Starting phenix.real_space_refine on Thu May 15 19:00:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c9x_16513/05_2025/8c9x_16513.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c9x_16513/05_2025/8c9x_16513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c9x_16513/05_2025/8c9x_16513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c9x_16513/05_2025/8c9x_16513.map" model { file = "/net/cci-nas-00/data/ceres_data/8c9x_16513/05_2025/8c9x_16513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c9x_16513/05_2025/8c9x_16513.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13485 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1765 Chain: "B" Number of atoms: 1726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1765 Chain: "C" Number of atoms: 1726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1765 Chain: "D" Number of atoms: 1726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1765 Chain: "E" Number of atoms: 1726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 207, 1719 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 193} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1765 Chain: "F" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "G" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "J" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.88, per 1000 atoms: 0.81 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: 2.95 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.94 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: 3.93 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4225 1.34 - 1.46: 3523 1.46 - 1.58: 6042 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 13880 Sorted by residual: bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.29e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.11e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.09e+00 ... (remaining 13875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 18293 1.70 - 3.41: 477 3.41 - 5.11: 85 5.11 - 6.82: 15 6.82 - 8.52: 5 Bond angle restraints: 18875 Sorted by residual: angle pdb=" CB LYS F 44 " pdb=" CG LYS F 44 " pdb=" CD LYS F 44 " ideal model delta sigma weight residual 111.30 119.82 -8.52 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CB LYS I 44 " pdb=" CG LYS I 44 " pdb=" CD LYS I 44 " ideal model delta sigma weight residual 111.30 119.82 -8.52 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CB LYS H 44 " pdb=" CG LYS H 44 " pdb=" CD LYS H 44 " ideal model delta sigma weight residual 111.30 119.81 -8.51 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CB LYS G 44 " pdb=" CG LYS G 44 " pdb=" CD LYS G 44 " ideal model delta sigma weight residual 111.30 119.79 -8.49 2.30e+00 1.89e-01 1.36e+01 angle pdb=" CB LYS J 44 " pdb=" CG LYS J 44 " pdb=" CD LYS J 44 " ideal model delta sigma weight residual 111.30 119.77 -8.47 2.30e+00 1.89e-01 1.36e+01 ... (remaining 18870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 7094 17.45 - 34.90: 856 34.90 - 52.35: 245 52.35 - 69.80: 85 69.80 - 87.25: 25 Dihedral angle restraints: 8305 sinusoidal: 3540 harmonic: 4765 Sorted by residual: dihedral pdb=" CA ASP B 174 " pdb=" CB ASP B 174 " pdb=" CG ASP B 174 " pdb=" OD1 ASP B 174 " ideal model delta sinusoidal sigma weight residual -30.00 -88.18 58.18 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 174 " pdb=" CB ASP A 174 " pdb=" CG ASP A 174 " pdb=" OD1 ASP A 174 " ideal model delta sinusoidal sigma weight residual -30.00 -88.15 58.15 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP E 174 " pdb=" CB ASP E 174 " pdb=" CG ASP E 174 " pdb=" OD1 ASP E 174 " ideal model delta sinusoidal sigma weight residual -30.00 -88.13 58.13 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 8302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1603 0.052 - 0.104: 323 0.104 - 0.156: 69 0.156 - 0.207: 10 0.207 - 0.259: 10 Chirality restraints: 2015 Sorted by residual: chirality pdb=" C1 NAG D 402 " pdb=" ND2 ASN D 67 " pdb=" C2 NAG D 402 " pdb=" O5 NAG D 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG C 402 " pdb=" ND2 ASN C 67 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 67 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2012 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 401 " 0.021 2.00e-02 2.50e+03 1.83e-02 4.19e+00 pdb=" C7 NAG A 401 " -0.003 2.00e-02 2.50e+03 pdb=" C8 NAG A 401 " -0.005 2.00e-02 2.50e+03 pdb=" N2 NAG A 401 " -0.030 2.00e-02 2.50e+03 