Starting phenix.real_space_refine on Fri Jul 3 09:48:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c9x_16513/07_2026/8c9x_16513.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c9x_16513/07_2026/8c9x_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_16513/07_2026/8c9x_16513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c9x_16513/07_2026/8c9x_16513.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8c9x_16513/07_2026/8c9x_16513.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c9x_16513/07_2026/8c9x_16513.cif" model { file = "/net/cci-nas-00/data/ceres_data/8c9x_16513/07_2026/8c9x_16513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c9x_16513/07_2026/8c9x_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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 4.47, 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: 1.23 Conformation dependent library (CDL) restraints added in 895.7 milliseconds 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: 0.43 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: 2.35 Time building geometry restraints manager: 1.67 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: 6744 17.45 - 34.90: 834 34.90 - 52.35: 212 52.35 - 69.80: 70 69.80 - 87.25: 25 Dihedral angle restraints: 7885 sinusoidal: 3120 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 7882 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 4.280 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.600 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 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 : 17.361 87.247 4840 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 are 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/Z covalent geometry : bond 0.00363 / 0.17 (13880) covalent geometry : angle 0.68009 / 0.35 (18875) SS BOND : bond 0.00267 / 0.15 ( 5) SS BOND : angle 0.69375 / 0.37 ( 10) hydrogen bonds : bond 0.09957 / 6.28 ( 436) hydrogen bonds : angle 6.26084 / 4.37 ( 1533) link_BETA1-4 : bond 0.01888 / 1.05 ( 5) link_BETA1-4 : angle 7.00962 / 3.97 ( 15) link_NAG-ASN : bond 0.00534 / 0.33 ( 15) link_NAG-ASN : angle 2.37786 / 1.55 ( 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 : 0.467 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: 0.7021 time to fit residues: 265.8748 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 : 0.585 ------------------------------------------------------------------------------- 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... 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 = 0.3098 r_free = 0.3098 target = 0.078591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.051800 restraints weight = 53853.786| |-----------------------------------------------------------------------------| r_work (start): 0.2534 rms_B_bonded: 3.74 r_work: 0.2386 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2385 r_free = 0.2385 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 = 0.2385 r_free = 0.2385 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13905 Z= 0.217 Angle : 0.724 9.114 18945 Z= 0.357 Chirality : 0.051 0.317 2015 Planarity : 0.004 0.030 2395 Dihedral : 6.319 41.557 1851 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.11 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 are not related in a simple way. whole: -0.93 (0.20), residues: 1620 helix: 0.82 (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 0.006 0.001 ARG E 204 TYR 0.022 0.002 TYR J 95 PHE 0.016 0.001 PHE G 38 TRP 0.020 0.001 TRP D 133 HIS 0.002 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (13880) covalent geometry : angle 0.69853 / 0.35 (18875) SS BOND : bond 0.00383 / 0.22 ( 5) SS BOND : angle 0.23249 / 0.12 ( 10) hydrogen bonds : bond 0.03630 / 2.36 ( 436) hydrogen bonds : angle 5.41466 / 3.77 ( 1533) link_BETA1-4 : bond 0.01602 / 0.90 ( 5) link_BETA1-4 : angle 5.08639 / 2.85 ( 15) link_NAG-ASN : bond 0.00495 / 0.30 ( 15) link_NAG-ASN : angle 2.76865 / 1.92 ( 