Starting phenix.real_space_refine on Sun Jun 8 07:30:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bla_16104/06_2025/8bla_16104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bla_16104/06_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_16104/06_2025/8bla_16104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bla_16104/06_2025/8bla_16104.map" model { file = "/net/cci-nas-00/data/ceres_data/8bla_16104/06_2025/8bla_16104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bla_16104/06_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-5710/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: 6.11, per 1000 atoms: 0.65 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: 2.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.28 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: 2.57 Time building geometry restraints manager: 3.08 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: 0.05 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.490 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9705 Z= 0.213 Angle : 0.651 8.821 13290 Z= 0.288 Chirality : 0.047 0.145 1490 Planarity : 0.005 0.057 1620 Dihedral : 15.400 125.353 3980 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 15) link_NAG-ASN : angle 1.04548 ( 45) link_BETA1-4 : bond 0.00109 ( 10) link_BETA1-4 : angle 1.09335 ( 30) hydrogen bonds : bond 0.21399 ( 290) hydrogen bonds : angle 9.04104 ( 1020) SS BOND : bond 0.00146 ( 5) SS BOND : angle 0.29140 ( 10) covalent geometry : bond 0.00448 ( 9675) covalent geometry : angle 0.64791 (13205) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.945 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: 0.2575 time to fit residues: 33.6812 Evaluate side-chains 88 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 9705 Z= 0.187 Angle : 0.626 6.823 13290 Z= 0.327 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 15) link_NAG-ASN : angle 1.50899 ( 45) link_BETA1-4 : bond 0.00311 ( 10) link_BETA1-4 : angle 1.24959 ( 30) hydrogen bonds : bond 0.04887 ( 290) hydrogen bonds : angle 6.16706 ( 1020) SS BOND : bond 0.00402 ( 5) SS BOND : angle 0.60571 ( 10) covalent geometry : bond 0.00449 ( 9675) covalent geometry : angle 0.61898 (13205) *********************** 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 : 0.952 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: 0.2563 time to fit residues: 38.8634 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 : 1.004 ------------------------------------------------------------------------------- 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: 0.6980 chunk 29 optimal weight: 0.0270 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: 0.7038 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.116790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.100279 restraints weight = 12272.287| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.10 r_work: 0.2912 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9705 Z= 0.124 Angle : 0.557 6.038 13290 Z= 0.288 Chirality : 0.048 0.143 1490 Planarity : 0.004 0.029 1620 Dihedral : 10.958 118.403 1795 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.08 % Allowed : 11.88 % Favored : 86.04 % 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: -1.41 (0.26), residues: 1045 helix: 0.36 (0.56), residues: 95 sheet: -1.28 (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 0.002 0.000 ARG B 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 15) link_NAG-ASN : angle 1.35390 ( 45) link_BETA1-4 : bond 0.00225 ( 10) link_BETA1-4 : angle 1.14885 ( 30) hydrogen bonds : bond 0.03885 ( 290) hydrogen bonds : angle 5.54812 ( 1020) SS BOND : bond 0.00237 ( 5) SS BOND : angle 0.49035 ( 10) covalent geometry : bond 0.00285 ( 9675) covalent geometry : angle 0.55034 (13205) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.943 Fit side-chains REVERT: A 56 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8709 (ttm110) REVERT: B 232 MET cc_start: 0.8483 (tpp) cc_final: 0.8248 (ttm) REVERT: C 46 ARG cc_start: 0.7071 (ptp90) cc_final: 0.6366 (ptm160) REVERT: C 56 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8777 (ttm110) REVERT: C 130 LYS cc_start: 0.8483 (mmtp) cc_final: 0.8249 (mttp) REVERT: D 56 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7732 (mtm110) REVERT: E 56 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7561 (mtm110) outliers start: 21 outliers final: 16 residues processed: 116 average time/residue: 0.2601 time to fit residues: 40.0592 Evaluate side-chains 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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: 