Starting phenix.real_space_refine on Thu Jun 12 02:56:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c9x_16513/06_2025/8c9x_16513.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c9x_16513/06_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_16513/06_2025/8c9x_16513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c9x_16513/06_2025/8c9x_16513.map" model { file = "/net/cci-nas-00/data/ceres_data/8c9x_16513/06_2025/8c9x_16513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c9x_16513/06_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-5710/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: 12.74, per 1000 atoms: 0.94 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: 3.25 Conformation dependent library (CDL) restraints added in 2.7 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: 2.35 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: 4.28 Time building geometry restraints manager: 3.81 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: 0.11 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: 4.550 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 39.120 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.090 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.240 ------------------------------------------------------------------------------- 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 : 1.573 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: 1.4211 time to fit residues: 538.9243 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 : 1.397 ------------------------------------------------------------------------------- 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 = 0.080744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.054482 restraints weight = 42213.878| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 3.46 r_work: 0.2459 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 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 8.990 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 5.29177 ( 15) hydrogen bonds : bond 0.03421 ( 436) hydrogen bonds : angle 5.30689 ( 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 : 1.562 Fit side-chains revert: symmetry clash REVERT: F 74 ASP cc_start: 0.8703 (t0) cc_final: 0.8446 (t0) REVERT: G 74 ASP cc_start: 0.8773 (t0) cc_final: 0.8549 (t0) REVERT: G 77 LYS cc_start: 0.9444 (mtmm) cc_final: 0.9217 (mtmm) REVERT: H 2 GLN cc_start: 0.7880 (mp10) cc_final: 0.7591 (pm20) REVERT: H 74 ASP cc_start: 0.8763 (t0) cc_final: 0.8527 (t0) REVERT: H 77 LYS cc_start: 0.9467 (mtmm) cc_final: 0.9230 (mtmm) REVERT: I 74 ASP cc_start: 0.8752 (t0) cc_final: 0.8511 (t0) REVERT: J 46 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7586 (ttm110) REVERT: J 96 TYR cc_start: 0.8574 (p90) cc_final: 0.8314 (p90) outliers start: 59 outliers final: 32 residues processed: 350 average time/residue: 1.5316 time to fit residues: 577.4691 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 : 1.388 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3104 r_free = 0.3104 target = 0.078934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.052455 restraints weight = 43303.289| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 3.46 r_work: 0.2408 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 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 = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13905 Z= 0.187 Angle : 0.689 9.435 18945 Z= 0.336 Chirality : 0.049 0.294 2015 Planarity : 0.004 0.037 2395 Dihedral : 8.487 56.075 2250 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.23 % Allowed : 25.35 % Favored : 70.42 % 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: -0.93 (0.20), residues: 1620 helix: 0.65 (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 C 133 HIS 0.001 0.000 HIS A 140 PHE 0.011 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 2.73557 ( 45) link_BETA1-4 : bond 0.01684 ( 5) link_BETA1-4 : angle 5.38188 ( 15) hydrogen bonds : bond 0.03385 ( 436) hydrogen bonds : angle 5.18687 ( 1533) SS BOND : bond 0.00409 ( 5) SS BOND : angle 0.34584 ( 10) covalent geometry : bond 0.00419 (13880) covalent geometry : angle 0.66019 (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 : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 185 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8266 (ptm-80) REVERT: F 47 GLU cc_start: 0.8677 (pp20) cc_final: 0.8469 (pp20) REVERT: F 74 ASP cc_start: 0.8795 (t0) cc_final: 0.8468 (t0) REVERT: G 74 ASP cc_start: 0.8767 (t0) cc_final: 0.8503 (t0) REVERT: G 77 LYS cc_start: 0.9458 (mtmm) cc_final: 0.9199 (mtmm) REVERT: G 83 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8274 (tp-100) REVERT: H 2 GLN cc_start: 0.7979 (mp10) cc_final: 0.7737 (pm20) REVERT: I 46 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7923 (ttm170) REVERT: I 74 ASP cc_start: 0.8815 (t0) cc_final: 0.8520 (t0) REVERT: I 83 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8315 (tp-100) outliers start: 60 outliers final: 37 residues processed: 333 average time/residue: 1.7880 time to fit residues: 641.5672 Evaluate side-chains 316 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 118 optimal weight: 0.0010 chunk 126 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.8388 ------------------------------------------------------------------------------- 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 116 GLN F 4 GLN I 4 GLN I 115 GLN J 4 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.052647 restraints weight = 62241.036| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 3.91 r_work: 0.2398 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2396 r_free = 0.2396 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 = 0.2396 r_free = 0.2396 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13905 Z= 0.149 Angle : 0.664 9.513 18945 Z= 0.323 Chirality : 0.048 0.283 2015 Planarity : 0.004 0.032 2395 Dihedral : 8.285 56.033 2245 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.08 % Allowed : 25.70 % 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: -0.91 (0.20), residues: 1620 helix: 0.67 (0.71), residues: 45 sheet: -0.14 (0.19), residues: 680 loop : -1.02 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 133 HIS 0.001 0.000 HIS C 140 PHE 0.009 0.001 PHE J 38 TYR 0.016 0.001 TYR A 128 ARG 0.004 0.001 ARG A 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 15) link_NAG-ASN : angle 2.62593 ( 45) link_BETA1-4 : bond 0.01712 ( 5) link_BETA1-4 : angle 5.23207 ( 15) hydrogen bonds : bond 0.03095 ( 436) hydrogen bonds : angle 5.05328 ( 1533) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.35745 ( 10) covalent geometry : bond 0.00332 (13880) covalent geometry : angle 0.63634 (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 346 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 288 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 185 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8251 (ptm-80) REVERT: D 185 ARG cc_start: 0.8604 (ttt-90) cc_final: 0.8342 (ptm-80) REVERT: E 185 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8240 (ttt-90) REVERT: F 20 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8548 (tptp) REVERT: G 47 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7067 (pp20) REVERT: G 74 ASP cc_start: 0.8766 (t0) cc_final: 0.8502 (t0) REVERT: G 77 LYS cc_start: 0.9465 (mtmm) cc_final: 0.9220 (mtmm) REVERT: I 74 ASP cc_start: 0.8827 (t0) cc_final: 0.8498 (t0) REVERT: I 83 GLN cc_start: 0.8526 (tp-100) cc_final: 0.8302 (tp-100) REVERT: J 83 GLN cc_start: 0.8582 (tp-100) cc_final: 0.8346 (tp-100) outliers start: 58 outliers final: 31 residues processed: 327 average time/residue: 2.6515 time to fit residues: 929.3733 Evaluate side-chains 311 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 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 20 LYS Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 46 ARG 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: 0.6980 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 56 optimal weight: 0.0000 chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 overall best weight: 0.7464 ------------------------------------------------------------------------------- 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 = 0.3123 r_free = 0.3123 target = 0.079960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.053319 restraints weight = 46930.976| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 3.59 r_work: 0.2425 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 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 = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1551 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= 0.141 Angle : 0.660 9.541 18945 Z= 0.320 Chirality : 0.047 0.275 2015 Planarity : 0.004 0.032 2395 Dihedral : 8.193 56.021 2240 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.45 % Allowed : 26.06 % 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: -0.89 (0.20), residues: 1620 helix: 0.64 (0.72), residues: 45 sheet: -0.14 (0.19), residues: 680 loop : -0.99 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 133 HIS 0.001 0.000 HIS A 140 PHE 0.009 0.001 PHE G 38 TYR 0.016 