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 357 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 290 time to evaluate : 0.578 Fit side-chains REVERT: A 205 ARG cc_start: 0.8909 (ttp-170) cc_final: 0.8646 (ttp-170) REVERT: F 74 ASP cc_start: 0.8749 (t0) cc_final: 0.8456 (t0) REVERT: G 74 ASP cc_start: 0.8788 (t0) cc_final: 0.8508 (t0) REVERT: G 77 LYS cc_start: 0.9454 (mtmm) cc_final: 0.9207 (mtmm) REVERT: H 2 GLN cc_start: 0.7940 (mp10) cc_final: 0.7690 (pm20) REVERT: H 74 ASP cc_start: 0.8776 (t0) cc_final: 0.8541 (t0) REVERT: H 77 LYS cc_start: 0.9461 (mtmm) cc_final: 0.9221 (mtmm) REVERT: I 74 ASP cc_start: 0.8787 (t0) cc_final: 0.8540 (t0) REVERT: J 46 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7603 (ttm110) REVERT: J 96 TYR cc_start: 0.8581 (p90) cc_final: 0.8321 (p90) outliers start: 67 outliers final: 39 residues processed: 340 average time/residue: 0.7210 time to fit residues: 263.8505 Evaluate side-chains 319 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 B residue 189 CYS 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 E residue 189 CYS 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 20 LYS 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: 0.9980 chunk 149 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3112 r_free = 0.3112 target = 0.079405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.052842 restraints weight = 45446.257| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 3.54 r_work: 0.2413 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2412 r_free = 0.2412 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 = 0.2412 r_free = 0.2412 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13905 Z= 0.157 Angle : 0.675 9.440 18945 Z= 0.328 Chirality : 0.048 0.289 2015 Planarity : 0.004 0.029 2395 Dihedral : 5.588 47.418 1830 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.80 % Allowed : 25.92 % Favored : 70.28 % 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 are not related in a simple way. whole: -0.94 (0.20), residues: 1620 helix: 0.78 (0.71), residues: 45 sheet: -0.15 (0.19), residues: 680 loop : -1.06 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 204 TYR 0.023 0.001 TYR I 95 PHE 0.012 0.001 PHE F 38 TRP 0.022 0.001 TRP A 133 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (13880) covalent geometry : angle 0.64759 / 0.32 (18875) SS BOND : bond 0.00359 / 0.20 ( 5) SS BOND : angle 0.47643 / 0.25 ( 10) hydrogen bonds : bond 0.03265 / 2.11 ( 436) hydrogen bonds : angle 5.13751 / 3.58 ( 1533) link_BETA1-4 : bond 0.01763 / 0.98 ( 5) link_BETA1-4 : angle 4.91874 / 2.75 ( 15) link_NAG-ASN : bond 0.00477 / 0.31 ( 15) link_NAG-ASN : angle 2.78725 / 1.91 ( 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 343 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 289 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: D 185 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8256 (ptm-80) REVERT: F 74 ASP cc_start: 0.8790 (t0) cc_final: 0.8460 (t0) REVERT: G 74 ASP cc_start: 0.8771 (t0) cc_final: 0.8513 (t0) REVERT: G 77 LYS cc_start: 0.9464 (mtmm) cc_final: 0.9245 (mtmm) REVERT: G 83 GLN cc_start: 0.8582 (tp-100) cc_final: 0.8292 (tp-100) REVERT: H 2 GLN cc_start: 0.8011 (mp10) cc_final: 0.7788 (pm20) REVERT: H 74 ASP cc_start: 0.8771 (t0) cc_final: 0.7998 (t0) REVERT: H 77 LYS cc_start: 0.9478 (mtmm) cc_final: 0.8876 (mtmm) REVERT: I 46 ARG cc_start: 0.8109 (ttm170) cc_final: 0.7888 (ttm170) REVERT: I 74 ASP cc_start: 0.8800 (t0) cc_final: 0.8471 (t0) REVERT: I 83 GLN cc_start: 0.8569 (tp-100) cc_final: 0.8312 (tp-100) outliers start: 54 outliers final: 32 residues processed: 330 average time/residue: 0.7458 time to fit residues: 264.3201 Evaluate side-chains 310 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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 F residue 20 LYS 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 H residue 20 LYS Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 