pdb=" O7 NAG A 401 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 133 " 0.010 2.00e-02 2.50e+03 1.03e-02 2.66e+00 pdb=" CG TRP A 133 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 133 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 133 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 133 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 133 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 133 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 133 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 133 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 133 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 88 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO F 89 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 89 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 89 " 0.022 5.00e-02 4.00e+02 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 429 2.69 - 3.25: 12130 3.25 - 3.80: 22356 3.80 - 4.35: 30302 4.35 - 4.90: 49700 Nonbonded interactions: 114917 Sorted by model distance: nonbonded pdb=" OE2 GLU A 9 " pdb=" OH TYR F 33 " model vdw 2.143 3.040 nonbonded pdb=" OE2 GLU D 9 " pdb=" OH TYR I 33 " model vdw 2.166 3.040 nonbonded pdb=" N GLU I 90 " pdb=" OE1 GLU I 90 " model vdw 2.175 3.120 nonbonded pdb=" N GLU J 90 " pdb=" OE1 GLU J 90 " model vdw 2.175 3.120 nonbonded pdb=" N GLU G 90 " pdb=" OE1 GLU G 90 " model vdw 2.175 3.120 ... (remaining 114912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.150 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.080 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:9.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13905 Z= 0.166 Angle : 0.717 11.086 18945 Z= 0.356 Chirality : 0.048 0.259 2015 Planarity : 0.005 0.040 2395 Dihedral : 17.444 87.247 5260 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (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 TRP 0.028 0.002 TRP A 133 HIS 0.002 0.000 HIS E 140 PHE 0.012 0.001 PHE H 48 TYR 0.012 0.001 TYR I 95 ARG 0.008 0.001 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 15) link_NAG-ASN : angle 2.37786 ( 45) link_BETA1-4 : bond 0.01888 ( 5) link_BETA1-4 : angle 7.00962 ( 15) hydrogen bonds : bond 0.09957 ( 436) hydrogen bonds : angle 6.26084 ( 1533) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.69375 ( 10) covalent geometry : bond 0.00363 (13880) covalent geometry : angle 0.68009 (18875) *********************** 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 : 1.447 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: 1.4205 time to fit residues: 537.8202 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 : 1.359 ------------------------------------------------------------------------------- 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 135 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 116 GLN B 3 GLN B 170 ASN C 3 GLN D 3 GLN D 170 ASN E 3 GLN F 4 GLN G 40 GLN H 4 GLN I 4 GLN I 115 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.080743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.054484 restraints weight = 42214.573| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 3.46 r_work: 0.2461 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13905 Z= 0.154 Angle : 0.691 8.989 18945 Z= 0.339 Chirality : 0.049 0.305 2015 Planarity : 0.004 0.030 2395 Dihedral : 9.124 56.970 2271 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.15 % Allowed : 23.80 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1620 helix: 1.09 (0.69), residues: 45 sheet: -0.15 (0.18), residues: 735 loop : -1.07 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 133 HIS 0.001 0.000 HIS D 140 PHE 0.015 0.001 PHE G 38 TYR 0.022 0.002 TYR J 95 ARG 0.005 0.001 ARG E 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 15) link_NAG-ASN : angle 2.50856 ( 45) link_BETA1-4 : bond 0.01833 ( 5) link_BETA1-4 : angle 5.29178 ( 15) hydrogen bonds : bond 0.03421 ( 436) hydrogen bonds : angle 5.30690 ( 1533) SS BOND : bond 0.00276 ( 5) SS BOND : angle 0.40843 ( 10) covalent geometry : bond 0.00342 (13880) covalent geometry : angle 0.66454 (18875) *********************** 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 362 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 303 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: F 74 ASP cc_start: 0.8699 (t0) cc_final: 0.8442 (t0) REVERT: G 74 ASP cc_start: 0.8770 (t0) cc_final: 0.8546 (t0) REVERT: G 77 LYS cc_start: 0.9443 (mtmm) cc_final: 0.9216 (mtmm) REVERT: H 2 GLN cc_start: 0.7877 (mp10) cc_final: 0.7589 (pm20) REVERT: H 74 ASP cc_start: 0.8759 (t0) cc_final: 0.8523 (t0) REVERT: H 77 LYS cc_start: 0.9465 (mtmm) cc_final: 0.9229 (mtmm) REVERT: I 74 ASP cc_start: 0.8750 (t0) cc_final: 0.8509 (t0) REVERT: J 46 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7586 (ttm110) REVERT: J 96 TYR cc_start: 0.8570 (p90) cc_final: 0.8311 (p90) outliers start: 59 outliers final: 32 residues processed: 350 average time/residue: 1.4589 time to fit residues: 549.8043 Evaluate side-chains 321 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 288 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 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 46 ARG 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 I residue 36 VAL 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 8 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 147 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 170 ASN B 170 ASN C 47 GLN C 170 ASN D 47 GLN D 116 GLN D 170 ASN E 47 GLN E 116 GLN F 4 GLN I 4 GLN I 115 GLN J 4 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.079097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.052666 restraints weight = 43332.929| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 3.47 r_work: 0.2414 rms_B_bonded: 3.35 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 = 0.47 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 | |-----------------------------------------------------------------------------| r_final: 0.2413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13905 Z= 0.183 Angle : 0.685 9.432 18945 Z= 0.334 Chirality : 0.049 0.291 2015 Planarity : 0.004 0.036 2395 Dihedral : 8.489 56.055 2250 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.23 % Allowed : 25.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1620 helix: 0.73 (0.70), residues: 45 sheet: -0.12 (0.19), residues: 680 loop : -1.06 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 133 HIS 0.001 0.000 HIS A 140 PHE 0.010 0.001 PHE F 48 TYR 0.023 0.002 TYR I 95 ARG 0.005 0.001 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 15) link_NAG-ASN : angle 2.70723 ( 45) link_BETA1-4 : bond 0.01709 ( 5) link_BETA1-4 : angle 5.36004 ( 15) hydrogen bonds : bond 0.03363 ( 436) hydrogen bonds : angle 5.17914 ( 1533) SS BOND : bond 0.00406 ( 5) SS BOND : angle 0.35050 ( 10) covalent geometry : bond 0.00412 (13880) covalent geometry : angle 0.65647 (18875) *********************** 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 349 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 289 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 185 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8265 (ptm-80) REVERT: F 20 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8359 (tptp) REVERT: F 47 GLU cc_start: 0.8672 (pp20) cc_final: 0.8465 (pp20) REVERT: F 74 ASP cc_start: 0.8783 (t0) cc_final: 0.8455 (t0) REVERT: G 74 ASP cc_start: 0.8766 (t0) cc_final: 0.8506 (t0) REVERT: G 77 LYS cc_start: 0.9457 (mtmm) cc_final: 0.9201 (mtmm) REVERT: G 83 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8266 (tp-100) REVERT: H 2 GLN cc_start: 0.7969 (mp10) cc_final: 0.7724 (pm20) REVERT: I 74 ASP cc_start: 0.8813 (t0) cc_final: 0.8513 (t0) REVERT: I 83 GLN cc_start: 0.8569 (tp-100) cc_final: 0.8315 (tp-100) outliers start: 60 outliers final: 38 residues processed: 333 average time/residue: 1.4813 time to fit residues: 531.1159 Evaluate side-chains 319 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 280 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 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 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 E residue 191 LYS 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 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 46 ARG 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 64 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 100 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 0.0010 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 170 ASN B 139 GLN B 170 ASN C 47 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.080381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.053308 restraints weight = 62173.504| |-----------------------------------------------------------------------------| r_work (start): 0.2568 rms_B_bonded: 3.97 r_work: 