0.3980 chunk 30 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 53 optimal weight: 0.0030 chunk 71 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.117528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.101453 restraints weight = 12107.890| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.04 r_work: 0.2982 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9705 Z= 0.100 Angle : 0.530 5.655 13290 Z= 0.271 Chirality : 0.047 0.142 1490 Planarity : 0.004 0.031 1620 Dihedral : 10.797 117.303 1795 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.37 % Allowed : 12.97 % Favored : 83.66 % 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: -1.37 (0.25), residues: 1045 helix: 0.52 (0.57), residues: 95 sheet: -1.17 (0.23), residues: 395 loop : -0.86 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 178 HIS 0.001 0.000 HIS B 180 PHE 0.012 0.001 PHE E 221 TYR 0.010 0.001 TYR B 89 ARG 0.002 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 15) link_NAG-ASN : angle 1.27005 ( 45) link_BETA1-4 : bond 0.00224 ( 10) link_BETA1-4 : angle 1.13375 ( 30) hydrogen bonds : bond 0.03277 ( 290) hydrogen bonds : angle 5.22005 ( 1020) SS BOND : bond 0.00206 ( 5) SS BOND : angle 0.33149 ( 10) covalent geometry : bond 0.00228 ( 9675) covalent geometry : angle 0.52360 (13205) *********************** 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 139 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 1.071 Fit side-chains REVERT: A 56 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8836 (ttm110) REVERT: B 197 LYS cc_start: 0.6863 (ttpp) cc_final: 0.6564 (ttmt) REVERT: C 56 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8666 (ttm110) REVERT: C 130 LYS cc_start: 0.8731 (mmtp) cc_final: 0.8449 (mttp) REVERT: D 56 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7846 (mtm110) REVERT: D 93 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8316 (mt-10) REVERT: D 197 LYS cc_start: 0.6866 (ttpp) cc_final: 0.6573 (ttmt) REVERT: E 56 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.7566 (mtm110) REVERT: E 93 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8394 (mt-10) REVERT: E 197 LYS cc_start: 0.6718 (ttpp) cc_final: 0.6207 (ttpt) outliers start: 34 outliers final: 25 residues processed: 138 average time/residue: 0.2535 time to fit residues: 47.1461 Evaluate side-chains 124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 97 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.114788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.098805 restraints weight = 12335.105| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.06 r_work: 0.2902 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9705 Z= 0.145 Angle : 0.559 6.184 13290 Z= 0.286 Chirality : 0.048 0.148 1490 Planarity : 0.004 0.029 1620 Dihedral : 10.966 119.508 1795 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: -1.22 (0.25), residues: 1045 helix: 0.72 (0.57), residues: 95 sheet: -0.94 (0.23), residues: 430 loop : -0.87 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 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 0.002 0.000 ARG B 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 15) link_NAG-ASN : angle 1.40261 ( 45) link_BETA1-4 : bond 0.00105 ( 10) link_BETA1-4 : angle 1.26531 ( 30) hydrogen bonds : bond 0.03350 ( 290) hydrogen bonds : angle 5.22617 ( 1020) SS BOND : bond 0.00234 ( 5) SS BOND : angle 0.57564 ( 10) covalent geometry : bond 0.00347 ( 9675) covalent geometry : angle 0.55136 (13205) *********************** 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 : 0.929 Fit side-chains REVERT: A 56 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.7907 (mtm110) REVERT: B 184 ASP cc_start: 0.8028 (m-30) cc_final: 0.7792 (m-30) REVERT: B 197 LYS cc_start: 0.6613 (ttpp) cc_final: 0.6101 (ttpt) REVERT: C 56 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8610 (ttm110) REVERT: C 130 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8349 (mttp) REVERT: D 56 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7700 (mtm110) REVERT: D 93 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8331 (mt-10) REVERT: D 197 LYS cc_start: 0.6606 (ttpp) cc_final: 0.6347 (ttmt) REVERT: E 56 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.7620 (mtm110) REVERT: E 197 LYS cc_start: 0.6404 (ttpp) cc_final: 0.5943 (ttpt) outliers start: 39 outliers final: 29 residues processed: 135 average time/residue: 0.2926 time to fit residues: 52.6626 Evaluate side-chains 129 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.114278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.098346 