Starting phenix.real_space_refine on Sat Aug 23 17:00:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c9x_16513/08_2025/8c9x_16513.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c9x_16513/08_2025/8c9x_16513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c9x_16513/08_2025/8c9x_16513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c9x_16513/08_2025/8c9x_16513.map" model { file = "/net/cci-nas-00/data/ceres_data/8c9x_16513/08_2025/8c9x_16513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c9x_16513/08_2025/8c9x_16513.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 60 5.16 5 C 8645 2.51 5 N 2230 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13485 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1765 Chain: "B" Number of atoms: 1726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1765 Chain: "C" Number of atoms: 1726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1765 Chain: "D" Number of atoms: 1726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1765 Chain: "E" Number of atoms: 1726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1765 Chain: "F" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "G" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "J" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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 Time building chain proxies: 4.45, per 1000 atoms: 0.33 Number of scatterers: 13485 At special positions: 0 Unit cell: (95.03, 95.03, 112.574, 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 60 16.00 O 2550 8.00 N 2230 7.00 C 8645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 401 " - " ASN A 23 " " NAG A 402 " - " ASN A 67 " " NAG B 401 " - " ASN B 23 " " NAG B 402 " - " ASN B 67 " " NAG C 401 " - " ASN C 23 " " NAG C 402 " - " ASN C 67 " " NAG D 401 " - " ASN D 23 " " NAG D 402 " - " ASN D 67 " " NAG E 401 " - " ASN E 23 " " NAG E 402 " - " ASN E 67 " " NAG P 1 " - " ASN A 110 " " NAG Q 1 " - " ASN B 110 " " NAG R 1 " - " ASN C 110 " " NAG S 1 " - " ASN D 110 " " NAG T 1 " - " ASN E 110 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 679.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 35 sheets defined 5.3% alpha, 57.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.978A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.977A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 136 Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.978A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 136 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.978A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 136 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.977A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.989A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.989A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.815A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.808A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.808A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.981A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.981A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.815A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.807A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.807A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.979A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.979A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.807A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.807A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.982A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.982A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.815A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.808A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.808A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.982A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.982A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.807A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.807A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 8 Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.291A pdb=" N GLY F 11 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.291A pdb=" N GLY F 11 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL F 97 " --> pdb=" O TRP F 113 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TRP F 113 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA F 99 " --> pdb=" O SER F 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 4 through 8 Processing sheet with id=AC7, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.291A pdb=" N GLY G 11 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ARG G 39 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.291A