64 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: 0.7980 chunk 98 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 170 ASN B 65 GLN C 170 ASN D 47 GLN D 116 GLN D 170 ASN E 116 GLN F 4 GLN I 4 GLN I 115 GLN J 4 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.078450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.051676 restraints weight = 44965.369| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 3.53 r_work: 0.2384 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2382 r_free = 0.2382 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 = 0.2382 r_free = 0.2382 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13905 Z= 0.190 Angle : 0.686 9.501 18945 Z= 0.334 Chirality : 0.049 0.289 2015 Planarity : 0.004 0.032 2395 Dihedral : 5.761 55.158 1825 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % 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 are not related in a simple way. whole: -0.93 (0.20), residues: 1620 helix: 0.47 (0.71), residues: 45 sheet: -0.16 (0.19), residues: 680 loop : -1.02 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 204 TYR 0.015 0.001 TYR A 128 PHE 0.010 0.001 PHE F 48 TRP 0.022 0.001 TRP C 133 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (13880) covalent geometry : angle 0.65839 / 0.33 (18875) SS BOND : bond 0.00365 / 0.20 ( 5) SS BOND : angle 0.18389 / 0.10 ( 10) hydrogen bonds : bond 0.03295 / 2.13 ( 436) hydrogen bonds : angle 5.11111 / 3.56 ( 1533) link_BETA1-4 : bond 0.01607 / 0.89 ( 5) link_BETA1-4 : angle 4.97870 / 2.78 ( 15) link_NAG-ASN : bond 0.00438 / 0.28 ( 15) link_NAG-ASN : angle 2.84472 / 1.96 ( 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 345 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 47 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7138 (pp20) REVERT: G 74 ASP cc_start: 0.8773 (t0) cc_final: 0.8506 (t0) REVERT: G 77 LYS cc_start: 0.9477 (mtmm) cc_final: 0.9222 (mtmm) REVERT: I 46 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7901 (ttp80) REVERT: I 74 ASP cc_start: 0.8841 (t0) cc_final: 0.8492 (t0) REVERT: I 83 GLN cc_start: 0.8528 (tp-100) cc_final: 0.8286 (tp-100) REVERT: J 2 GLN cc_start: 0.7755 (pm20) cc_final: 0.7555 (pm20) REVERT: J 74 ASP cc_start: 0.8876 (t0) cc_final: 0.8570 (t0) outliers start: 63 outliers final: 37 residues processed: 327 average time/residue: 0.7472 time to fit residues: 261.9575 Evaluate side-chains 309 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 271 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 F residue 119 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 64 SER 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: 3.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 75 optimal weight: 0.0570 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 134 optimal weight: 0.0870 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 0.0670 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 170 ASN B 116 GLN D 47 GLN D 116 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.080430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.053657 restraints weight = 59523.126| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 3.88 r_work: 0.2425 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2423 r_free = 0.2423 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 = 0.2423 r_free = 0.2423 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13905 Z= 0.117 Angle : 0.655 9.458 18945 Z= 0.317 Chirality : 0.047 0.265 2015 Planarity : 0.004 0.032 2395 Dihedral : 5.667 58.871 1820 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.96 % Allowed : 26.55 % Favored : 70.49 % 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 are not related in a simple way. whole: -0.90 (0.20), residues: 1620 helix: 0.79 (0.74), residues: 45 sheet: -0.15 (0.19), residues: 680 loop : -1.00 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 204 TYR 0.016 0.001 TYR G 60 PHE 0.010 