Starting phenix.real_space_refine on Fri Mar 14 00:28:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bla_16104/03_2025/8bla_16104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bla_16104/03_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_16104/03_2025/8bla_16104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bla_16104/03_2025/8bla_16104.map" model { file = "/net/cci-nas-00/data/ceres_data/8bla_16104/03_2025/8bla_16104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bla_16104/03_2025/8bla_16104.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.20, per 1000 atoms: 0.66 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: 2.69 Conformation dependent library (CDL) restraints added in 990.6 milliseconds 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: 1.17 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: 2.73 Time building geometry restraints manager: 3.17 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: 0.06 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: 1.300 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.200 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.010 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.550 ------------------------------------------------------------------------------- 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 9675 Z= 0.266 Angle : 0.648 8.821 13205 Z= 0.287 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP B 190 HIS 0.001 0.000 HIS E 141 PHE 0.007 0.001 PHE C 221 TYR 0.009 0.001 TYR C 89 ARG 0.008 0.001 ARG A 46 *********************** 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 : 1.136 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: 0.2634 time to fit residues: 35.3072 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 : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 152 GLN D 152 GLN E 152 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.113453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.098075 restraints weight = 12236.883| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.95 r_work: 0.2914 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9675 Z= 0.296 Angle : 0.619 6.823 13205 Z= 0.326 Chirality : 0.050 0.152 1490 Planarity : 0.004 0.033 1620 Dihedral : 11.334 120.901 1795 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.18 % Allowed : 12.48 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.26), residues: 1045 helix: 0.07 (0.57), residues: 95 sheet: -1.16 (0.23), residues: 420 loop : -0.78 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 190 HIS 0.002 0.001 HIS E 141 PHE 0.015 0.002 PHE D 221 TYR 0.016 0.002 TYR B 89 ARG 0.002 0.000 ARG C 31 *********************** 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 113 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.107 Fit side-chains REVERT: A 149 LYS cc_start: 0.8288 (ptmt) cc_final: 0.7901 (pttt) REVERT: B 46 ARG cc_start: 0.7277 (ptp90) cc_final: 0.7004 (ptp90) REVERT: B 232 MET cc_start: 0.8598 (tpp) cc_final: 0.8377 (ttm) REVERT: C 46 ARG cc_start: 0.7241 (ptp90) cc_final: 0.6701 (ptm-80) REVERT: E 46 ARG cc_start: 0.7399 (ptp90) cc_final: 0.6712 (ptm160) REVERT: E 232 MET cc_start: 0.8637 (tpp) cc_final: 0.8343 (ttm) outliers start: 22 outliers final: 21 residues processed: 112 average time/residue: 0.2613 time to fit residues: 39.5070 Evaluate side-chains 107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 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 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 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 122 ILE Chi-restraints excluded: chain E residue 154 VAL 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 70 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.0070 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 123 ASN C 123 ASN D 123 ASN E 123 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.116878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.100419 restraints weight = 12256.384| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.10 r_work: 0.2911 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9675 Z= 0.187 Angle : 0.552 6.128 13205 Z= 0.286 Chirality : 0.048 0.144 1490 Planarity : 0.004 0.029 1620 Dihedral : 10.924 117.919 1795 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.08 % Allowed : 12.18 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.26), residues: 1045 helix: 0.37 (0.56), residues: 95 sheet: -1.31 (0.22), residues: 420 loop : -0.73 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.001 0.000 HIS E 141 PHE 0.013 0.001 PHE E 221 TYR 0.012 0.001 TYR D 89 ARG 0.001 0.000 ARG D 140 *********************** 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 118 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.969 Fit side-chains REVERT: A 56 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8721 (ttm110) REVERT: B 232 MET cc_start: 0.8497 (tpp) cc_final: 0.8284 (ttm) REVERT: C 46 ARG cc_start: 0.7076 (ptp90) cc_final: 0.6366 (ptm160) REVERT: C 56 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8775 (ttm110) REVERT: C 130 LYS cc_start: 0.8480 (mmtp) cc_final: 0.8248 (mttp) REVERT: D 56 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7732 (mtm110) REVERT: D 197 LYS cc_start: 0.6688 (ttpp) cc_final: 0.6354 (ttmt) REVERT: E 56 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7492 (mtm110) outliers start: 21 outliers final: 16 residues processed: 117 average time/residue: 0.2694 time to fit residues: 41.7390 Evaluate side-chains 105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 43 THR 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 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 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 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 75 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 102 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 94 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.116922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.100502 restraints weight = 12131.746| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.08 r_work: 0.2918 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9675 Z= 0.173 Angle : 0.530 5.722 13205 Z= 0.274 Chirality : 0.047 0.145 1490 Planarity : 0.004 0.030 1620 Dihedral : 10.858 118.029 1795 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.26), residues: 1045 helix: 0.56 (0.57), residues: 95 sheet: -1.28 (0.23), residues: 420 loop : -0.77 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 178 HIS 0.001 0.000 HIS D 180 PHE 0.013 0.001 PHE E 221 TYR 0.012 0.001 TYR D 89 ARG 0.002 0.000 ARG B 46 *********************** 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 137 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 1.013 Fit side-chains REVERT: A 56 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.7876 (mtm110) REVERT: B 197 LYS cc_start: 0.6579 (ttpp) cc_final: 0.6306 (ttmt) REVERT: C 56 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8579 (ttm110) REVERT: C 130 LYS cc_start: 0.8604 (mmtp) cc_final: 0.8380 (mttp) REVERT: D 56 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7728 (mtm110) REVERT: D 93 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 197 LYS cc_start: 0.6582 (ttpp) cc_final: 0.6313 (ttmt) REVERT: E 56 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.7458 (mtm110) REVERT: E 93 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8494 (mt-10) REVERT: E 197 LYS cc_start: 0.6505 (ttpp) cc_final: 0.6032 (ttpt) outliers start: 34 outliers final: 26 residues processed: 136 average time/residue: 0.2605 time to fit residues: 47.2545 Evaluate side-chains 125 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 40 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.0040 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.114929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.099091 restraints weight = 12313.243| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.02 r_work: 0.2951 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9675 Z= 0.222 Angle : 0.551 6.184 13205 Z= 0.284 Chirality : 0.048 0.149 1490 Planarity : 0.004 0.030 1620 Dihedral : 10.925 119.199 1795 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.86 % Allowed : 12.38 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.26), residues: 1045 helix: 0.74 (0.58), residues: 95 sheet: -0.97 (0.23), residues: 430 loop : -0.85 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 178 HIS 0.001 0.000 HIS D 180 PHE 0.012 0.001 PHE B 221 TYR 0.013 0.001 TYR D 89 ARG 0.003 0.000 ARG B 31 *********************** 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 139 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.971 Fit side-chains REVERT: A 56 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8066 (mtm110) REVERT: B 184 ASP cc_start: 0.8159 (m-30) cc_final: 0.7906 (m-30) REVERT: B 197 LYS cc_start: 0.7005 (ttpp) cc_final: 0.6496 (ttpt) REVERT: C 56 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8733 (ttm110) REVERT: C 130 LYS cc_start: 0.8754 (mmtp) cc_final: 0.8489 (mttp) REVERT: D 56 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.7816 (mtm110) REVERT: D 197 LYS cc_start: 0.6959 (ttpp) cc_final: 0.6660 (ttmt) REVERT: E 56 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.7719 (mtm110) REVERT: E 197 LYS cc_start: 0.6765 (ttpp) cc_final: 0.6275 (ttpt) outliers start: 39 outliers final: 29 residues processed: 135 average time/residue: 0.2879 time to fit residues: 51.2252 Evaluate side-chains 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 98 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 0.0030 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 8 optimal weight: 0.0000 chunk 27 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.116541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.099967 restraints weight = 12259.652| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.11 r_work: 0.2915 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9675 Z= 0.197 Angle : 0.543 5.904 13205 Z= 0.280 Chirality : 0.047 0.146 1490 Planarity : 0.004 0.028 1620 Dihedral : 10.844 118.791 1795 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.76 % Allowed : 11.