restraints weight = 12341.653| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.01 r_work: 0.2926 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9705 Z= 0.171 Angle : 0.576 6.569 13290 Z= 0.294 Chirality : 0.048 0.153 1490 Planarity : 0.004 0.030 1620 Dihedral : 10.982 120.080 1795 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.86 % Allowed : 11.98 % Favored : 84.16 % 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: -1.34 (0.25), residues: 1045 helix: 0.87 (0.58), residues: 95 sheet: -1.04 (0.23), residues: 430 loop : -0.98 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 178 HIS 0.002 0.001 HIS E 141 PHE 0.013 0.001 PHE E 94 TYR 0.015 0.001 TYR D 89 ARG 0.002 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 15) link_NAG-ASN : angle 1.42544 ( 45) link_BETA1-4 : bond 0.00078 ( 10) link_BETA1-4 : angle 1.27611 ( 30) hydrogen bonds : bond 0.03401 ( 290) hydrogen bonds : angle 5.23251 ( 1020) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.70078 ( 10) covalent geometry : bond 0.00413 ( 9675) covalent geometry : angle 0.56871 (13205) *********************** 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 133 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 1.089 Fit side-chains REVERT: A 56 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8066 (mtm110) REVERT: B 197 LYS cc_start: 0.7022 (ttpp) cc_final: 0.6446 (ttpt) REVERT: C 56 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.7969 (mtm110) REVERT: C 130 LYS cc_start: 0.8731 (mmtp) cc_final: 0.8484 (mttp) REVERT: D 56 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.7841 (mtm110) REVERT: D 197 LYS cc_start: 0.6961 (ttpp) cc_final: 0.6675 (ttmt) REVERT: D 233 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7913 (mtpp) REVERT: E 56 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.7921 (mtm110) REVERT: E 197 LYS cc_start: 0.6873 (ttpp) cc_final: 0.6365 (ttpt) outliers start: 39 outliers final: 32 residues processed: 127 average time/residue: 0.2921 time to fit residues: 48.7818 Evaluate side-chains 125 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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: 0.6980 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.115359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.099566 restraints weight = 12385.051| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.97 r_work: 0.2903 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9705 Z= 0.143 Angle : 0.562 6.339 13290 Z= 0.287 Chirality : 0.048 0.150 1490 Planarity : 0.004 0.029 1620 Dihedral : 10.892 119.342 1795 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.86 % Allowed : 11.78 % Favored : 84.36 % 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: -1.39 (0.25), residues: 1045 helix: 0.80 (0.58), residues: 95 sheet: -1.07 (0.23), residues: 430 loop : -1.00 (0.27), residues: 520 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 0.012 0.001 PHE A 221 TYR 0.020 0.001 TYR E 86 ARG 0.003 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 15) link_NAG-ASN : angle 1.34147 ( 45) link_BETA1-4 : bond 0.00119 ( 10) link_BETA1-4 : angle 1.19650 ( 30) hydrogen bonds : bond 0.03238 ( 290) hydrogen bonds : angle 5.14711 ( 1020) SS BOND : bond 0.00198 ( 5) SS BOND : angle 0.54460 ( 10) covalent geometry : bond 0.00341 ( 9675) covalent geometry : angle 0.55518 (13205) *********************** 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 139 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 1.024 Fit side-chains REVERT: A 56 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8018 (mtm110) REVERT: B 197 LYS cc_start: 0.6837 (ttpp) cc_final: 0.6632 (ttmm) REVERT: C 56 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8021 (mtm110) REVERT: C 130 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8451 (mttp) REVERT: D 56 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.7791 (mtm110) REVERT: D 197 LYS cc_start: 0.6825 (ttpp) cc_final: 0.6562 (ttmt) REVERT: D 233 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7820 (mtpp) REVERT: E 46 ARG cc_start: 0.7355 (ptp90) cc_final: 0.7128 (ptp90) REVERT: E 56 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.7731 (mtm110) REVERT: E 93 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8257 (mt-10) REVERT: E 197 LYS cc_start: 0.6786 (ttpp) cc_final: 0.6125 (ttpt) outliers start: 39 outliers final: 33 residues processed: 133 average time/residue: 0.2695 time to fit residues: 47.3792 Evaluate side-chains 134 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 173 