed : 12.77 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.26), residues: 1045 helix: 0.58 (0.57), residues: 95 sheet: -0.91 (0.22), residues: 485 loop : -0.80 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 31 TYR 0.012 0.001 TYR D 89 PHE 0.012 0.001 PHE E 221 TRP 0.007 0.001 TRP B 178 HIS 0.001 0.000 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9675) covalent geometry : angle 0.53583 (13205) SS BOND : bond 0.00223 ( 5) SS BOND : angle 0.46538 ( 10) hydrogen bonds : bond 0.03392 ( 290) hydrogen bonds : angle 5.32488 ( 1020) link_BETA1-4 : bond 0.00200 ( 10) link_BETA1-4 : angle 1.17131 ( 30) link_NAG-ASN : bond 0.00148 ( 15) link_NAG-ASN : angle 1.33477 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.348 Fit side-chains REVERT: C 56 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8587 (ttm110) REVERT: C 130 LYS cc_start: 0.8635 (mmtp) cc_final: 0.8406 (mttp) REVERT: D 56 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7743 (mtm110) REVERT: D 93 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 197 LYS cc_start: 0.6659 (ttpp) cc_final: 0.6374 (ttmt) REVERT: E 56 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7556 (mtm110) REVERT: E 93 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8400 (mt-10) REVERT: E 197 LYS cc_start: 0.6562 (ttpp) cc_final: 0.6080 (ttpt) outliers start: 34 outliers final: 26 residues processed: 135 average time/residue: 0.1052 time to fit residues: 19.1099 Evaluate side-chains 124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.098156 restraints weight = 12402.255| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.13 r_work: 0.2887 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9705 Z= 0.156 Angle : 0.568 6.264 13290 Z= 0.290 Chirality : 0.048 0.150 1490 Planarity : 0.004 0.029 1620 Dihedral : 10.964 119.406 1795 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.56 % Allowed : 12.48 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.25), residues: 1045 helix: 0.73 (0.58), residues: 95 sheet: -1.01 (0.23), residues: 430 loop : -0.86 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 31 TYR 0.014 0.001 TYR D 89 PHE 0.012 0.001 PHE B 221 TRP 0.008 0.001 TRP B 178 HIS 0.001 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9675) covalent geometry : angle 0.56030 (13205) SS BOND : bond 0.00235 ( 5) SS BOND : angle 0.60288 ( 10) hydrogen bonds : bond 0.03428 ( 290) hydrogen bonds : angle 5.27282 ( 1020) link_BETA1-4 : bond 0.00080 ( 10) link_BETA1-4 : angle 1.25600 ( 30) link_NAG-ASN : bond 0.00218 ( 15) link_NAG-ASN : angle 1.41181 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.373 Fit side-chains REVERT: A 56 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.7852 (mtm110) REVERT: B 184 ASP cc_start: 0.8045 (m-30) cc_final: 0.7797 (m-30) REVERT: C 56 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8609 (ttm110) REVERT: C 130 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8378 (mttp) REVERT: D 56 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7707 (mtm110) REVERT: D 197 LYS cc_start: 0.6597 (ttpp) cc_final: 0.6344 (ttmt) REVERT: E 56 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7546 (mtm110) REVERT: E 197 LYS cc_start: 0.6499 (ttpp) cc_final: 0.6037 (ttpt) outliers start: 36 outliers final: 29 residues processed: 129 average time/residue: 0.1061 time to fit residues: 17.9724 Evaluate side-chains 126 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.115001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.098335 restraints weight = 12485.885| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.11 r_work: 0.2894 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9705 Z= 0.149 Angle : 0.561 6.214 13290 Z= 0.286 Chirality : 0.048 0.149 1490 Planarity : 0.004 0.029 1620 Dihedral : 10.924 119.566 1795 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.96 % Allowed : 11.98 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.25), residues: 1045 helix: 0.81 (0.58), residues: 95 sheet: -1.02 (0.23), residues: 430 loop : -0.90 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 31 TYR 0.013 0.001 TYR D 89 PHE 0.012 0.001 PHE B 221 TRP 0.008 0.001 TRP B 178 HIS 0.001 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9675) covalent geometry : angle 0.55340 (13205) SS BOND : bond 0.00194 ( 5) SS BOND : angle 0.63577 ( 10) hydrogen bonds : bond 0.03320 ( 290) hydrogen bonds : angle 5.18675 ( 1020) link_BETA1-4 : bond 0.00103 ( 10) link_BETA1-4 : angle 1.22133 ( 30) link_NAG-ASN : bond 0.00212 ( 15) link_NAG-ASN : angle 1.38186 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 94 time to evaluate : 0.242 Fit side-chains REVERT: A 56 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7975 (mtm110) REVERT: C 56 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.7991 (mtm110) REVERT: C 130 LYS cc_start: 0.8650 (mmtp) cc_final: 0.8419 (mttp) REVERT: D 56 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.7780 (mtm110) REVERT: D 197 LYS cc_start: 0.6705 (ttpp) cc_final: 0.6445 (ttmt) REVERT: E 56 