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.25), residues: 1045 helix: 0.80 (0.58), residues: 95 sheet: -1.02 (0.23), residues: 430 loop : -0.89 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.001 0.000 HIS D 180 PHE 0.013 0.001 PHE A 221 TYR 0.012 0.001 TYR D 89 ARG 0.006 0.000 ARG A 31 *********************** 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 131 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.969 Fit side-chains REVERT: A 56 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7971 (mtm110) REVERT: B 184 ASP cc_start: 0.8081 (m-30) cc_final: 0.7818 (m-30) REVERT: C 56 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8050 (mtm110) REVERT: C 130 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8424 (mttp) REVERT: D 56 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7779 (mtm110) REVERT: D 93 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8367 (mt-10) REVERT: D 197 LYS cc_start: 0.6776 (ttpp) cc_final: 0.6516 (ttmt) REVERT: D 233 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7705 (mtpp) REVERT: E 56 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.7711 (mtm110) REVERT: E 197 LYS cc_start: 0.6604 (ttpp) cc_final: 0.6153 (ttpt) outliers start: 38 outliers final: 32 residues processed: 125 average time/residue: 0.2774 time to fit residues: 45.4619 Evaluate side-chains 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 98 ASN 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 86 optimal weight: 0.3980 chunk 43 optimal weight: 0.0570 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 overall best weight: 0.3498 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.117109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.101322 restraints weight = 12333.900| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.07 r_work: 0.2937 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9675 Z= 0.138 Angle : 0.517 5.601 13205 Z= 0.266 Chirality : 0.047 0.141 1490 Planarity : 0.004 0.028 1620 Dihedral : 10.690 117.565 1795 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.56 % Allowed : 11.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.25), residues: 1045 helix: 0.71 (0.57), residues: 95 sheet: -1.00 (0.23), residues: 430 loop : -0.83 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 178 HIS 0.001 0.000 HIS E 141 PHE 0.010 0.001 PHE E 221 TYR 0.009 0.001 TYR E 89 ARG 0.006 0.000 ARG A 31 *********************** 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 142 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 1.019 Fit side-chains REVERT: A 56 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8076 (mtm110) REVERT: A 231 GLU cc_start: 0.8084 (pt0) cc_final: 0.7750 (pt0) REVERT: B 184 ASP cc_start: 0.8034 (m-30) cc_final: 0.7784 (m-30) REVERT: C 56 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8056 (mtm110) REVERT: C 130 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8434 (mttp) REVERT: D 56 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7757 (mtm110) REVERT: D 93 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8286 (mt-10) REVERT: D 197 LYS cc_start: 0.6712 (ttpp) cc_final: 0.6466 (ttmt) REVERT: E 56 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.7606 (mtm110) REVERT: E 93 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8267 (mt-10) REVERT: E 197 LYS cc_start: 0.6650 (ttpp) cc_final: 0.5998 (ttpt) outliers start: 36 outliers final: 28 residues processed: 139 average time/residue: 0.2588 time to fit residues: 48.4020 Evaluate side-chains 123 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.116379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.099921 restraints weight = 12416.418| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.10 r_work: 0.2920 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9675 Z= 0.203 Angle : 0.543 6.046 13205 Z= 0.279 Chirality : 0.047 0.147 1490 Planarity : 0.004 0.027 1620 Dihedral : 10.840 119.330 1795 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.25), residues: 1045 helix: 0.75 (0.57), residues: 95 sheet: -1.03 (0.23), residues: 430 loop : -0.90 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.002 0.001 HIS E 141 PHE 0.011 0.001 PHE E 221 TYR 0.013 0.001 TYR C 89 ARG 0.006 0.000 ARG A 31 *********************** 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 133 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 1.065 Fit side-chains REVERT: A 56 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8081 (mtm110) REVERT: B 184 ASP cc_start: 0.8019 (m-30) cc_final: 0.7754 (m-30) REVERT: C 56 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8039 (mtm110) REVERT: C 130 LYS cc_start: 0.8639 (mmtp) cc_final: 0.8433 (mttp) REVERT: D 31 ARG cc_start: 0.7360 (mtp180) cc_final: 0.7098 (tpt-90) REVERT: D 56 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7770 (mtm110) REVERT: D 197 LYS cc_start: 0.6626 (ttpp) cc_final: 0.6381 (ttmt) REVERT: D 233 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7728 (mtpp) REVERT: E 56 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.7636 (mtm110) REVERT: E 142 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8146 (mm-40) REVERT: E 197 LYS cc_start: 0.6709 (ttpp) cc_final: 0.6068 (ttpt) outliers start: 39 outliers final: 32 residues processed: 129 average time/residue: 0.2767 time to fit residues: 47.8383 Evaluate side-chains 127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 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 138 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 2 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.0370 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.118050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.101371 restraints weight = 12328.518| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.13 r_work: 0.2939 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9675 Z= 0.154 Angle : 0.525 5.707 13205 Z= 0.270 Chirality : 0.047 0.142 1490 Planarity : 0.004 0.028 1620 Dihedral : 10.697 117.940 1795 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.47 % Allowed : 12.