0.001 PHE G 38 TRP 0.026 0.001 TRP A 133 HIS 0.000 0.000 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (13880) covalent geometry : angle 0.63006 / 0.31 (18875) SS BOND : bond 0.00243 / 0.14 ( 5) SS BOND : angle 0.49292 / 0.26 ( 10) hydrogen bonds : bond 0.02827 / 1.82 ( 436) hydrogen bonds : angle 4.86856 / 3.39 ( 1533) link_BETA1-4 : bond 0.01718 / 0.95 ( 5) link_BETA1-4 : angle 4.59927 / 2.57 ( 15) link_NAG-ASN : bond 0.00486 / 0.32 ( 15) link_NAG-ASN : angle 2.68338 / 1.83 ( 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 333 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8540 (tp30) REVERT: G 74 ASP cc_start: 0.8766 (t0) cc_final: 0.8512 (t0) REVERT: G 77 LYS cc_start: 0.9475 (mtmm) cc_final: 0.9241 (mtmm) REVERT: G 83 GLN cc_start: 0.8530 (tp-100) cc_final: 0.8258 (tp-100) REVERT: I 45 GLU cc_start: 0.8283 (pm20) cc_final: 0.7961 (pm20) REVERT: I 74 ASP cc_start: 0.8859 (t0) cc_final: 0.8527 (t0) REVERT: I 83 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8113 (tp-100) REVERT: J 45 GLU cc_start: 0.8387 (pm20) cc_final: 0.8064 (pm20) REVERT: J 74 ASP cc_start: 0.8869 (t0) cc_final: 0.8566 (t0) REVERT: J 83 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8301 (tp-100) outliers start: 42 outliers final: 28 residues processed: 321 average time/residue: 0.6818 time to fit residues: 235.4045 Evaluate side-chains 308 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 119 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 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 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: 1.9990 chunk 99 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 GLN E 116 GLN F 4 GLN H 4 GLN I 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.080162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.053287 restraints weight = 59572.984| |-----------------------------------------------------------------------------| r_work (start): 0.2568 rms_B_bonded: 3.87 r_work: 0.2414 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2413 r_free = 0.2413 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 = 0.2413 r_free = 0.2413 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13905 Z= 0.136 Angle : 0.661 9.505 18945 Z= 0.321 Chirality : 0.047 0.263 2015 Planarity : 0.004 0.038 2395 Dihedral : 5.675 59.508 1820 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.96 % Allowed : 26.69 % 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 are not related in a simple way. whole: -0.84 (0.20), residues: 1620 helix: 0.83 (0.73), residues: 45 sheet: -0.14 (0.19), residues: 680 loop : -0.93 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 204 TYR 0.025 0.001 TYR I 95 PHE 0.008 0.001 PHE G 38 TRP 0.025 0.001 TRP A 133 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (13880) covalent geometry : angle 0.63587 / 0.32 (18875) SS BOND : bond 0.00218 / 0.12 ( 5) SS BOND : angle 0.25406 / 0.14 ( 10) hydrogen bonds : bond 0.02912 / 1.88 ( 436) hydrogen bonds : angle 4.81214 / 3.34 ( 1533) link_BETA1-4 : bond 0.01603 / 0.89 ( 5) link_BETA1-4 : angle 4.64573 / 2.59 ( 15) link_NAG-ASN : bond 0.00443 / 0.29 ( 15) link_NAG-ASN : angle 2.65460 / 1.81 ( 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 328 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 TRP cc_start: 0.8285 (m-10) cc_final: 0.8067 (m-90) REVERT: F 45 GLU cc_start: 0.8286 (pm20) cc_final: 0.7994 (pm20) REVERT: G 74 ASP cc_start: 0.8755 (t0) cc_final: 0.8462 (t0) REVERT: G 77 LYS cc_start: 0.9484 (mtmm) cc_final: 0.9245 (mtmm) REVERT: G 83 GLN cc_start: 0.8511 (tp-100) cc_final: 0.8176 (tp-100) REVERT: H 66 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8493 (ttpt) REVERT: I 40 GLN cc_start: 0.8167 (tp-100) cc_final: 0.7906 (tp40) REVERT: I 45 GLU cc_start: 0.8334 (pm20) cc_final: 0.7997 (pm20) REVERT: I 74 ASP cc_start: 0.8859 (t0) cc_final: 0.8431 (t0) REVERT: I 77 LYS cc_start: 0.9501 (mtmm) cc_final: 0.9259 (mtmm) REVERT: I 83 