pdb=" N GLY G 11 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL G 97 " --> pdb=" O TRP G 113 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TRP G 113 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA G 99 " --> pdb=" O SER G 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 4 through 8 Processing sheet with id=AD1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.291A pdb=" N GLY H 11 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG H 39 " --> pdb=" O PHE H 48 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.291A pdb=" N GLY H 11 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL H 97 " --> pdb=" O TRP H 113 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TRP H 113 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA H 99 " --> pdb=" O SER H 111 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 4 through 8 Processing sheet with id=AD4, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.291A pdb=" N GLY I 11 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ARG I 39 " --> pdb=" O PHE I 48 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.291A pdb=" N GLY I 11 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL I 97 " --> pdb=" O TRP I 113 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TRP I 113 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA I 99 " --> pdb=" O SER I 111 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 4 through 8 Processing sheet with id=AD7, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.290A pdb=" N GLY J 11 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ARG J 39 " --> pdb=" O PHE J 48 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE J 48 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.290A pdb=" N GLY J 11 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL J 97 " --> pdb=" O TRP J 113 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TRP J 113 " --> pdb=" O VAL J 97 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA J 99 " --> pdb=" O SER J 111 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1533 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: 2.54 Time building geometry restraints manager: 1.19 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: 4225 1.34 - 1.46: 3523 1.46 - 1.58: 6042 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 13880 Sorted by residual: bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.29e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.11e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.09e+00 ... (remaining 13875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 18293 1.70 - 3.41: 477 3.41 - 5.11: 85 5.11 - 6.82: 15 6.82 - 8.52: 5 Bond angle restraints: 18875 Sorted by residual: angle pdb=" CB LYS F 44 " pdb=" CG LYS F 44 " pdb=" CD LYS F 44 " ideal model delta sigma weight residual 111.30 119.82 -8.52 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CB LYS I 44 " pdb=" CG LYS I 44 " pdb=" CD LYS I 44 " ideal model delta sigma weight residual 111.30 119.82 -8.52 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CB LYS H 44 " pdb=" CG LYS H 44 " pdb=" CD LYS H 44 " ideal model delta sigma weight residual 111.30 119.81 -8.51 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CB LYS G 44 " pdb=" CG LYS G 44 " pdb=" CD LYS G 44 " ideal model delta sigma weight residual 111.30 119.79 -8.49 2.30e+00 1.89e-01 1.36e+01 angle pdb=" CB LYS J 44 " pdb=" CG LYS J 44 " pdb=" CD LYS J 44 " ideal model delta sigma weight residual 111.30 119.77 -8.47 2.30e+00 1.89e-01 1.36e+01 ... (remaining 18870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 7094 17.45 - 34.90: 856 34.90 - 52.35: 245 52.35 - 69.80: 85 69.80 - 87.25: 25 Dihedral angle restraints: 8305 sinusoidal: 3540 harmonic: 4765 Sorted by residual: dihedral pdb=" CA ASP B 174 " pdb=" CB ASP B 174 " pdb=" CG ASP B 174 " pdb=" OD1 ASP B 174 " ideal model delta sinusoidal sigma weight residual -30.00 -88.18 58.18 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 174 " pdb=" CB ASP A 174 " pdb=" CG ASP A 174 " pdb=" OD1 ASP A 174 " ideal model delta sinusoidal sigma weight residual -30.00 -88.15 58.15 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP E 174 " pdb=" CB ASP E 174 " pdb=" CG ASP E 174 " pdb=" OD1 ASP E 174 " ideal model delta sinusoidal sigma weight residual -30.00 -88.13 58.13 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 8302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1603 0.052 - 0.104: 323 0.104 - 0.156: 69 0.156 - 0.207: 10 0.207 - 0.259: 10 Chirality restraints: 2015 Sorted by residual: chirality pdb=" C1 NAG D 402 " pdb=" ND2 ASN D 67 " pdb=" C2 NAG D 402 " pdb=" O5 NAG D 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG C 402 " pdb=" ND2 ASN C 67 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 67 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2012 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 401 " 0.021 2.00e-02 2.50e+03 1.83e-02 4.19e+00 pdb=" C7 NAG A 401 " -0.003 2.00e-02 2.50e+03 pdb=" C8 NAG A 401 " -0.005 2.00e-02 2.50e+03 pdb=" N2 NAG A 401 " -0.030 2.00e-02 2.50e+03 pdb=" O7 NAG A 401 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 133 " 0.010 2.00e-02 2.50e+03 1.03e-02 2.66e+00 pdb=" CG TRP A 133 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 133 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 133 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 133 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 133 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 133 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 133 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 133 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 133 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 88 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO F 89 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 89 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 89 " 0.022 5.00e-02 4.00e+02 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 429 2.69 - 3.25: 12130 3.25 - 3.80: 22356 3.80 - 4.35: 30302 4.35 - 4.90: 49700 Nonbonded interactions: 114917 Sorted by model distance: nonbonded pdb=" OE2 GLU A 9 " pdb=" OH TYR F 33 " model vdw 2.143 3.040 nonbonded pdb=" OE2 GLU D 9 " pdb=" OH TYR I 33 " model vdw 2.166 3.040 nonbonded pdb=" N GLU I 90 " pdb=" OE1 GLU I 90 " model vdw 2.175 3.120 nonbonded pdb=" N GLU J 90 " pdb=" OE1 GLU J 90 " model vdw 2.175 3.120 nonbonded pdb=" N GLU G 90 " pdb=" OE1 GLU G 90 " model vdw 2.175 3.120 ... (remaining 114912 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: 0.04 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' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 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: 5.380 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: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.200 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 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 13905 Z= 0.166 Angle : 0.717 11.086 18945 Z= 0.356 Chirality : 0.048 0.259 2015 Planarity : 0.005 0.040 2395 Dihedral : 17.444 87.247 5260 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.46 % Allowed : 28.03 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.20), residues: 1620 helix: 1.34 (0.71), residues: 45 sheet: -0.29 (0.18), residues: 735 loop : -1.12 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 204 TYR 0.012 0.001 TYR I 95 PHE 0.012 0.001 PHE H 48 TRP 0.028 0.002 TRP A 133 HIS 0.002 0.000 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00363 (13880) covalent geometry : angle 0.68009 (18875) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.69375 ( 10) hydrogen bonds : bond 0.09957 ( 436) hydrogen bonds : angle 6.26084 ( 1533) link_BETA1-4 : bond 0.01888 ( 5) link_BETA1-4 : angle 7.00962 ( 15) link_NAG-ASN : bond 0.00534 ( 15) link_NAG-ASN : angle 2.37786 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 316 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 26 residues processed: 351 average time/residue: 0.5741 time to fit residues: 216.8010 Evaluate side-chains 314 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 288 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 116 GLN B 3 GLN B 170 ASN C 3 GLN D 3 GLN D 170 ASN E 3 GLN F 4 GLN G 40 GLN H 4 GLN I 4 GLN I 115 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.078791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.052002 restraints weight = 53850.269| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 3.76 r_work: 0.2391 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2389 r_free = 0.2389 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2389 r_free = 0.2389 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13905 Z= 0.217 Angle : 0.720 9.222 18945 Z= 0.355 Chirality : 0.050 0.309 2015 Planarity : 0.004 0.031 2395 Dihedral : 9.237 56.609 2271 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.72 % Allowed : 23.03 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.20), residues: 1620 helix: 0.88 (0.67), residues: 45 sheet: -0.16 (0.18), residues: 735 loop : -1.08 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 204 TYR 0.021 0.002 TYR J 95 PHE 0.014 0.001 PHE G 38 TRP 0.019 0.001 TRP C 133 HIS 0.002 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00493 (13880) covalent geometry : angle 0.69196 (18875) SS BOND : bond 0.00368 ( 5) SS