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.25), residues: 1045 helix: 0.64 (0.56), residues: 95 sheet: -1.04 (0.23), residues: 430 loop : -0.87 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 178 HIS 0.002 0.000 HIS E 141 PHE 0.011 0.001 PHE E 221 TYR 0.010 0.001 TYR D 89 ARG 0.005 0.000 ARG A 31 *********************** 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 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 1.062 Fit side-chains REVERT: A 56 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8097 (mtm110) REVERT: B 184 ASP cc_start: 0.8031 (m-30) cc_final: 0.7765 (m-30) REVERT: C 56 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8012 (mtm110) REVERT: D 31 ARG cc_start: 0.7398 (mtp180) cc_final: 0.7137 (tpt-90) REVERT: D 56 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.7774 (mtm110) REVERT: D 93 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8290 (mt-10) REVERT: D 197 LYS cc_start: 0.6578 (ttpp) cc_final: 0.6327 (ttmt) REVERT: D 233 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7689 (mtpp) REVERT: E 56 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7635 (mtm110) REVERT: E 142 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8100 (mm-40) REVERT: E 197 LYS cc_start: 0.6677 (ttpp) cc_final: 0.6077 (ttpt) outliers start: 35 outliers final: 29 residues processed: 126 average time/residue: 0.2564 time to fit residues: 43.4315 Evaluate side-chains 123 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain B residue 154 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 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 = 0.3226 r_free = 0.3226 target = 0.116280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.099925 restraints weight = 12450.143| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.08 r_work: 0.2922 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9675 Z= 0.206 Angle : 0.540 5.970 13205 Z= 0.277 Chirality : 0.047 0.146 1490 Planarity : 0.004 0.027 1620 Dihedral : 10.812 119.181 1795 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.25), residues: 1045 helix: -0.67 (0.48), residues: 125 sheet: -1.04 (0.23), residues: 430 loop : -1.02 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.002 0.001 HIS E 141 PHE 0.011 0.001 PHE E 221 TYR 0.012 0.001 TYR D 89 ARG 0.005 0.000 ARG A 31 ********************** 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 127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 1.426 Fit side-chains REVERT: A 56 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8139 (mtm110) REVERT: A 100 GLU cc_start: 0.7803 (pm20) cc_final: 0.7590 (pm20) REVERT: A 197 LYS cc_start: 0.6702 (ttpp) cc_final: 0.6135 (ttmt) REVERT: C 56 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8041 (mtm110) REVERT: C 93 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8395 (mt-10) REVERT: D 31 ARG cc_start: 0.7526 (mtp180) cc_final: 0.7259 (tpt-90) REVERT: D 56 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7789 (mtm110) REVERT: D 93 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8347 (mt-10) REVERT: D 197 LYS cc_start: 0.6630 (ttpp) cc_final: 0.6372 (ttmt) REVERT: D 233 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7707 (mtpp) REVERT: E 56 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.7655 (mtm110) REVERT: E 197 LYS cc_start: 0.6734 (ttpp) cc_final: 0.6141 (ttpt) outliers start: 34 outliers final: 30 residues processed: 124 average time/residue: 0.3246 time to fit residues: 55.7281 Evaluate side-chains 126 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain B residue 154 VAL 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 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 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 54 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.116418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.099917 restraints weight = 12275.495| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.08 r_work: 0.2917 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9675 Z= 0.205 Angle : 0.538 6.014 13205 Z= 0.276 Chirality : 0.047 0.147 1490 Planarity : 0.004 0.028 1620 Dihedral : 10.797 119.167 1795 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.25), residues: 1045 helix: -0.67 (0.48), residues: 125 sheet: -1.07 (0.23), residues: 430 loop : -1.02 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 178 HIS 0.002 0.001 HIS E 141 PHE 0.011 0.001 PHE E 221 TYR 0.012 0.001 TYR D 89 ARG 0.005 0.000 ARG A 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.92 seconds wall clock time: 79 minutes 27.77 seconds (4767.77 seconds total)