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8179 (tp-100) REVERT: J 74 ASP cc_start: 0.8851 (t0) cc_final: 0.8538 (t0) REVERT: J 83 GLN cc_start: 0.8470 (tp-100) cc_final: 0.8192 (tp-100) REVERT: J 91 ASP cc_start: 0.7917 (m-30) cc_final: 0.7708 (m-30) outliers start: 42 outliers final: 25 residues processed: 317 average time/residue: 0.6886 time to fit residues: 234.8239 Evaluate side-chains 304 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 279 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 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 F residue 119 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 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 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: 0.8980 chunk 75 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN C 65 GLN D 65 GLN E 65 GLN E 116 GLN F 4 GLN H 4 GLN I 4 GLN I 115 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.078512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.051468 restraints weight = 59566.987| |-----------------------------------------------------------------------------| r_work (start): 0.2520 rms_B_bonded: 3.85 r_work: 0.2370 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2369 r_free = 0.2369 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 = 0.2369 r_free = 0.2369 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13905 Z= 0.188 Angle : 0.695 9.536 18945 Z= 0.338 Chirality : 0.048 0.277 2015 Planarity : 0.004 0.034 2395 Dihedral : 5.717 57.384 1820 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.31 % Allowed : 26.20 % Favored : 70.49 % 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 are not related in a simple way. whole: -0.83 (0.20), residues: 1620 helix: 0.51 (0.71), residues: 45 sheet: -0.11 (0.19), residues: 680 loop : -0.92 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 204 TYR 0.020 0.001 TYR I 95 PHE 0.010 0.001 PHE F 48 TRP 0.026 0.001 TRP D 133 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (13880) covalent geometry : angle 0.66856 / 0.33 (18875) SS BOND : bond 0.00298 / 0.17 ( 5) SS BOND : angle 0.08095 / 0.04 ( 10) hydrogen bonds : bond 0.03145 / 2.03 ( 436) hydrogen bonds : angle 4.93367 / 3.43 ( 1533) link_BETA1-4 : bond 0.01653 / 0.93 ( 5) link_BETA1-4 : angle 4.92324 / 2.74 ( 15) link_NAG-ASN : bond 0.00437 / 0.28 ( 15) link_NAG-ASN : angle 2.75727 / 1.89 ( 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 325 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 278 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: B 185 ARG cc_start: 0.8546 (tmt170) cc_final: 0.8221 (tmt170) REVERT: B 192 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8598 (tp30) REVERT: F 45 GLU cc_start: 0.8299 (pm20) cc_final: 0.8019 (pm20) REVERT: G 74 ASP cc_start: 0.8763 (t0) cc_final: 0.8453 (t0) REVERT: G 77 LYS cc_start: 0.9482 (mtmm) cc_final: 0.9224 (mtmm) REVERT: G 83 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8157 (tp-100) REVERT: H 66 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8543 (ttpt) REVERT: I 2 GLN cc_start: 0.7734 (pm20) cc_final: 0.7515 (pm20) REVERT: I 45 GLU cc_start: 0.8371 (pm20) cc_final: 0.8056 (pm20) REVERT: I 74 ASP cc_start: 0.8871 (t0) cc_final: 0.8520 (t0) REVERT: I 83 GLN cc_start: 0.8471 (tp-100) cc_final: 0.8186 (tp-100) REVERT: J 74 ASP cc_start: 0.8884 (t0) cc_final: 0.8536 (t0) REVERT: J 83 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8124 (tp-100) outliers start: 47 outliers final: 38 residues processed: 316 average time/residue: 0.6804 time to fit residues: 231.7739 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 : 0.557 ------------------------------------------------------------------------------- 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 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 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 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 F residue 119 VAL Chi-restraints