0.2418 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2415 r_free = 0.2415 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 = 0.2415 r_free = 0.2415 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13905 Z= 0.133 Angle : 0.657 9.526 18945 Z= 0.319 Chirality : 0.047 0.276 2015 Planarity : 0.004 0.034 2395 Dihedral : 8.207 55.939 2245 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.94 % Allowed : 26.20 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1620 helix: 0.79 (0.72), residues: 45 sheet: -0.13 (0.19), residues: 680 loop : -1.02 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 133 HIS 0.001 0.000 HIS B 140 PHE 0.009 0.001 PHE J 38 TYR 0.015 0.001 TYR A 128 ARG 0.007 0.001 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 15) link_NAG-ASN : angle 2.56445 ( 45) link_BETA1-4 : bond 0.01731 ( 5) link_BETA1-4 : angle 5.12895 ( 15) hydrogen bonds : bond 0.02994 ( 436) hydrogen bonds : angle 4.98775 ( 1533) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.39699 ( 10) covalent geometry : bond 0.00296 (13880) covalent geometry : angle 0.62934 (18875) *********************** 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 349 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 293 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: F 74 ASP cc_start: 0.8800 (t0) cc_final: 0.8447 (t0) REVERT: G 47 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7017 (pp20) REVERT: G 74 ASP cc_start: 0.8767 (t0) cc_final: 0.8498 (t0) REVERT: G 77 LYS cc_start: 0.9468 (mtmm) cc_final: 0.9225 (mtmm) REVERT: I 45 GLU cc_start: 0.8317 (pm20) cc_final: 0.7975 (pm20) REVERT: I 74 ASP cc_start: 0.8824 (t0) cc_final: 0.8523 (t0) REVERT: I 83 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8276 (tp-100) REVERT: J 2 GLN cc_start: 0.7705 (pm20) cc_final: 0.7494 (pm20) REVERT: J 83 GLN cc_start: 0.8571 (tp-100) cc_final: 0.8327 (tp-100) outliers start: 56 outliers final: 32 residues processed: 333 average time/residue: 1.4708 time to fit residues: 526.3679 Evaluate side-chains 319 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 189 CYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 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 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 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 0.3980 chunk 34 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 170 ASN D 47 GLN D 116 GLN E 116 GLN F 4 GLN I 4 GLN I 115 GLN J 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.081055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.054568 restraints weight = 46876.312| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 3.58 r_work: 0.2454 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2452 r_free = 0.2452 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 = 0.2452 r_free = 0.2452 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1562 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= 0.119 Angle : 0.648 9.521 18945 Z= 0.314 Chirality : 0.047 0.268 2015 Planarity : 0.004 0.033 2395 Dihedral : 8.103 55.946 2240 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.03 % Allowed : 26.83 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.20), residues: 1620 helix: 0.91 (0.72), residues: 45 sheet: -0.11 (0.19), residues: 680 loop : -0.98 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 133 HIS 0.000 0.000 HIS H 32 PHE 0.011 0.001 PHE H 38 TYR 0.017 0.001 TYR I 96 ARG 0.006 0.001 ARG A 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 15) link_NAG-ASN : angle 2.48213 ( 45) link_BETA1-4 : bond 0.01706 ( 5) link_BETA1-4 : angle 5.04448 ( 15) hydrogen bonds : bond 0.02807 ( 436) hydrogen bonds : angle 4.85588 ( 1533) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.40873 ( 10) covalent geometry : bond 0.00265 (13880) covalent geometry : angle 0.62115 (18875) *********************** 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 341 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: B 185 ARG cc_start: 0.8564 (ttt-90) cc_final: 0.8355 (ptm-80) REVERT: C 185 ARG cc_start: 0.8542 (ttt-90) cc_final: 0.8340 (ptm-80) REVERT: G 47 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.6952 (pp20) REVERT: G 66 LYS cc_start: 0.8958 (ttmm) cc_final: 0.8655 (ttpt) REVERT: G 74 ASP cc_start: 0.8763 (t0) cc_final: 0.8465 (t0) REVERT: G 77 LYS cc_start: 0.9481 (mtmm) cc_final: 0.9149 (mtmm) REVERT: G 83 GLN cc_start: 0.8499 (tp-100) cc_final: 