BOND : angle 0.25841 ( 10) hydrogen bonds : bond 0.03702 ( 436) hydrogen bonds : angle 5.44198 ( 1533) link_BETA1-4 : bond 0.01446 ( 5) link_BETA1-4 : angle 5.55533 ( 15) link_NAG-ASN : bond 0.00590 ( 15) link_NAG-ASN : angle 2.68616 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 291 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: G 74 ASP cc_start: 0.8783 (t0) cc_final: 0.8560 (t0) REVERT: G 77 LYS cc_start: 0.9437 (mtmm) cc_final: 0.9213 (mtmm) REVERT: H 2 GLN cc_start: 0.7924 (mp10) cc_final: 0.7656 (pm20) REVERT: H 74 ASP cc_start: 0.8769 (t0) cc_final: 0.8549 (t0) REVERT: H 77 LYS cc_start: 0.9454 (mtmm) cc_final: 0.9217 (mtmm) REVERT: H 83 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8234 (tp-100) REVERT: I 74 ASP cc_start: 0.8782 (t0) cc_final: 0.8546 (t0) outliers start: 67 outliers final: 37 residues processed: 341 average time/residue: 0.6128 time to fit residues: 225.0181 Evaluate side-chains 317 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 2 optimal weight: 0.5980 chunk 149 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 170 ASN B 170 ASN C 47 GLN C 170 ASN D 47 GLN D 116 GLN D 170 ASN E 47 GLN E 116 GLN F 4 GLN H 4 GLN I 4 GLN I 115 GLN J 4 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.079468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.052988 restraints weight = 45454.979| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 3.54 r_work: 0.2418 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13905 Z= 0.154 Angle : 0.675 9.446 18945 Z= 0.329 Chirality : 0.048 0.289 2015 Planarity : 0.004 0.029 2395 Dihedral : 8.539 55.895 2250 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.73 % Allowed : 26.06 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.20), residues: 1620 helix: 0.83 (0.71), residues: 45 sheet: -0.13 (0.19), residues: 680 loop : -1.06 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 204 TYR 0.022 0.001 TYR I 95 PHE 0.012 0.001 PHE F 38 TRP 0.022 0.001 TRP D 133 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00342 (13880) covalent geometry : angle 0.64694 (18875) SS BOND : bond 0.00339 ( 5) SS BOND : angle 0.46564 ( 10) hydrogen bonds : bond 0.03269 ( 436) hydrogen bonds : angle 5.16126 ( 1533) link_BETA1-4 : bond 0.01720 ( 5) link_BETA1-4 : angle 5.26412 ( 15) link_NAG-ASN : bond 0.00501 ( 15) link_NAG-ASN : angle 2.64559 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 289 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 74 ASP cc_start: 0.8762 (t0) cc_final: 0.8505 (t0) REVERT: G 77 LYS cc_start: 0.9458 (mtmm) cc_final: 0.9244 (mtmm) REVERT: H 2 GLN cc_start: 0.7987 (mp10) cc_final: 0.7746 (pm20) REVERT: I 46 ARG cc_start: 0.8074 (ttm170) cc_final: 0.7857 (ttm170) REVERT: I 74 ASP cc_start: 0.8798 (t0) cc_final: 0.8482 (t0) REVERT: I 83 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8295 (tp-100) outliers start: 53 outliers final: 34 residues processed: 328 average time/residue: 0.6178 time to fit residues: 217.3110 Evaluate side-chains 315 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 189 CYS Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 72 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 170 ASN B 65 GLN B 170 ASN C 65 GLN C 170 ASN D 47 GLN D 65 GLN D 116 GLN D 170 ASN E 116 GLN F 4 GLN I 4 GLN I 115 GLN ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.077600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.050887 restraints weight = 45042.133| |-----------------------------------------------------------------------------| r_work (start): 0.2509 rms_B_bonded: 3.51 r_work: 0.2361 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2360 r_free = 0.2360 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2360 r_free = 0.2360 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13905 Z= 0.232 Angle : 0.707 9.601 18945 Z= 0.345 Chirality : 0.050 0.300 2015 Planarity : 0.004 0.030 2395 Dihedral : 8.542 56.408 2245 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.44 % Allowed : 25.49 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.20), residues: 1620 helix: 0.39 (0.69), residues: 45 sheet: -0.15 (0.19), residues: 680 loop : -1.03 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 185 TYR 0.019 0.002 TYR I 96 PHE 0.012 0.001 PHE I 48 TRP 0.021 0.001 TRP C 133 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00523 (13880) covalent geometry : angle 0.67703 (18875) SS BOND : bond 0.00413 ( 5) SS BOND : angle 0.07777 ( 10) hydrogen bonds : bond 0.03478 ( 436) hydrogen bonds : angle 5.21662 ( 1533) link_BETA1-4 : bond 0.01600 ( 5) link_BETA1-4 : angle 5.56990 ( 15) link_NAG-ASN : bond 0.00474 ( 15) link_NAG-ASN : angle 2.81719 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: C 185 ARG cc_start: 0.8594 (ttt-90) cc_final: 0.8271 (ttt-90) REVERT: G 47 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7242 (pp20) REVERT: G 74 ASP cc_start: 0.8782 (t0) cc_final: 0.8518 (t0) REVERT: G 77 LYS cc_start: 0.9475 (mtmm) cc_final: 0.9224 (mtmm) REVERT: I 46 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7778 (ttp80) REVERT: I 74 ASP cc_start: 0.8856 (t0) cc_final: 0.8513 (t0) REVERT: I 83 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8292 (tp-100) outliers start: 63 outliers final: 36 residues processed: 327 average time/residue: 0.5970 time to fit residues: 209.6079 Evaluate side-chains 305 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 189 CYS Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 122 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 75 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 170 ASN B 116 GLN D 47 GLN D 116 GLN D 170 ASN E 116 GLN F 4 GLN I 4 GLN I 115 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.079535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.052462 restraints weight = 59442.272| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 3.89 r_work: 0.2395 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2395 r_free = 0.2395 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2395 r_free = 0.2395 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13905 Z= 0.134 Angle : 0.665 9.521 18945 Z= 0.324 Chirality : 0.048 0.277 2015 Planarity : 0.004 0.031 2395 Dihedral : 8.379 58.585 2240 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.73 % Allowed : 26.13 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.20), residues: 1620 helix: 0.64 (0.74), residues: 45 sheet: -0.15 (0.19), residues: 680 loop : -0.99 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 204 TYR 0.016 0.001 TYR G 60 PHE 0.010 0.001 PHE G 38 TRP 0.025 0.001 TRP E 133 HIS 0.001 0.000 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00296 (13880) covalent geometry : angle 0.63708 (18875) SS BOND : bond 0.00264 ( 5) SS BOND : angle 0.39133 ( 10) hydrogen bonds : bond 0.03011 ( 436) hydrogen bonds : angle 4.97758 ( 1533) link_BETA1-4 : bond 0.01737 ( 5) link_BETA1-4 : angle 5.18892 ( 15) link_NAG-ASN : bond 0.00480 ( 15) link_NAG-ASN : angle 2.59522 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: B 185 ARG cc_start: 0.8633 (ttt-90) cc_final: 0.8428 (ptm-80) REVERT: B 192 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8596 (tp30) REVERT: C 185 ARG cc_start: 0.8593 (ttt-90) cc_final: 0.8390 (ptm-80) REVERT: E 192 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8553 (tp30) REVERT: F 45 GLU cc_start: 0.8290 (pm20) cc_final: 0.7988 (pm20) REVERT: G 74 ASP cc_start: 0.8748 (t0) cc_final: 0.8469 (t0) REVERT: G 77 LYS cc_start: 0.9475 (mtmm) cc_final: 0.9231 (mtmm) REVERT: H 74 ASP cc_start: 0.8754 (t0) cc_final: 0.8111 (t0) REVERT: H 77 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.8790 (mtmm) REVERT: I 74 ASP cc_start: 0.8850 (t0) cc_final: 0.8519 (t0) REVERT: I 83 GLN cc_start: 0.8474 (tp-100) cc_final: 0.8115 (tp-100) REVERT: J 46 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7456 (ttm170) outliers start: 53 outliers final: 31 residues processed: 317 average time/residue: 0.5737 time to fit residues: 195.7084 Evaluate side-chains 307 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 272 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 10 optimal weight: 0.8980 chunk 99 optimal weight: 0.0870 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 153 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 GLN F 4 GLN H 4 GLN I 4 GLN I 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.080336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.053459 restraints weight = 59127.561| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 3.87 r_work: 0.2419 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2419 r_free = 0.2419 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2419 r_free = 0.2419 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13905 Z= 0.124 Angle : 0.654 9.545 18945 Z= 0.318 Chirality : 0.047 0.265 2015 Planarity : 0.004 0.037 2395 Dihedral : 8.286 59.570 2240 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.17 % Allowed : 26.76 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1620 helix: 0.81 (0.73), residues: 45 sheet: -0.13 (0.19), residues: 680 loop : -0.95 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 204 TYR 0.024 0.001 TYR I 95 PHE 0.009 0.001 PHE G 38 TRP 0.027 0.001 TRP A 133 HIS 0.001 0.000 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00279 (13880) covalent geometry : angle 0.62786 (18875) SS BOND : bond 0.00200 ( 5) SS BOND : angle 0.34004 ( 10) hydrogen bonds : bond 0.02867 ( 436) hydrogen bonds : angle 4.82025 ( 1533) link_BETA1-4 : bond 0.01705 ( 5) link_BETA1-4 : angle 5.06925 ( 15) link_NAG-ASN : bond 0.00482 ( 15) link_NAG-ASN : angle 2.49431 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 296 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8601 (ttt180) cc_final: 0.8400 (ttp80) REVERT: B 8 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9192 (ttpp) REVERT: B 185 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.8408 (ptm-80) REVERT: B 192 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8520 (tp30) REVERT: F 45 GLU cc_start: 0.8282 (pm20) cc_final: 0.7970 (pm20) REVERT: F 74 ASP cc_start: 0.8804 (t0) cc_final: 0.8443 (t0) REVERT: G 47 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.6947 (pp20) REVERT: G 74 ASP cc_start: 0.8763 (t0) cc_final: 0.8496 (t0) REVERT: G 77 LYS cc_start: 0.9481 (mtmm) cc_final: 0.9249 (mtmm) REVERT: H 74 ASP cc_start: 0.8797 (t0) cc_final: 0.8351 (t0) REVERT: H 77 LYS cc_start: 0.9430 (mtmm) cc_final: 0.8875 (mtmm) REVERT: I 40 GLN cc_start: 0.8160 (tp-100) cc_final: 0.7911 (tp40) REVERT: I 74 ASP cc_start: 0.8859 (t0) cc_final: 0.8437 (t0) REVERT: I 77 LYS cc_start: 0.9499 (mtmm) cc_final: 0.9254 (mtmm) REVERT: I 83 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8196 (tp-100) REVERT: J 74 ASP cc_start: 0.8860 (t0) cc_final: 0.8553 (t0) outliers start: 45 outliers final: 30 residues processed: 327 average time/residue: 0.6438 time to fit residues: 226.0372 Evaluate side-chains 319 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 132 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 67 optimal weight: 0.3980 chunk 158 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN B 116 GLN E 65 GLN E 116 GLN F 4 GLN H 4 GLN I 2 GLN I 4 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.050535 restraints weight = 59274.699| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 3.87 r_work: 0.2346 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2346 r_free = 0.2346 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2346 r_free = 0.2346 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13905 Z= 0.221 Angle : 0.709 9.646 18945 Z= 0.347 Chirality : 0.049 0.286 2015 Planarity : 0.004 0.035 2395 Dihedral : 8.423 57.307 2240 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.08 % Allowed : 25.56 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.20), residues: 1620 helix: 0.43 (0.70), residues: 45 sheet: -0.10 (0.19), residues: 680 loop : -0.94 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 204 TYR 0.019 0.002 TYR I 95 PHE 0.011 0.001 PHE G 48 TRP 0.024 0.001 TRP C 133 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00499 (13880) covalent geometry : angle 0.68123 (18875) SS BOND : bond 0.00304 ( 5) SS BOND : angle 0.16243 ( 10) hydrogen bonds : bond 0.03292 ( 436) hydrogen bonds : angle 5.02821 ( 1533) link_BETA1-4 : bond 0.01546 ( 5) link_BETA1-4 : angle 5.44117 ( 15) link_NAG-ASN : bond 0.00467 ( 15) link_NAG-ASN : angle 2.70681 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 277 time to evaluate : 0.534 Fit side-chains REVERT: A 185 ARG cc_start: 0.8609 (ttt180) cc_final: 0.8385 (ttp80) REVERT: B 133 TRP cc_start: 0.8309 (m-10) cc_final: 0.8076 (m-90) REVERT: B 185 ARG cc_start: 0.8631 (ttt-90) cc_final: 0.8375 (ptm-80) REVERT: B 192 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8589 (tp30) REVERT: D 185 ARG cc_start: 0.8581 (ttt-90) cc_final: 0.8294 (ttt-90) REVERT: E 188 GLU cc_start: 0.8827 (pm20) cc_final: 0.8619 (pm20) REVERT: F 45 GLU cc_start: 0.8303 (pm20) cc_final: 0.7991 (pm20) REVERT: F 74 ASP cc_start: 0.8823 (t0) cc_final: 0.8439 (t0) REVERT: G 74 ASP cc_start: 0.8752 (t0) cc_final: 0.8442 (t0) REVERT: G 77 LYS cc_start: 0.9475 (mtmm) cc_final: 0.9216 (mtmm) REVERT: H 77 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.8783 (mtmm) REVERT: I 74 ASP cc_start: 0.8874 (t0) cc_final: 0.8498 (t0) REVERT: I 83 GLN cc_start: 0.8485 (tp-100) cc_final: 0.8196 (tp-100) REVERT: J 46 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7891 (ttm110) REVERT: J 74 ASP cc_start: 0.8880 (t0) cc_final: 0.8579 (t0) outliers start: 58 outliers final: 37 residues processed: 318 average time/residue: 0.6295 time to fit residues: 215.4347 Evaluate side-chains 310 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 155 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN B 116 GLN E 116 GLN F 4 GLN H 4 GLN I 2 GLN I 4 GLN I 115 GLN J 2 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.052162 restraints weight = 63202.359| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 3.99 r_work: 0.2388 