excluded: chain G residue 64 SER 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 66 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 8 optimal weight: 0.0770 chunk 155 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.080252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.052942 restraints weight = 63239.544| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 4.00 r_work: 0.2405 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2403 r_free = 0.2403 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 = 0.2403 r_free = 0.2403 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13905 Z= 0.132 Angle : 0.673 9.501 18945 Z= 0.327 Chirality : 0.047 0.263 2015 Planarity : 0.004 0.043 2395 Dihedral : 5.597 55.855 1820 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.96 % Allowed : 26.69 % 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 are not related in a simple way. whole: -0.79 (0.20), residues: 1620 helix: 0.67 (0.73), residues: 45 sheet: -0.11 (0.19), residues: 680 loop : -0.89 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 204 TYR 0.018 0.001 TYR I 95 PHE 0.010 0.001 PHE G 38 TRP 0.028 0.001 TRP D 133 HIS 0.000 0.000 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (13880) covalent geometry : angle 0.64850 / 0.32 (18875) SS BOND : bond 0.00236 / 0.13 ( 5) SS BOND : angle 0.31822 / 0.17 ( 10) hydrogen bonds : bond 0.02846 / 1.83 ( 436) hydrogen bonds : angle 4.77883 / 3.32 ( 1533) link_BETA1-4 : bond 0.01696 / 0.95 ( 5) link_BETA1-4 : angle 4.62022 / 2.57 ( 15) link_NAG-ASN : bond 0.00461 / 0.31 ( 15) link_NAG-ASN : angle 2.65398 / 1.81 ( 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 326 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: B 192 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8517 (tp30) REVERT: F 45 GLU cc_start: 0.8309 (pm20) cc_final: 0.8018 (pm20) REVERT: F 74 ASP cc_start: 0.8780 (t0) cc_final: 0.8530 (t0) REVERT: G 74 ASP cc_start: 0.8751 (t0) cc_final: 0.8467 (t0) REVERT: G 77 LYS cc_start: 0.9489 (mtmm) cc_final: 0.9235 (mtmm) REVERT: G 83 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8143 (tp-100) REVERT: H 47 GLU cc_start: 0.8516 (pp20) cc_final: 0.8266 (pp20) REVERT: H 74 ASP cc_start: 0.8768 (t0) cc_final: 0.8458 (t0) REVERT: H 77 LYS cc_start: 0.9430 (mtmm) cc_final: 0.9167 (ptpp) REVERT: H 96 TYR cc_start: 0.8579 (p90) cc_final: 0.8343 (p90) REVERT: I 40 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7902 (tp40) REVERT: I 45 GLU cc_start: 0.8394 (pm20) cc_final: 0.8064 (pm20) REVERT: I 74 ASP cc_start: 0.8872 (t0) cc_final: 0.8456 (t0) REVERT: I 77 LYS cc_start: 0.9510 (mtmm) cc_final: 0.9279 (mtmm) REVERT: I 83 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8242 (tp-100) REVERT: J 74 ASP cc_start: 0.8868 (t0) cc_final: 0.8490 (t0) REVERT: J 83 GLN cc_start: 0.8331 (tp-100) cc_final: 0.8048 (tp-100) REVERT: J 84 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7984 (mtp) outliers start: 42 outliers final: 34 residues processed: 315 average time/residue: 0.6933 time to fit residues: 235.2451 Evaluate side-chains 314 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 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 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 F residue 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 119 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 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 2 GLN Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 1 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3127 r_free = 0.3127 target = 0.080272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.053886 restraints weight = 39264.311| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 3.36 r_work: 0.2442 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 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 = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13905 Z= 0.135 Angle : 0.677 9.513 18945 Z= 