0.8219 (tp-100) REVERT: I 45 GLU cc_start: 0.8311 (pm20) cc_final: 0.7978 (pm20) REVERT: I 74 ASP cc_start: 0.8825 (t0) cc_final: 0.8497 (t0) REVERT: I 83 GLN cc_start: 0.8494 (tp-100) cc_final: 0.8225 (tp-100) REVERT: J 74 ASP cc_start: 0.8723 (t0) cc_final: 0.8486 (t0) REVERT: J 83 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8282 (tp-100) outliers start: 43 outliers final: 27 residues processed: 327 average time/residue: 1.4320 time to fit residues: 504.0866 Evaluate side-chains 308 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 136 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 67 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN D 47 GLN D 116 GLN E 116 GLN F 4 GLN I 4 GLN I 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.080704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.053743 restraints weight = 58294.334| |-----------------------------------------------------------------------------| r_work (start): 0.2580 rms_B_bonded: 3.87 r_work: 0.2428 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2427 r_free = 0.2427 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 = 0.2427 r_free = 0.2427 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1677 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= 0.133 Angle : 0.654 9.536 18945 Z= 0.317 Chirality : 0.047 0.267 2015 Planarity : 0.004 0.039 2395 Dihedral : 8.163 56.890 2240 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.89 % Allowed : 26.90 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1620 helix: 0.83 (0.71), residues: 45 sheet: -0.08 (0.19), residues: 680 loop : -0.94 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 133 HIS 0.001 0.000 HIS A 140 PHE 0.009 0.001 PHE H 38 TYR 0.018 0.001 TYR I 96 ARG 0.009 0.001 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 15) link_NAG-ASN : angle 2.48223 ( 45) link_BETA1-4 : bond 0.01629 ( 5) link_BETA1-4 : angle 5.07453 ( 15) hydrogen bonds : bond 0.02861 ( 436) hydrogen bonds : angle 4.81944 ( 1533) SS BOND : bond 0.00239 ( 5) SS BOND : angle 0.26421 ( 10) covalent geometry : bond 0.00299 (13880) covalent geometry : angle 0.62790 (18875) *********************** 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 330 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: B 8 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9178 (ttpp) REVERT: B 192 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8601 (tp30) REVERT: C 185 ARG cc_start: 0.8552 (ttt-90) cc_final: 0.8348 (ptm-80) REVERT: E 192 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8534 (tp30) REVERT: F 45 GLU cc_start: 0.8277 (pm20) cc_final: 0.7977 (pm20) REVERT: G 66 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8705 (ttpt) REVERT: G 74 ASP cc_start: 0.8768 (t0) cc_final: 0.8456 (t0) REVERT: G 77 LYS cc_start: 0.9495 (mtmm) cc_final: 0.9157 (mtmm) REVERT: G 83 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8158 (tp-100) REVERT: I 45 GLU cc_start: 0.8338 (pm20) cc_final: 0.8027 (pm20) REVERT: I 74 ASP cc_start: 0.8854 (t0) cc_final: 0.8519 (t0) REVERT: I 83 GLN cc_start: 0.8455 (tp-100) cc_final: 0.8173 (tp-100) REVERT: J 83 GLN cc_start: 0.8513 (tp-100) cc_final: 0.8244 (tp-100) outliers start: 41 outliers final: 29 residues processed: 319 average time/residue: 1.4572 time to fit residues: 500.4207 Evaluate side-chains 314 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 282 time to evaluate : 1.557 ------------------------------------------------------------------------------- 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 8 LYS 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 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 26 GLN Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain F residue 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 22 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 I residue 119 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 116 GLN B 65 GLN D 65 GLN E 116 GLN F 4 GLN I 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.052118 restraints weight = 52269.830| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 3.73 r_work: 0.2391 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2389 r_free = 0.2389 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2389 r_free = 0.2389 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13905 Z= 0.180 Angle : 0.681 9.589 18945 Z= 0.332 Chirality : 0.048 0.279 2015 Planarity : 0.004 0.036 2395 Dihedral : 8.323 59.728 2240 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.31 % Allowed : 26.