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2387 r_free = 0.2387 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2387 r_free = 0.2387 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13905 Z= 0.146 Angle : 0.681 9.541 18945 Z= 0.333 Chirality : 0.048 0.275 2015 Planarity : 0.004 0.040 2395 Dihedral : 8.291 56.222 2240 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.52 % Allowed : 25.92 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.20), residues: 1620 helix: 0.64 (0.73), residues: 45 sheet: -0.09 (0.19), residues: 680 loop : -0.90 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 204 TYR 0.017 0.001 TYR I 95 PHE 0.009 0.001 PHE F 38 TRP 0.028 0.001 TRP D 133 HIS 0.001 0.000 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00331 (13880) covalent geometry : angle 0.65491 (18875) SS BOND : bond 0.00274 ( 5) SS BOND : angle 0.26909 ( 10) hydrogen bonds : bond 0.02945 ( 436) hydrogen bonds : angle 4.84081 ( 1533) link_BETA1-4 : bond 0.01742 ( 5) link_BETA1-4 : angle 5.16926 ( 15) link_NAG-ASN : bond 0.00476 ( 15) link_NAG-ASN : angle 2.54617 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 281 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 TRP cc_start: 0.8310 (m-10) cc_final: 0.8059 (m-90) REVERT: B 185 ARG cc_start: 0.8648 (ttt-90) cc_final: 0.8402 (ptm-80) REVERT: B 192 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8611 (tp30) REVERT: D 185 ARG cc_start: 0.8564 (ttt-90) cc_final: 0.8291 (ptm-80) REVERT: F 45 GLU cc_start: 0.8313 (pm20) cc_final: 0.8026 (pm20) REVERT: F 47 GLU cc_start: 0.8528 (pp20) cc_final: 0.8294 (pp20) REVERT: G 74 ASP cc_start: 0.8725 (t0) cc_final: 0.8437 (t0) REVERT: G 77 LYS cc_start: 0.9478 (mtmm) cc_final: 0.9214 (mtmm) REVERT: I 74 ASP cc_start: 0.8866 (t0) cc_final: 0.8424 (t0) REVERT: I 77 LYS cc_start: 0.9506 (mtmm) cc_final: 0.9259 (mtmm) REVERT: I 83 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8173 (tp-100) REVERT: J 74 ASP cc_start: 0.8855 (t0) cc_final: 0.8563 (t0) outliers start: 50 outliers final: 38 residues processed: 317 average time/residue: 0.6012 time to fit residues: 204.6516 Evaluate side-chains 308 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 144 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 1 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN E 116 GLN F 2 GLN F 4 GLN H 4 GLN I 2 GLN I 4 GLN I 115 GLN J 85 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.080037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.053514 restraints weight = 39294.929| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 3.38 r_work: 0.2434 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2433 r_free = 0.2433 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2433 r_free = 0.2433 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13905 Z= 0.135 Angle : 0.685 9.572 18945 Z= 0.334 Chirality : 0.047 0.280 2015 Planarity : 0.004 0.046 2395 Dihedral : 8.233 55.955 2240 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.75 % Allowed : 26.27 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.20), residues: 1620 helix: 0.73 (0.72), residues: 45 sheet: -0.08 (0.19), residues: 680 loop : -0.88 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 204 TYR 0.017 0.001 TYR G 60 PHE 0.010 0.001 PHE G 38 TRP 0.028 0.001 TRP E 133 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00310 (13880) covalent geometry : angle 0.66005 (18875) SS BOND : bond 0.00211 ( 5) SS BOND : angle 0.26599 ( 10) hydrogen bonds : bond 0.02848 ( 436) hydrogen bonds : angle 4.77288 ( 1533) link_BETA1-4 : bond 0.01695 ( 5) link_BETA1-4 : angle 5.08912 ( 15) link_NAG-ASN : bond 0.00471 ( 15) link_NAG-ASN : angle 2.52006 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 185 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.8378 (ptm-80) REVERT: B 192 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8528 (tp30) REVERT: D 185 ARG cc_start: 0.8509 (ttt-90) cc_final: 0.8240 (ptm-80) REVERT: F 45 GLU cc_start: 0.8290 (pm20) cc_final: 0.7988 (pm20) REVERT: F 47 GLU cc_start: 0.8447 (pp20) cc_final: 0.8220 (pp20) REVERT: G 74 ASP cc_start: 0.8729 (t0) cc_final: 0.8458 (t0) REVERT: G 77 LYS cc_start: 0.9483 (mtmm) cc_final: 0.9252 (mtmm) REVERT: H 74 ASP cc_start: 0.8729 (t0) cc_final: 0.8473 (t0) REVERT: H 77 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9196 (ptpp) REVERT: I 40 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7922 (tp40) REVERT: I 74 ASP cc_start: 0.8853 (t0) cc_final: 0.8402 (t0) REVERT: I 77 LYS cc_start: 0.9504 (mtmm) cc_final: 0.9248 (mtmm) REVERT: I 83 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8264 (tp-100) REVERT: J 66 LYS cc_start: 0.8899 (ptmm) cc_final: 0.8685 (ptmm) REVERT: J 74 ASP cc_start: 