LEU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.114345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.098343 restraints weight = 12505.328| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.07 r_work: 0.2914 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.003 0.035 9705 Z= 0.139 Angle : 0.562 6.230 13290 Z= 0.287 Chirality : 0.048 0.149 1490 Planarity : 0.004 0.029 1620 Dihedral : 10.869 119.319 1795 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.86 % Allowed : 11.98 % Favored : 84.16 % 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 (0.25), residues: 1045 helix: 0.76 (0.57), residues: 95 sheet: -1.08 (0.23), residues: 430 loop : -1.01 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 178 HIS 0.002 0.001 HIS E 141 PHE 0.013 0.001 PHE A 221 TYR 0.023 0.001 TYR E 86 ARG 0.003 0.000 ARG C 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 15) link_NAG-ASN : angle 1.33099 ( 45) link_BETA1-4 : bond 0.00131 ( 10) link_BETA1-4 : angle 1.20200 ( 30) hydrogen bonds : bond 0.03188 ( 290) hydrogen bonds : angle 5.11518 ( 1020) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.51264 ( 10) covalent geometry : bond 0.00330 ( 9675) covalent geometry : angle 0.55525 (13205) *********************** 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 145 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.963 Fit side-chains REVERT: A 56 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8028 (mtm110) REVERT: B 103 ASP cc_start: 0.8530 (t0) cc_final: 0.8282 (t0) REVERT: B 197 LYS cc_start: 0.6862 (ttpp) cc_final: 0.6660 (ttmm) REVERT: C 56 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.7966 (mtm110) REVERT: D 56 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.7823 (mtm110) REVERT: D 197 LYS cc_start: 0.6689 (ttpp) cc_final: 0.6432 (ttmt) REVERT: D 233 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7819 (mtpp) REVERT: E 46 ARG cc_start: 0.7376 (ptp90) cc_final: 0.7160 (ptp90) REVERT: E 56 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.7822 (mtm110) REVERT: E 93 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8268 (mt-10) REVERT: E 197 LYS cc_start: 0.6775 (ttpp) cc_final: 0.6119 (ttpt) outliers start: 39 outliers final: 32 residues processed: 139 average time/residue: 0.2670 time to fit residues: 48.9759 Evaluate side-chains 139 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 2 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.116212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.100812 restraints weight = 12402.369| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.94 r_work: 0.2940 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9705 Z= 0.129 Angle : 0.555 6.105 13290 Z= 0.283 Chirality : 0.047 0.149 1490 Planarity : 0.004 0.035 1620 Dihedral : 10.819 119.008 1795 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.96 % Allowed : 11.88 % Favored : 84.16 % 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: -1.41 (0.25), residues: 1045 helix: 0.71 (0.57), residues: 95 sheet: -1.07 (0.23), residues: 430 loop : -1.02 (0.27), residues: 520 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 0.013 0.001 PHE A 221 TYR 0.023 0.001 TYR E 86 ARG 0.008 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 15) link_NAG-ASN : angle 1.29503 ( 45) link_BETA1-4 : bond 0.00156 ( 10) link_BETA1-4 : angle 1.16834 ( 30) hydrogen bonds : bond 0.03142 ( 290) hydrogen bonds : angle 5.07198 ( 1020) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.46808 ( 10) covalent geometry : bond 0.00306 ( 9675) covalent geometry : angle 0.54902 (13205) *********************** 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 143 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 0.982 Fit side-chains REVERT: A 56 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8129 (mtm110) REVERT: A 197 LYS cc_start: 0.6947 (ttpp) cc_final: 0.6353 (ttmt) REVERT: B 103 ASP cc_start: 0.8608 (t0) cc_final: 0.8336 (t0) REVERT: B 197 LYS cc_start: 0.6982 (ttpp) cc_final: 0.6733 (ttmm) REVERT: C 56 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8074 (mtm110) REVERT: C 93 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8394 (mt-10) REVERT: D 56 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.7834 (mtm110) REVERT: D 197 LYS cc_start: 0.6794 (ttpp) cc_final: 0.6515 (ttmt) REVERT: D 233 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7877 (mtpp) REVERT: E 56 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.7752 (mtm110) REVERT: E 93 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8275 (mt-10) REVERT: E 197 LYS cc_start: 0.6871 (ttpp) cc_final: 0.6213 (ttpt) outliers start: 40 outliers final: 34 residues processed: 137 average time/residue: 0.2550 time to fit residues: 46.7403 Evaluate side-chains 138 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 142 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 84 optimal weight: 0.0870 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 = 0.116368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.099810 restraints weight = 12463.181| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.12 r_work: 0.2913 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9705 Z= 0.117 Angle : 0.548 5.945 13290 Z= 0.280 Chirality : 0.047 0.147 1490 Planarity : 0.004 0.039 1620 Dihedral : 10.769 118.960 1795 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.76 % Allowed : 12.18 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.39 (0.25), residues: 1045 helix: 0.65 (0.57), residues: 95 sheet: -1.04 (0.23), residues: 430 loop : -1.01 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 178 HIS 0.002 0.000 HIS E 141 PHE 0.011 0.001 PHE A 221 TYR 0.023 0.001 TYR E 86 ARG 0.008 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 15) link_NAG-ASN : angle 1.25028 ( 45) link_BETA1-4 : bond 0.00205 ( 10) link_BETA1-4 : angle 1.14001 ( 30) hydrogen bonds : bond 0.03080 ( 290) hydrogen bonds : angle 5.01646 ( 1020) SS BOND : bond 0.00156 ( 5) SS BOND : angle 0.39042 ( 10) covalent geometry : bond 0.00274 ( 9675) covalent geometry : angle 0.54234 (13205) ********************** 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 145 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.965 Fit side-chains REVERT: A 46 ARG cc_start: 0.7168 (ptp90) cc_final: 0.6812 (ptp90) REVERT: A 56 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8046 (mtm110) REVERT: A 197 LYS cc_start: 0.6706 (ttpp) cc_final: 0.6134 (ttmt) REVERT: B 39 ASP cc_start: 0.8288 (m-30) cc_final: 0.8056 (m-30) REVERT: B 103 ASP cc_start: 0.8451 (t0) cc_final: 0.8214 (t0) REVERT: B 197 LYS cc_start: 0.6764 (ttpp) cc_final: 0.6525 (ttmm) REVERT: C 56 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8011 (mtm110) REVERT: C 93 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8410 (mt-10) REVERT: D 56 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7769 (mtm110) REVERT: D 93 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8267 (mt-10) REVERT: D 197 LYS cc_start: 0.6585 (ttpp) cc_final: 0.6337 (ttmt) REVERT: D 233 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7686 (mtpp) REVERT: E 56 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.7701 (mtm110) REVERT: E 93 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8256 (mt-10) REVERT: E 114 SER cc_start: 0.9192 (t) cc_final: 0.8920 (p) REVERT: E 197 LYS cc_start: 0.6677 (ttpp) cc_final: 0.6082 (ttpt) outliers start: 38 outliers final: 33 residues processed: 141 average time/residue: 0.2330 time to fit residues: 44.9675 Evaluate side-chains 139 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 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 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 54 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.0170 overall best weight: 0.5916 ------------------------------------------------------------------------------- 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 = 0.116714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.100392 restraints weight = 12285.882| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.08 r_work: 0.2927 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9705 Z= 0.115 Angle : 0.550 5.858 13290 Z= 0.280 Chirality : 0.047 0.147 1490 Planarity : 0.004 0.036 1620 Dihedral : 10.750 118.401 1795 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.66 % Allowed : 12.57 % 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: -1.41 (0.25), residues: 1045 helix: 0.55 (0.56), residues: 95 sheet: -1.06 (0.23), residues: 430 loop : -0.99 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.002 0.001 HIS E 141 PHE 0.011 0.001 PHE A 221 TYR 0.022 0.001 TYR E 86 ARG 0.008 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 15) link_NAG-ASN : angle 1.24033 ( 45) link_BETA1-4 : bond 0.00208 ( 10) link_BETA1-4 : angle 1.13064 ( 30) hydrogen bonds : bond 0.03076 ( 290) hydrogen bonds : angle 4.98760 ( 1020) SS BOND : bond 0.00157 ( 5) SS BOND : angle 0.38649 ( 10) covalent geometry : bond 0.00269 ( 9675) covalent geometry : angle 0.54394 (13205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4458.80 seconds wall clock time: 77 minutes 27.42 seconds (4647.42 seconds total)