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1620 helix: 0.55 (0.70), residues: 45 sheet: -0.05 (0.19), residues: 680 loop : -0.93 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 133 HIS 0.002 0.000 HIS A 140 PHE 0.010 0.001 PHE J 48 TYR 0.016 0.001 TYR I 96 ARG 0.005 0.001 ARG E 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 15) link_NAG-ASN : angle 2.61658 ( 45) link_BETA1-4 : bond 0.01604 ( 5) link_BETA1-4 : angle 5.26073 ( 15) hydrogen bonds : bond 0.03092 ( 436) hydrogen bonds : angle 4.93967 ( 1533) SS BOND : bond 0.00306 ( 5) SS BOND : angle 0.09162 ( 10) covalent geometry : bond 0.00403 (13880) covalent geometry : angle 0.65341 (18875) *********************** 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 328 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: B 133 TRP cc_start: 0.8296 (m-10) cc_final: 0.8049 (m-90) REVERT: B 192 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8584 (tp30) REVERT: C 185 ARG cc_start: 0.8577 (ttt-90) cc_final: 0.8374 (ptm-80) REVERT: D 185 ARG cc_start: 0.8522 (ttt-90) cc_final: 0.8306 (tmt170) REVERT: F 45 GLU cc_start: 0.8308 (pm20) cc_final: 0.8016 (pm20) REVERT: G 74 ASP cc_start: 0.8774 (t0) cc_final: 0.8493 (t0) REVERT: G 77 LYS cc_start: 0.9484 (mtmm) cc_final: 0.9243 (mtmm) REVERT: G 83 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8149 (tp-100) REVERT: I 45 GLU cc_start: 0.8378 (pm20) cc_final: 0.8051 (pm20) REVERT: I 74 ASP cc_start: 0.8862 (t0) cc_final: 0.8412 (t0) REVERT: I 77 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9209 (mtmm) REVERT: I 83 GLN cc_start: 0.8385 (tp-100) cc_final: 0.8072 (tp-100) REVERT: J 83 GLN cc_start: 0.8432 (tp-100) cc_final: 0.8155 (tp-100) outliers start: 47 outliers final: 31 residues processed: 315 average time/residue: 1.4219 time to fit residues: 482.4361 Evaluate side-chains 309 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 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 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 22 SER Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain I residue 94 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 70 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 GLN F 4 GLN I 2 GLN I 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.053069 restraints weight = 52342.878| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 3.71 r_work: 0.2411 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2410 r_free = 0.2410 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 = 0.2410 r_free = 0.2410 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13905 Z= 0.149 Angle : 0.681 9.571 18945 Z= 0.332 Chirality : 0.048 0.273 2015 Planarity : 0.004 0.046 2395 Dihedral : 8.271 59.443 2240 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.46 % Allowed : 27.89 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.20), residues: 1620 helix: 0.54 (0.72), residues: 45 sheet: -0.05 (0.19), residues: 680 loop : -0.89 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 133 HIS 0.001 0.000 HIS A 140 PHE 0.009 0.001 PHE H 38 TYR 0.017 0.001 TYR G 60 ARG 0.010 0.001 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 15) link_NAG-ASN : angle 2.53952 ( 45) link_BETA1-4 : bond 0.01697 ( 5) link_BETA1-4 : angle 5.14917 ( 15) hydrogen bonds : bond 0.02931 ( 436) hydrogen bonds : angle 4.83525 ( 1533) SS BOND : bond 0.00276 ( 5) SS BOND : angle 0.24826 ( 10) covalent geometry : bond 0.00337 (13880) covalent geometry : angle 0.65508 (18875) *********************** 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 319 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 1.475 Fit side-chains REVERT: B 133 TRP cc_start: 0.8281 (m-10) cc_final: 0.8053 (m-90) REVERT: B 192 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8601 (tp30) REVERT: D 185 ARG cc_start: 0.8516 (ttt-90) cc_final: 0.8282 (tmt170) REVERT: F 45 GLU cc_start: 0.8296 (pm20) cc_final: 0.8012 (pm20) REVERT: F 74 ASP cc_start: 0.8783 (t0) cc_final: 0.8405 (t0) REVERT: G 74 ASP cc_start: 0.8756 (t0) cc_final: 0.8465 (t0) REVERT: G 77 LYS cc_start: 0.9491 (mtmm) cc_final: 0.9240 (mtmm) REVERT: G 83 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8115 (tp-100) REVERT: I 45 GLU cc_start: 0.8378 (pm20) cc_final: 0.8079 (pm20) REVERT: I 74 ASP cc_start: 0.8866 (t0) cc_final: 