0.001 TYR G 60 ARG 0.006 0.001 ARG A 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 15) link_NAG-ASN : angle 2.55980 ( 45) link_BETA1-4 : bond 0.01703 ( 5) link_BETA1-4 : angle 5.16235 ( 15) hydrogen bonds : bond 0.02948 ( 436) hydrogen bonds : angle 4.94460 ( 1533) SS BOND : bond 0.00265 ( 5) SS BOND : angle 0.33325 ( 10) covalent geometry : bond 0.00314 (13880) covalent geometry : angle 0.63305 (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 339 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 290 time to evaluate : 1.622 Fit side-chains REVERT: C 185 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8165 (ttt-90) REVERT: C 188 GLU cc_start: 0.8660 (pm20) cc_final: 0.8361 (pm20) REVERT: D 185 ARG cc_start: 0.8580 (ttt-90) cc_final: 0.8338 (ttp80) REVERT: G 47 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.6996 (pp20) REVERT: G 74 ASP cc_start: 0.8749 (t0) cc_final: 0.8450 (t0) REVERT: G 77 LYS cc_start: 0.9469 (mtmm) cc_final: 0.9122 (mtmm) REVERT: G 83 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8217 (tp-100) REVERT: H 74 ASP cc_start: 0.8697 (t0) cc_final: 0.8482 (t0) REVERT: H 77 LYS cc_start: 0.9480 (mtmm) cc_final: 0.9225 (mtmm) REVERT: I 45 GLU cc_start: 0.8287 (pm20) cc_final: 0.7955 (pm20) REVERT: I 74 ASP cc_start: 0.8834 (t0) cc_final: 0.8499 (t0) REVERT: I 83 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8137 (tp-100) REVERT: J 83 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8312 (tp-100) outliers start: 49 outliers final: 30 residues processed: 325 average time/residue: 1.7944 time to fit residues: 626.1773 Evaluate side-chains 306 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain C residue 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 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 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 136 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 67 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN B 65 GLN D 65 GLN E 116 GLN F 4 GLN I 4 GLN I 85 ASN I 115 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.078843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.051908 restraints weight = 58423.046| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 3.83 r_work: 0.2385 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2383 r_free = 0.2383 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 = 0.2383 r_free = 0.2383 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13905 Z= 0.180 Angle : 0.677 9.571 18945 Z= 0.329 Chirality : 0.048 0.281 2015 Planarity : 0.004 0.040 2395 Dihedral : 8.312 57.734 2240 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.24 % Allowed : 26.41 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.71), residues: 45 sheet: -0.12 (0.19), residues: 680 loop : -0.95 (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 A 140 PHE 0.011 0.001 PHE H 38 TYR 0.015 0.001 TYR A 128 ARG 0.009 0.001 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 15) link_NAG-ASN : angle 2.62634 ( 45) link_BETA1-4 : bond 0.01631 ( 5) link_BETA1-4 : angle 5.28587 ( 15) hydrogen bonds : bond 0.03109 ( 436) hydrogen bonds : angle 4.97690 ( 1533) SS BOND : bond 0.00306 ( 5) SS BOND : angle 0.11515 ( 10) covalent geometry : bond 0.00403 (13880) covalent geometry : angle 0.64946 (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 322 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 1.630 Fit side-chains REVERT: B 8 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9187 (ttpp) REVERT: B 192 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8586 (tp30) REVERT: D 185 ARG cc_start: 0.8608 (ttt-90) cc_final: 0.8344 (ptm-80) REVERT: F 20 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8872 (tptp) REVERT: G 47 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7070 (pp20) REVERT: G 74 ASP cc_start: 0.8759 (t0) cc_final: 0.8459 (t0) REVERT: G 77 LYS cc_start: 0.9477 (mtmm) cc_final: 0.9134 (mtmm) REVERT: G 83 GLN cc_start: 0.8510 (tp-100) cc_final: 0.8183 (tp-100) REVERT: H 66 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8602 (ttmt) REVERT: H 74 ASP cc_start: 0.8747 (t0) cc_final: 0.8534 (t0) REVERT: I 74 ASP cc_start: 0.8867 (t0) cc_final: 0.8529 (t0) REVERT: I 83 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8185 (tp-100) REVERT: J 74 ASP cc_start: 0.8869 (t0) cc_final: 0.8566 (t0) REVERT: J 83 GLN cc_start: 0.8535 (tp-100) cc_final: 0.8268 (tp-100) outliers start: 46 outliers final: 30 residues processed: 310 average time/residue: 1.5598 time to fit residues: 519.6022 Evaluate side-chains 307 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 