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.7587 (mtm110) REVERT: E 197 LYS cc_start: 0.6580 (ttpp) cc_final: 0.6096 (ttpt) outliers start: 40 outliers final: 31 residues processed: 129 average time/residue: 0.1027 time to fit residues: 17.5914 Evaluate side-chains 124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.0470 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.115814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.099428 restraints weight = 12347.962| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.10 r_work: 0.2906 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9705 Z= 0.118 Angle : 0.541 5.781 13290 Z= 0.277 Chirality : 0.047 0.146 1490 Planarity : 0.004 0.028 1620 Dihedral : 10.798 118.485 1795 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.66 % Allowed : 11.78 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.25), residues: 1045 helix: 0.71 (0.57), residues: 95 sheet: -1.03 (0.23), residues: 430 loop : -0.88 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 31 TYR 0.019 0.001 TYR E 86 PHE 0.011 0.001 PHE A 221 TRP 0.007 0.001 TRP B 178 HIS 0.001 0.000 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9675) covalent geometry : angle 0.53521 (13205) SS BOND : bond 0.00180 ( 5) SS BOND : angle 0.41646 ( 10) hydrogen bonds : bond 0.03115 ( 290) hydrogen bonds : angle 5.02982 ( 1020) link_BETA1-4 : bond 0.00178 ( 10) link_BETA1-4 : angle 1.14440 ( 30) link_NAG-ASN : bond 0.00145 ( 15) link_NAG-ASN : angle 1.27248 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.290 Fit side-chains REVERT: A 56 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.7931 (mtm110) REVERT: B 184 ASP cc_start: 0.8014 (m-30) cc_final: 0.7755 (m-30) REVERT: C 56 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8006 (mtm110) REVERT: C 130 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8451 (mttp) REVERT: D 56 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.7783 (mtm110) REVERT: D 197 LYS cc_start: 0.6596 (ttpp) cc_final: 0.6332 (ttmt) REVERT: E 56 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7623 (mtm110) REVERT: E 93 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8316 (mt-10) REVERT: E 197 LYS cc_start: 0.6697 (ttpp) cc_final: 0.6044 (ttpt) outliers start: 37 outliers final: 31 residues processed: 131 average time/residue: 0.0941 time to fit residues: 16.5674 Evaluate side-chains 123 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.115272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099133 restraints weight = 12338.589| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.07 r_work: 0.2911 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9705 Z= 0.129 Angle : 0.553 5.870 13290 Z= 0.281 Chirality : 0.047 0.148 1490 Planarity : 0.004 0.028 1620 Dihedral : 10.834 119.181 1795 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.86 % Allowed : 12.08 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.25), residues: 1045 helix: 0.67 (0.57), residues: 95 sheet: -1.05 (0.23), residues: 430 loop : -0.94 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 31 TYR 0.016 0.001 TYR E 86 PHE 0.011 0.001 PHE E 221 TRP 0.008 0.001 TRP E 178 HIS 0.001 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9675) covalent geometry : angle 0.54599 (13205) SS BOND : bond 0.00179 ( 5) SS BOND : angle 0.47755 ( 10) hydrogen bonds : bond 0.03126 ( 290) hydrogen bonds : angle 5.02067 ( 1020) link_BETA1-4 : bond 0.00148 ( 10) link_BETA1-4 : angle 1.18595 ( 30) link_NAG-ASN : bond 0.00176 ( 15) link_NAG-ASN : angle 1.30797 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.265 Fit side-chains REVERT: A 56 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.7966 (mtm110) REVERT: B 184 ASP cc_start: 0.8021 (m-30) cc_final: 0.7760 (m-30) REVERT: C 56 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8007 (mtm110) REVERT: C 130 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8463 (mttp) REVERT: D 56 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.7795 (mtm110) REVERT: D 197 LYS cc_start: 0.6636 (ttpp) cc_final: 0.6368 (ttmt) REVERT: E 56 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.7638 (mtm110) REVERT: E 197 LYS cc_start: 0.6715 (ttpp) cc_final: 0.6063 (ttpt) outliers start: 39 outliers final: 34 residues processed: 124 average time/residue: 0.1063 time to fit residues: 17.5824 Evaluate side-chains 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 76 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.114040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.097626 restraints weight = 12429.384| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.08 r_work: 0.2894 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9705 Z= 0.160 Angle : 0.573 6.432 13290 Z= 0.291 Chirality : 0.048 0.154 1490 Planarity : 0.004 0.030 1620 Dihedral : 10.932 119.906 1795 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.16 % Allowed : 11.98 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.25), residues: 1045 helix: 0.66 (0.57), residues: 95 sheet: -1.08 (0.23), residues: 430 loop : -1.01 