0.8435 (t0) REVERT: I 77 LYS cc_start: 0.9489 (mtmm) cc_final: 0.9246 (mtmm) REVERT: I 83 GLN cc_start: 0.8352 (tp-100) cc_final: 0.8035 (tp-100) outliers start: 35 outliers final: 28 residues processed: 310 average time/residue: 1.4248 time to fit residues: 475.8059 Evaluate side-chains 303 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 274 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 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 191 LYS 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 22 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 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 75 optimal weight: 0.0020 chunk 126 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 62 optimal weight: 0.3980 chunk 132 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN B 116 GLN E 116 GLN F 4 GLN I 2 GLN J 2 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.080507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.053720 restraints weight = 46776.121| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 3.59 r_work: 0.2432 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2430 r_free = 0.2430 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 = 0.2430 r_free = 0.2430 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13905 Z= 0.137 Angle : 0.678 9.555 18945 Z= 0.331 Chirality : 0.047 0.265 2015 Planarity : 0.004 0.044 2395 Dihedral : 8.207 57.587 2240 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.61 % Allowed : 27.82 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1620 helix: 0.65 (0.71), residues: 45 sheet: -0.02 (0.19), residues: 680 loop : -0.86 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 133 HIS 0.001 0.000 HIS A 140 PHE 0.010 0.001 PHE I 38 TYR 0.027 0.001 TYR I 95 ARG 0.010 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 15) link_NAG-ASN : angle 2.46429 ( 45) link_BETA1-4 : bond 0.01728 ( 5) link_BETA1-4 : angle 5.07925 ( 15) hydrogen bonds : bond 0.02842 ( 436) hydrogen bonds : angle 4.75770 ( 1533) SS BOND : bond 0.00244 ( 5) SS BOND : angle 0.30361 ( 10) covalent geometry : bond 0.00311 (13880) covalent geometry : angle 0.65336 (18875) *********************** 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 325 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 1.612 Fit side-chains REVERT: A 133 TRP cc_start: 0.8285 (m-10) cc_final: 0.8083 (m-90) REVERT: B 192 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8589 (tp30) REVERT: C 188 GLU cc_start: 0.8690 (pm20) cc_final: 0.8431 (pm20) REVERT: D 185 ARG cc_start: 0.8516 (ttt-90) cc_final: 0.8267 (tmt170) REVERT: E 133 TRP cc_start: 0.8322 (m-90) cc_final: 0.8112 (m-10) REVERT: F 45 GLU cc_start: 0.8291 (pm20) cc_final: 0.8025 (pm20) REVERT: F 74 ASP cc_start: 0.8801 (t0) cc_final: 0.8586 (t0) REVERT: G 74 ASP cc_start: 0.8743 (t0) cc_final: 0.8449 (t0) REVERT: G 77 LYS cc_start: 0.9492 (mtmm) cc_final: 0.9243 (mtmm) REVERT: G 83 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8100 (tp-100) REVERT: H 74 ASP cc_start: 0.8781 (t0) cc_final: 0.8491 (t0) REVERT: H 77 LYS cc_start: 0.9425 (mtmm) cc_final: 0.9176 (ptpp) REVERT: I 40 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7911 (tp40) REVERT: I 45 GLU cc_start: 0.8382 (pm20) cc_final: 0.8080 (pm20) REVERT: I 47 GLU cc_start: 0.8466 (pp20) cc_final: 0.8158 (pp20) REVERT: I 74 ASP cc_start: 0.8849 (t0) cc_final: 0.8462 (t0) REVERT: I 77 LYS cc_start: 0.9488 (mtmm) cc_final: 0.9284 (mtmm) REVERT: I 83 GLN cc_start: 0.8354 (tp-100) cc_final: 0.8058 (tp-100) outliers start: 37 outliers final: 32 residues processed: 315 average time/residue: 1.4044 time to fit residues: 477.1614 Evaluate side-chains 315 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 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 191 LYS 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 22 SER 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 94 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 36 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN E 116 GLN F 2 GLN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 GLN I 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.053900 restraints weight = 46849.770| |-----------------------------------------------------------------------------| r_work (start): 0.2580 rms_B_bonded: 3.57 r_work: 0.2439 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 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 = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13905 Z= 0.139 Angle : 0.694 9.561 18945 Z= 0.339 Chirality : 0.047 0.264 2015 Planarity : 0.004 0.044 2395 Dihedral : 8.194 56.840 2240 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.39 % Allowed : 28.31 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1620 helix: 0.65 (0.71), residues: 45 sheet: 0.00 (0.19), residues: 680 loop : -0.82 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 133 HIS 0.001 0.000 HIS A 140 PHE 0.009 0.001 PHE I 38 TYR 0.025 0.001 TYR I 95 ARG 0.010 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 15) link_NAG-ASN : angle 2.44777 ( 45) link_BETA1-4 : bond 0.01688 ( 5) link_BETA1-4 : angle 5.06682 ( 15) hydrogen bonds : bond 0.02825 ( 436) hydrogen bonds : angle 4.74754 ( 1533) SS BOND : bond 0.00235 ( 5) SS BOND : angle 0.29489 ( 10) covalent geometry : bond 0.00320 (13880) covalent geometry : angle 0.67013 (18875) ********************** 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 315 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 1.395 Fit side-chains REVERT: A 133 TRP cc_start: 0.8288 (m-10) cc_final: 0.8069 (m-90) REVERT: B 192 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8596 (tp30) REVERT: C 41 ASP cc_start: 0.8896 (t0) cc_final: 0.8659 (t0) REVERT: C 188 GLU cc_start: 0.8667 (pm20) cc_final: 0.8391 (pm20) REVERT: D 185 ARG cc_start: 0.8520 (ttt-90) cc_final: 0.8271 (tmt170) REVERT: E 133 TRP cc_start: 0.8323 (m-90) cc_final: 0.8115 (m-10) REVERT: F 45 GLU cc_start: 0.8288 (pm20) cc_final: 0.8030 (pm20) REVERT: F 74 ASP cc_start: 0.8774 (t0) cc_final: 0.8381 (t0) REVERT: G 74 ASP cc_start: 0.8744 (t0) cc_final: 0.8447 (t0) REVERT: G 77 LYS cc_start: 0.9493 (mtmm) cc_final: 0.9242 (mtmm) REVERT: G 83 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8121 (tp-100) REVERT: H 47 GLU cc_start: 0.8462 (pp20) cc_final: 0.8216 (pp20) REVERT: H 74 ASP cc_start: 0.8797 (t0) cc_final: 0.8498 (t0) REVERT: H 77 LYS cc_start: 0.9418 (mtmm) cc_final: 0.9176 (ptpp) REVERT: I 40 GLN cc_start: 0.8230 (tp-100) cc_final: 0.7949 (tp40) REVERT: I 45 GLU cc_start: 0.8375 (pm20) cc_final: 0.8097 (pm20) REVERT: I 47 GLU cc_start: 0.8430 (pp20) cc_final: 0.8125 (pp20) REVERT: I 74 ASP cc_start: 0.8853 (t0) cc_final: 0.8459 (t0) REVERT: I 83 GLN cc_start: 0.8392 (tp-100) cc_final: 0.8184 (tp-100) REVERT: J 74 ASP cc_start: 0.8869 (t0) cc_final: 0.8617 (t0) outliers start: 34 outliers final: 31 residues processed: 309 average time/residue: 1.4153 time to fit residues: 471.6962 Evaluate side-chains 308 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 276 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 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 191 LYS Chi-restraints excluded: chain F residue 2 GLN 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 22 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 I residue 106 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 129 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 152 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN B 116 GLN E 116 GLN F 2 GLN G 40 GLN I 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.053590 restraints weight = 58304.505| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 3.85 r_work: 0.2424 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2424 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.232 13905 Z= 0.211 Angle : 0.902 59.192 18945 Z= 0.486 Chirality : 0.047 0.264 2015 Planarity : 0.004 0.043 2395 Dihedral : 8.193 56.833 2240 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.25 % Allowed : 28.38 % Favored : 69.37 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1620 helix: 0.67 (0.72), residues: 45 sheet: 0.00 (0.19), residues: 680 loop : -0.82 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 133 HIS 0.001 0.000 HIS A 140 PHE 0.009 0.001 PHE I 38 TYR 0.021 0.001 TYR I 95 ARG 0.008 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 15) link_NAG-ASN : angle 2.44133 ( 45) link_BETA1-4 : bond 0.01767 ( 5) link_BETA1-4 : angle 5.16615 ( 15) hydrogen bonds : bond 0.02824 ( 436) hydrogen bonds : angle 4.74888 ( 1533) SS BOND : bond 0.00210 ( 5) SS BOND : angle 0.30284 ( 10) covalent geometry : bond 0.00458 (13880) covalent geometry : angle 0.88427 (18875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12855.05 seconds wall clock time: 221 minutes 18.89 seconds (13278.89 seconds total)