272 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 66 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 41 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN E 116 GLN F 4 GLN I 4 GLN I 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.080163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.053201 restraints weight = 52264.467| |-----------------------------------------------------------------------------| r_work (start): 0.2567 rms_B_bonded: 3.75 r_work: 0.2417 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2417 r_free = 0.2417 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2417 r_free = 0.2417 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13905 Z= 0.137 Angle : 0.669 9.543 18945 Z= 0.326 Chirality : 0.047 0.271 2015 Planarity : 0.004 0.041 2395 Dihedral : 8.284 59.781 2240 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.82 % Allowed : 27.11 % 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: -0.82 (0.20), residues: 1620 helix: 0.64 (0.72), residues: 45 sheet: -0.11 (0.19), residues: 680 loop : -0.92 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 133 HIS 0.000 0.000 HIS A 140 PHE 0.010 0.001 PHE H 38 TYR 0.016 0.001 TYR G 60 ARG 0.010 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 15) link_NAG-ASN : angle 2.52075 ( 45) link_BETA1-4 : bond 0.01708 ( 5) link_BETA1-4 : angle 5.10733 ( 15) hydrogen bonds : bond 0.02869 ( 436) hydrogen bonds : angle 4.85246 ( 1533) SS BOND : bond 0.00256 ( 5) SS BOND : angle 0.34099 ( 10) covalent geometry : bond 0.00308 (13880) covalent geometry : angle 0.64241 (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 329 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 1.554 Fit side-chains REVERT: B 192 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8603 (tp30) REVERT: C 185 ARG cc_start: 0.8513 (ttt-90) cc_final: 0.8286 (ptm-80) REVERT: D 185 ARG cc_start: 0.8583 (ttt-90) cc_final: 0.8312 (ptm-80) REVERT: F 45 GLU cc_start: 0.8299 (pm20) cc_final: 0.8029 (pm20) REVERT: G 47 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.6999 (pp20) REVERT: G 74 ASP cc_start: 0.8746 (t0) cc_final: 0.8433 (t0) REVERT: G 77 LYS cc_start: 0.9487 (mtmm) cc_final: 0.9147 (mtmm) REVERT: G 83 GLN cc_start: 0.8495 (tp-100) cc_final: 0.8145 (tp-100) REVERT: H 74 ASP cc_start: 0.8807 (t0) cc_final: 0.8364 (t0) REVERT: H 77 LYS cc_start: 0.9438 (mtmm) cc_final: 0.8918 (mtmm) REVERT: I 74 ASP cc_start: 0.8847 (t0) cc_final: 0.8521 (t0) REVERT: I 83 GLN cc_start: 0.8414 (tp-100) cc_final: 0.8127 (tp-100) REVERT: J 74 ASP cc_start: 0.8846 (t0) cc_final: 0.8596 (t0) REVERT: J 83 GLN cc_start: 0.8441 (tp-100) cc_final: 0.8228 (tp-100) REVERT: J 84 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8109 (mtp) outliers start: 40 outliers final: 30 residues processed: 318 average time/residue: 1.4966 time to fit residues: 512.6575 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 : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain 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 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 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 80 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL 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: 0.4980 chunk 67 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 158 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN E 116 GLN F 4 GLN I 2 GLN I 4 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 = 0.3128 r_free = 0.3128 target = 0.080276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.053274 restraints weight = 52230.972| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 3.75 r_work: 0.2419 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2418 r_free = 0.2418 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2418 r_free = 0.2418 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13905 Z= 0.139 Angle : 0.673 9.557 18945 Z= 0.328 Chirality : 0.047 0.267 2015 Planarity : 0.004 0.034 2395 Dihedral : 8.237 58.283 2240 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.75 % Allowed : 27.25 % Favored : 70.00 % 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: 0.62 (0.72), residues: 45 sheet: -0.08 (0.19), residues: 680 loop : -0.90 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 133 HIS 0.001 0.000 HIS A 140 PHE 0.010 0.001 PHE H 38 TYR 0.016 0.001 TYR G 60 ARG 0.007 0.001 ARG E 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 15) link_NAG-ASN : angle 2.47557 ( 45) link_BETA1-4 : bond 0.01679 ( 5) link_BETA1-4 : angle 5.08560 ( 15) hydrogen bonds : bond 0.02859 ( 436) hydrogen bonds : angle 4.80652 ( 1533) SS BOND : bond 0.00225 ( 5) SS BOND : angle 0.27930 ( 10) covalent geometry : bond 0.00313 (13880) covalent geometry : angle 0.64743 (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 323 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 1.398 Fit side-chains REVERT: B 133 TRP cc_start: 0.8268 (m-10) cc_final: 0.8053 (m-90) REVERT: B 192 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8604 (tp30) REVERT: E 185 ARG cc_start: 0.8603 (ttt-90) cc_final: 0.8371 (ptt90) REVERT: F 45 GLU cc_start: 0.8335 (pm20) cc_final: 0.8045 (pm20) REVERT: F 74 ASP cc_start: 0.8786 (t0) cc_final: 0.8429 (t0) REVERT: G 74 ASP cc_start: 0.8752 (t0) cc_final: 0.8469 (t0) REVERT: G 77 LYS cc_start: 0.9495 (mtmm) cc_final: 0.9247 (mtmm) REVERT: G 83 GLN cc_start: 0.8472 (tp-100) cc_final: 0.8111 (tp-100) REVERT: H 66 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8621 (ptmm) REVERT: H 74 ASP cc_start: 0.8821 (t0) cc_final: 0.8612 (t0) REVERT: I 74 ASP cc_start: 0.8870 (t0) cc_final: 0.8434 (t0) REVERT: I 77 LYS cc_start: 0.9506 (mtmm) cc_final: 0.9264 (mtmm) REVERT: I 83 GLN cc_start: 0.8332 (tp-100) cc_final: 0.8033 (tp-100) REVERT: J 74 ASP cc_start: 0.8847 (t0) cc_final: 0.8435 (t0) outliers start: 39 outliers final: 31 residues processed: 313 average time/residue: 1.4588 time to fit residues: 491.8219 Evaluate side-chains 311 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 0.0470 chunk 134 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 0.0050 chunk 126 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 62 optimal weight: 0.3980 chunk 132 optimal weight: 0.8980 overall best weight: 0.4692 ------------------------------------------------------------------------------- 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 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.081180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.054412 restraints weight = 46697.607| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 3.61 r_work: 0.2448 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1928 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= 0.125 Angle : 0.676 9.544 18945 Z= 0.329 Chirality : 0.047 0.261 2015 Planarity : 0.004 0.033 2395 Dihedral : 8.157 56.583 2240 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.32 % Allowed : 27.75 % Favored : 69.93 % 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: -0.75 (0.20), residues: 1620 helix: 0.72 (0.72), residues: 45 sheet: -0.04 (0.19), residues: 680 loop : -0.89 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 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 0.007 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 15) link_NAG-ASN : angle 2.40322 ( 45) link_BETA1-4 : bond 0.01695 ( 5) link_BETA1-4 : angle 4.97595 ( 15) hydrogen bonds : bond 0.02750 ( 436) hydrogen bonds : angle 4.71204 ( 1533) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.35893 ( 10) covalent geometry : bond 0.00286 (13880) covalent geometry : angle 0.65173 (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 321 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 288 time to evaluate : 1.533 Fit side-chains REVERT: B 133 TRP cc_start: 0.8267 (m-10) cc_final: 0.8060 (m-90) REVERT: B 192 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8512 (tp30) REVERT: C 185 ARG cc_start: 0.8540 (ttt-90) cc_final: 0.8340 (ptm-80) REVERT: F 45 GLU cc_start: 0.8363 (pm20) cc_final: 0.8090 (pm20) REVERT: F 74 ASP cc_start: 0.8782 (t0) cc_final: 0.8534 (t0) REVERT: G 74 ASP cc_start: 0.8753 (t0) cc_final: 0.8471 (t0) REVERT: G 77 LYS cc_start: 0.9503 (mtmm) cc_final: 0.9256 (mtmm) REVERT: G 83 GLN cc_start: 0.8485 (tp-100) cc_final: 0.8120 (tp-100) REVERT: H 66 LYS cc_start: 0.8887 (ptmm) cc_final: 0.8608 (ptmm) REVERT: H 74 ASP cc_start: 0.8831 (t0) cc_final: 0.8510 (t0) REVERT: I 40 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7948 (tp40) REVERT: I 74 ASP cc_start: 0.8877 (t0) cc_final: 0.8478 (t0) REVERT: I 77 LYS cc_start: 0.9509 (mtmm) cc_final: 0.9260 (mtmm) REVERT: I 83 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8071 (tp-100) REVERT: J 2 GLN cc_start: 0.7830 (pm20) cc_final: 0.7626 (pm20) REVERT: J 74 ASP cc_start: 0.8838 (t0) cc_final: 0.8595 (t0) outliers start: 33 outliers final: 28 residues processed: 313 average time/residue: 1.4603 time to fit residues: 492.4770 Evaluate side-chains 311 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 192 GLU 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 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 