0.329 Chirality : 0.047 0.260 2015 Planarity : 0.004 0.042 2395 Dihedral : 5.551 54.518 1820 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.89 % Allowed : 26.76 % 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 are not related in a simple way. whole: -0.75 (0.20), residues: 1620 helix: 0.75 (0.73), 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 0.009 0.001 ARG C 204 TYR 0.017 0.001 TYR G 60 PHE 0.009 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/Z covalent geometry : bond 0.00307 / 0.13 (13880) covalent geometry : angle 0.65321 / 0.32 (18875) SS BOND : bond 0.00218 / 0.12 ( 5) SS BOND : angle 0.25588 / 0.14 ( 10) hydrogen bonds : bond 0.02829 / 1.81 ( 436) hydrogen bonds : angle 4.74419 / 3.29 ( 1533) link_BETA1-4 : bond 0.01652 / 0.92 ( 5) link_BETA1-4 : angle 4.60314 / 2.56 ( 15) link_NAG-ASN : bond 0.00451 / 0.30 ( 15) link_NAG-ASN : angle 2.62570 / 1.79 ( 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 321 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 0.516 Fit side-chains REVERT: B 192 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8595 (tp30) REVERT: F 45 GLU cc_start: 0.8291 (pm20) cc_final: 0.8005 (pm20) REVERT: F 74 ASP cc_start: 0.8822 (t0) cc_final: 0.8449 (t0) REVERT: G 74 ASP cc_start: 0.8757 (t0) cc_final: 0.8467 (t0) REVERT: G 77 LYS cc_start: 0.9495 (mtmm) cc_final: 0.9237 (mtmm) REVERT: G 83 GLN cc_start: 0.8521 (tp-100) cc_final: 0.8158 (tp-100) REVERT: H 47 GLU cc_start: 0.8494 (pp20) cc_final: 0.8242 (pp20) REVERT: H 66 LYS cc_start: 0.8917 (ptmm) cc_final: 0.8616 (ptmm) REVERT: H 74 ASP cc_start: 0.8783 (t0) cc_final: 0.8457 (t0) REVERT: H 77 LYS cc_start: 0.9426 (mtmm) cc_final: 0.9171 (ptpp) REVERT: I 40 GLN cc_start: 0.8235 (tp-100) cc_final: 0.7942 (tp40) REVERT: I 45 GLU cc_start: 0.8372 (pm20) cc_final: 0.8049 (pm20) REVERT: I 74 ASP cc_start: 0.8864 (t0) cc_final: 0.8435 (t0) REVERT: I 77 LYS cc_start: 0.9510 (mtmm) cc_final: 0.9267 (mtmm) REVERT: I 83 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8275 (tp-100) REVERT: J 74 ASP cc_start: 0.8862 (t0) cc_final: 0.8534 (t0) outliers start: 41 outliers final: 33 residues processed: 312 average time/residue: 0.7024 time to fit residues: 236.1673 Evaluate side-chains 312 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 D residue 201 VAL 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 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 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 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 125 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 GLN E 116 GLN F 2 GLN F 4 GLN H 2 GLN H 4 GLN I 2 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 = 0.3055 r_free = 0.3055 target = 0.076384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.049825 restraints weight = 37453.927| |-----------------------------------------------------------------------------| r_work (start): 0.2485 rms_B_bonded: 3.27 r_work: 0.2341 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2222 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2220 r_free = 0.2220 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2220 r_free = 0.2220 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9189 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 13905 Z= 0.325 Angle : 0.775 9.613 18945 Z= 0.381 Chirality : 0.052 0.299 2015 Planarity : 0.005 0.046 2395 Dihedral : 5.908 55.635 1820 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.61 % Allowed : 27.11 % Favored : 70.28 % 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 are not related in a simple way. whole: -0.83 (0.20), residues: 1620 helix: -0.01 (0.67), residues: 45 sheet: -0.11 (0.19), residues: 680 loop : -0.90 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 204 TYR 0.019 0.002 TYR I 95 PHE 0.012 0.002 PHE G 48 TRP 0.030 0.002 TRP A 133 HIS 0.003 0.001 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.33 (13880) covalent geometry : angle 