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 31 TYR 0.017 0.001 TYR E 86 PHE 0.013 0.001 PHE E 221 TRP 0.009 0.001 TRP B 178 HIS 0.002 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9675) covalent geometry : angle 0.56508 (13205) SS BOND : bond 0.00199 ( 5) SS BOND : angle 0.67636 ( 10) hydrogen bonds : bond 0.03274 ( 290) hydrogen bonds : angle 5.08574 ( 1020) link_BETA1-4 : bond 0.00072 ( 10) link_BETA1-4 : angle 1.26818 ( 30) link_NAG-ASN : bond 0.00249 ( 15) link_NAG-ASN : angle 1.41468 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 0.342 Fit side-chains REVERT: A 46 ARG cc_start: 0.7212 (ptp90) cc_final: 0.6800 (ptp90) REVERT: A 56 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.7976 (mtm110) REVERT: C 56 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8046 (mtm110) REVERT: C 93 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8418 (mt-10) REVERT: C 130 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8437 (mttp) REVERT: D 56 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.7813 (mtm110) REVERT: D 93 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8323 (mt-10) REVERT: D 197 LYS cc_start: 0.6654 (ttpp) cc_final: 0.6394 (ttmt) REVERT: D 233 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7687 (mtpp) REVERT: E 56 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.7718 (mtm110) REVERT: E 197 LYS cc_start: 0.6743 (ttpp) cc_final: 0.6090 (ttpt) outliers start: 42 outliers final: 35 residues processed: 133 average time/residue: 0.1245 time to fit residues: 21.6503 Evaluate side-chains 141 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.115706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.099274 restraints weight = 12333.803| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.08 r_work: 0.2915 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9705 Z= 0.121 Angle : 0.551 6.069 13290 Z= 0.281 Chirality : 0.047 0.149 1490 Planarity : 0.004 0.032 1620 Dihedral : 10.781 118.737 1795 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.76 % Allowed : 11.98 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.25), residues: 1045 helix: 0.56 (0.56), residues: 95 sheet: -1.08 (0.23), residues: 430 loop : -0.97 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 56 TYR 0.020 0.001 TYR E 86 PHE 0.012 0.001 PHE A 221 TRP 0.007 0.001 TRP B 178 HIS 0.002 0.000 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9675) covalent geometry : angle 0.54501 (13205) SS BOND : bond 0.00155 ( 5) SS BOND : angle 0.38799 ( 10) hydrogen bonds : bond 0.03111 ( 290) hydrogen bonds : angle 5.01278 ( 1020) link_BETA1-4 : bond 0.00189 ( 10) link_BETA1-4 : angle 1.12870 ( 30) link_NAG-ASN : bond 0.00156 ( 15) link_NAG-ASN : angle 1.26817 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.315 Fit side-chains REVERT: A 56 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8001 (mtm110) REVERT: B 56 ARG cc_start: 0.8935 (ttm110) cc_final: 0.8648 (ttm110) REVERT: B 103 ASP cc_start: 0.8490 (t0) cc_final: 0.8198 (t0) REVERT: C 93 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8410 (mt-10) REVERT: C 130 LYS cc_start: 0.8676 (mmtp) cc_final: 0.8465 (mttp) REVERT: D 56 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.7801 (mtm110) REVERT: D 93 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8304 (mt-10) REVERT: D 197 LYS cc_start: 0.6644 (ttpp) cc_final: 0.6390 (ttmt) REVERT: D 233 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7692 (mtpp) REVERT: E 56 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.7708 (mtm110) REVERT: E 197 LYS cc_start: 0.6750 (ttpp) cc_final: 0.6148 (ttpt) outliers start: 38 outliers final: 34 residues processed: 136 average time/residue: 0.0991 time to fit residues: 18.1709 Evaluate side-chains 136 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.114492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.098567 restraints weight = 12275.794| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.06 r_work: 0.2903 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9705 Z= 0.136 Angle : 0.563 6.116 13290 Z= 0.288 Chirality : 0.048 0.150 1490 Planarity : 0.004 0.040 1620 Dihedral : 10.839 119.315 1795 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.76 % Allowed : 12.18 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.25), residues: 1045 helix: 0.59 (0.57), residues: 95 sheet: -1.09 (0.23), residues: 430 loop : -1.01 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 56 TYR 0.020 0.001 TYR E 86 PHE 0.013 0.001 PHE A 221 TRP 0.008 0.001 TRP B 178 HIS 0.002 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9675) covalent geometry : angle 0.55679 (13205) SS BOND : bond 0.00167 ( 5) SS BOND : angle 0.49678 ( 10) hydrogen bonds : bond 0.03150 ( 290) hydrogen bonds : angle 5.01520 ( 1020) link_BETA1-4 : bond 0.00145 ( 10) link_BETA1-4 : angle 1.19247 ( 30) link_NAG-ASN : bond 0.00180 ( 15) link_NAG-ASN : angle 1.31753 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1810.54 seconds wall clock time: 31 minutes 39.18 seconds (1899.18 seconds total)