J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 0.0000 chunk 39 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 0.0040 chunk 91 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN E 116 GLN F 2 GLN I 2 GLN I 115 GLN J 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.054509 restraints weight = 46677.306| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 3.62 r_work: 0.2453 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 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 = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13905 Z= 0.129 Angle : 0.686 9.551 18945 Z= 0.335 Chirality : 0.047 0.259 2015 Planarity : 0.004 0.033 2395 Dihedral : 8.132 55.911 2240 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.32 % Allowed : 27.89 % Favored : 69.79 % 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: -0.70 (0.20), residues: 1620 helix: 0.80 (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 0.036 0.001 TRP D 133 HIS 0.000 0.000 HIS A 140 PHE 0.009 0.001 PHE H 38 TYR 0.024 0.001 TYR I 95 ARG 0.007 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 15) link_NAG-ASN : angle 2.37812 ( 45) link_BETA1-4 : bond 0.01621 ( 5) link_BETA1-4 : angle 4.94805 ( 15) hydrogen bonds : bond 0.02728 ( 436) hydrogen bonds : angle 4.69525 ( 1533) SS BOND : bond 0.00196 ( 5) SS BOND : angle 0.35058 ( 10) covalent geometry : bond 0.00300 (13880) covalent geometry : angle 0.66293 (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 320 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 1.607 Fit side-chains REVERT: B 192 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8592 (tp30) REVERT: C 41 ASP cc_start: 0.8910 (t0) cc_final: 0.8651 (t0) REVERT: E 185 ARG cc_start: 0.8559 (tmt170) cc_final: 0.8170 (tmt170) REVERT: F 45 GLU cc_start: 0.8327 (pm20) cc_final: 0.8069 (pm20) REVERT: F 74 ASP cc_start: 0.8822 (t0) cc_final: 0.8440 (t0) REVERT: G 40 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7768 (tp40) REVERT: G 74 ASP cc_start: 0.8750 (t0) cc_final: 0.8468 (t0) REVERT: G 77 LYS cc_start: 0.9499 (mtmm) cc_final: 0.9253 (mtmm) REVERT: G 83 GLN cc_start: 0.8491 (tp-100) cc_final: 0.8125 (tp-100) REVERT: H 66 LYS cc_start: 0.8868 (ptmm) cc_final: 0.8531 (ptmm) REVERT: H 74 ASP cc_start: 0.8785 (t0) cc_final: 0.8536 (t0) REVERT: I 40 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7867 (tp40) REVERT: I 74 ASP cc_start: 0.8876 (t0) cc_final: 0.8474 (t0) REVERT: I 77 LYS cc_start: 0.9503 (mtmm) cc_final: 0.9248 (mtmm) REVERT: I 83 GLN cc_start: 0.8380 (tp-100) cc_final: 0.8163 (tp-100) REVERT: J 2 GLN cc_start: 0.7826 (pm20) cc_final: 0.7616 (pm20) REVERT: J 66 LYS cc_start: 0.8880 (ptmm) cc_final: 0.8657 (ptmm) REVERT: J 74 ASP cc_start: 0.8819 (t0) cc_final: 0.8575 (t0) outliers start: 33 outliers final: 29 residues processed: 311 average time/residue: 1.4802 time to fit residues: 496.1156 Evaluate side-chains 312 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 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 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 129 optimal weight: 0.0470 chunk 110 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 GLN F 2 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 = 0.3147 r_free = 0.3147 target = 0.081250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.054273 restraints weight = 58213.153| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 3.88 r_work: 0.2437 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- 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 = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 13905 Z= 0.211 Angle : 0.897 59.200 18945 Z= 0.484 Chirality : 0.047 0.259 2015 Planarity : 0.004 0.042 2395 Dihedral : 8.130 55.915 2240 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.18 % Allowed : 28.24 % Favored : 69.58 % 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: -0.70 (0.20), residues: 1620 helix: 0.82 (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 0.030 0.001 TRP D 133 HIS 0.000 0.000 HIS A 140 PHE 0.009 0.001 PHE H 38 TYR 0.020 0.001 TYR I 95 ARG 0.006 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 15) link_NAG-ASN : angle 2.38092 ( 45) link_BETA1-4 : bond 0.01423 ( 5) link_BETA1-4 : angle 4.94729 ( 15) hydrogen bonds : bond 0.02732 ( 436) hydrogen bonds : angle 4.69449 ( 1533) SS BOND : bond 0.00205 ( 5) SS BOND : angle 0.33759 ( 10) covalent geometry : bond 0.00459 (13880) covalent geometry : angle 0.88007 (18875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14595.46 seconds wall clock time: 257 minutes 17.60 seconds (15437.60 seconds total)