0.8845 (t0) cc_final: 0.8566 (t0) outliers start: 39 outliers final: 37 residues processed: 316 average time/residue: 0.5962 time to fit residues: 202.8361 Evaluate side-chains 319 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 280 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain F residue 2 GLN Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 2 GLN Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 125 optimal weight: 0.0970 chunk 133 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 68 optimal weight: 0.0270 chunk 75 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN B 116 GLN E 116 GLN F 4 GLN H 4 GLN I 4 GLN I 115 GLN J 2 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.079010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.052484 restraints weight = 37360.397| |-----------------------------------------------------------------------------| r_work (start): 0.2548 rms_B_bonded: 3.31 r_work: 0.2409 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13905 Z= 0.188 Angle : 0.708 9.578 18945 Z= 0.345 Chirality : 0.048 0.279 2015 Planarity : 0.004 0.046 2395 Dihedral : 8.285 56.211 2240 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.89 % Allowed : 26.55 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.20), residues: 1620 helix: 0.62 (0.71), residues: 45 sheet: -0.08 (0.19), residues: 680 loop : -0.86 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 204 TYR 0.017 0.001 TYR G 60 PHE 0.008 0.001 PHE F 48 TRP 0.031 0.001 TRP A 133 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00430 (13880) covalent geometry : angle 0.68177 (18875) SS BOND : bond 0.00275 ( 5) SS BOND : angle 0.07163 ( 10) hydrogen bonds : bond 0.03031 ( 436) hydrogen bonds : angle 4.81658 ( 1533) link_BETA1-4 : bond 0.01610 ( 5) link_BETA1-4 : angle 5.25097 ( 15) link_NAG-ASN : bond 0.00433 ( 15) link_NAG-ASN : angle 2.56851 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 185 ARG cc_start: 0.8628 (ttt-90) cc_final: 0.8400 (ttt-90) REVERT: B 192 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8608 (tp30) REVERT: C 41 ASP cc_start: 0.8893 (t0) cc_final: 0.8657 (t0) REVERT: F 45 GLU cc_start: 0.8317 (pm20) cc_final: 0.8023 (pm20) REVERT: F 47 GLU cc_start: 0.8479 (pp20) cc_final: 0.8248 (pp20) REVERT: G 74 ASP cc_start: 0.8750 (t0) cc_final: 0.8453 (t0) REVERT: G 77 LYS cc_start: 0.9487 (mtmm) cc_final: 0.9223 (mtmm) REVERT: H 46 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7521 (ttm170) REVERT: H 74 ASP cc_start: 0.8767 (t0) cc_final: 0.8501 (t0) REVERT: H 77 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9178 (ptpp) REVERT: I 74 ASP cc_start: 0.8864 (t0) cc_final: 0.8400 (t0) REVERT: I 77 LYS cc_start: 0.9509 (mtmm) cc_final: 0.9253 (mtmm) REVERT: I 83 GLN cc_start: 0.8464 (tp-100) cc_final: 0.8249 (tp-100) REVERT: J 74 ASP cc_start: 0.8855 (t0) cc_final: 0.8571 (t0) outliers start: 41 outliers final: 38 residues processed: 307 average time/residue: 0.6259 time to fit residues: 206.6504 Evaluate side-chains 309 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 0.0370 chunk 45 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN E 116 GLN I 4 GLN I 115 GLN J 2 GLN J 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.079129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.051586 restraints weight = 71736.566| |-----------------------------------------------------------------------------| r_work (start): 0.2527 rms_B_bonded: 4.15 r_work: 0.2367 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2366 r_free = 0.2366 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2366 r_free = 0.2366 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 13905 Z= 0.233 Angle : 0.906 58.815 18945 Z= 0.488 Chirality : 0.048 0.278 2015 Planarity : 0.004 0.053 2395 Dihedral : 8.285 56.191 2240 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.89 % Allowed : 26.27 % Favored : 70.85 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.20), residues: 1620 helix: 0.65 (0.71), residues: 45 sheet: -0.08 (0.19), residues: 680 loop : -0.85 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 204 TYR 0.015 0.001 TYR G 60 PHE 0.008 0.001 PHE F 48 TRP 0.025 0.001 TRP E 133 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00520 (13880) covalent geometry : angle 0.88765 (18875) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.09490 ( 10) hydrogen bonds : bond 0.03028 ( 436) hydrogen bonds : angle 4.81961 ( 1533) link_BETA1-4 : bond 0.01417 ( 5) link_BETA1-4 : angle 5.16862 ( 15) link_NAG-ASN : bond 0.00422 ( 15) link_NAG-ASN : angle 2.55669 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5734.97 seconds wall clock time: 98 minutes 7.19 seconds (5887.19 seconds total)