0.74848 / 0.37 (18875) SS BOND : bond 0.00464 / 0.27 ( 5) SS BOND : angle 0.49643 / 0.26 ( 10) hydrogen bonds : bond 0.03594 / 2.31 ( 436) hydrogen bonds : angle 5.10563 / 3.55 ( 1533) link_BETA1-4 : bond 0.01573 / 0.87 ( 5) link_BETA1-4 : angle 5.34974 / 2.97 ( 15) link_NAG-ASN : bond 0.00441 / 0.26 ( 15) link_NAG-ASN : angle 2.92624 / 2.02 ( 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 305 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.538 Fit side-chains REVERT: B 192 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8594 (tp30) REVERT: F 45 GLU cc_start: 0.8387 (pm20) cc_final: 0.8097 (pm20) REVERT: F 74 ASP cc_start: 0.8904 (t0) cc_final: 0.8507 (t0) REVERT: G 74 ASP cc_start: 0.8818 (t0) cc_final: 0.8490 (t0) REVERT: G 77 LYS cc_start: 0.9483 (mtmm) cc_final: 0.9198 (mtmm) REVERT: G 83 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8168 (tp-100) REVERT: H 46 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7623 (ttm170) REVERT: H 66 LYS cc_start: 0.8958 (ptmm) cc_final: 0.8579 (ptmm) REVERT: H 74 ASP cc_start: 0.8843 (t0) cc_final: 0.8215 (t0) REVERT: H 77 LYS cc_start: 0.9448 (mtmm) cc_final: 0.8789 (mtmm) REVERT: I 45 GLU cc_start: 0.8445 (pm20) cc_final: 0.8161 (pm20) REVERT: I 46 ARG cc_start: 0.8340 (ttm170) cc_final: 0.8065 (ttm170) REVERT: I 74 ASP cc_start: 0.8968 (t0) cc_final: 0.8587 (t0) REVERT: I 83 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8250 (tp-100) REVERT: J 74 ASP cc_start: 0.8946 (t0) cc_final: 0.8602 (t0) outliers start: 37 outliers final: 35 residues processed: 297 average time/residue: 0.6956 time to fit residues: 222.2851 Evaluate side-chains 300 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 D residue 201 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 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 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 2 GLN 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 J residue 2 GLN 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: 0.6980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 61 optimal weight: 0.1980 chunk 73 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN E 116 GLN F 2 GLN H 2 GLN H 4 GLN ** I 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN J 2 GLN J 85 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.076603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.049057 restraints weight = 71880.901| |-----------------------------------------------------------------------------| r_work (start): 0.2466 rms_B_bonded: 4.09 r_work: 0.2303 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2301 r_free = 0.2301 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2301 r_free = 0.2301 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.291 13905 Z= 0.472 Angle : 1.348 59.169 18945 Z= 0.785 Chirality : 0.056 0.845 2015 Planarity : 0.006 0.157 2395 Dihedral : 5.913 55.665 1820 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.96 % Allowed : 26.83 % Favored : 70.21 % Cbeta Deviations : 0.26 % 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 are not related in a simple way. whole: -0.84 (0.19), residues: 1620 helix: -0.01 (0.67), residues: 45 sheet: -0.13 (0.19), residues: 680 loop : -0.90 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 4 TYR 0.016 0.002 TYR I 95 PHE 0.012 0.002 PHE G 48 TRP 0.024 0.001 TRP A 133 HIS 0.003 0.001 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.01033 / 0.47 (13880) covalent geometry : angle 1.33409 / 0.78 (18875) SS BOND : bond 0.00309 / 0.17 ( 5) SS BOND : angle 0.41749 / 0.22 ( 10) hydrogen bonds : bond 0.03596 / 2.32 ( 436) hydrogen bonds : angle 5.10974 / 3.55 ( 1533) link_BETA1-4 : bond 0.01489 / 0.85 ( 5) link_BETA1-4 : angle 5.37879 / 2.98 ( 15) link_NAG-ASN : bond 0.00414 / 0.25 ( 15) link_NAG-ASN : angle 2.90362 / 2.00 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6509.45 seconds wall clock time: 111 minutes 36.91 seconds (6696.91 seconds total)