Starting phenix.real_space_refine on Sun Nov 17 10:27:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9x_16513/11_2024/8c9x_16513.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9x_16513/11_2024/8c9x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9x_16513/11_2024/8c9x_16513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9x_16513/11_2024/8c9x_16513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9x_16513/11_2024/8c9x_16513.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9x_16513/11_2024/8c9x_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-5513/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: 13.14, per 1000 atoms: 0.97 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: 3.38 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: 2.21 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: 4.83 Time building geometry restraints manager: 3.94 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 39.540 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 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:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.830 ------------------------------------------------------------------------------- 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 13880 Z= 0.241 Angle : 0.680 8.521 18875 Z= 0.349 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 *********************** 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 : 1.594 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: 1.4674 time to fit residues: 555.5702 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 : 1.521 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 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 13880 Z= 0.223 Angle : 0.665 8.989 18875 Z= 0.334 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 *********************** 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 : 1.479 Fit side-chains revert: symmetry clash REVERT: H 74 ASP cc_start: 0.8945 (t0) cc_final: 0.8717 (t0) REVERT: J 96 TYR cc_start: 0.8797 (p90) cc_final: 0.8558 (p90) outliers start: 59 outliers final: 32 residues processed: 350 average time/residue: 1.4956 time to fit residues: 563.9083 Evaluate side-chains 320 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 288 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 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 80 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 120 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 144 optimal weight: 0.0060 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13880 Z= 0.309 Angle : 0.673 9.411 18875 Z= 0.337 Chirality : 0.049 0.299 2015 Planarity : 0.004 0.033 2395 Dihedral : 8.560 56.259 2250 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.44 % Allowed : 25.14 % 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: 0.61 (0.69), 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 0.021 0.001 TRP C 133 HIS 0.002 0.001 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 E 185 *********************** 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 350 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 287 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: F 20 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.8826 (tptp) REVERT: G 83 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8819 (tp-100) REVERT: H 77 LYS cc_start: 0.9145 (mtmm) cc_final: 0.8640 (mtmm) REVERT: J 96 TYR cc_start: 0.8745 (p90) cc_final: 0.8540 (p90) outliers start: 63 outliers final: 40 residues processed: 332 average time/residue: 1.5216 time to fit residues: 544.1428 Evaluate side-chains 319 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 189 CYS Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 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 64 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 170 ASN B 139 GLN B 170 ASN C 47 GLN C 170 ASN D 47 GLN D 116 GLN D 170 ASN E 116 GLN F 4 GLN I 4 GLN I 115 GLN J 4 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13880 Z= 0.195 Angle : 0.636 9.515 18875 Z= 0.316 Chirality : 0.047 0.278 2015 Planarity : 0.004 0.032 2395 Dihedral : 8.276 55.881 2245 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.87 % Allowed : 26.48 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1620 helix: 0.81 (0.73), 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 0.023 0.001 TRP C 133 HIS 0.001 0.000 HIS H 32 PHE 0.009 0.001 PHE G 38 TYR 0.017 0.001 TYR I 96 ARG 0.006 0.001 ARG B 204 *********************** 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 343 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 288 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: G 47 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.6917 (pp20) REVERT: G 83 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8818 (tp-100) REVERT: H 74 ASP cc_start: 0.8943 (t0) cc_final: 0.8211 (t0) REVERT: H 77 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8615 (mtmm) outliers start: 55 outliers final: 31 residues processed: 329 average time/residue: 1.5626 time to fit residues: 551.5139 Evaluate side-chains 310 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 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 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 128 optimal weight: 7.9990 chunk 87 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 170 ASN B 65 GLN D 47 GLN D 65 GLN D 116 GLN E 116 GLN F 4 GLN I 4 GLN I 85 ASN I 115 GLN J 4 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13880 Z= 0.274 Angle : 0.653 9.574 18875 Z= 0.325 Chirality : 0.048 0.285 2015 Planarity : 0.004 0.033 2395 Dihedral : 8.336 56.336 2240 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.38 % Allowed : 26.62 % 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: -0.90 (0.20), residues: 1620 helix: 0.54 (0.70), residues: 45 sheet: -0.13 (0.19), residues: 680 loop : -1.00 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 133 HIS 0.001 0.000 HIS A 140 PHE 0.010 0.001 PHE G 48 TYR 0.021 0.001 TYR J 96 ARG 0.006 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 1.739 Fit side-chains REVERT: G 47 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.6984 (pp20) REVERT: G 83 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8842 (tp-100) REVERT: H 74 ASP cc_start: 0.8988 (t0) cc_final: 0.8298 (t0) REVERT: H 77 LYS cc_start: 0.9177 (mtmm) cc_final: 0.8689 (mtmm) outliers start: 48 outliers final: 32 residues processed: 316 average time/residue: 1.5655 time to fit residues: 531.6078 Evaluate side-chains 302 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain J residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN B 116 GLN D 47 GLN D 116 GLN E 116 GLN F 4 GLN H 4 GLN I 4 GLN I 85 ASN I 115 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13880 Z= 0.231 Angle : 0.651 9.556 18875 Z= 0.325 Chirality : 0.048 0.279 2015 Planarity : 0.004 0.041 2395 Dihedral : 8.352 58.741 2240 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.24 % Allowed : 26.90 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1620 helix: 0.54 (0.72), residues: 45 sheet: -0.13 (0.19), residues: 680 loop : -0.96 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 133 HIS 0.001 0.000 HIS A 140 PHE 0.011 0.001 PHE H 38 TYR 0.017 0.001 TYR A 128 ARG 0.010 0.001 ARG C 204 *********************** 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 325 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 1.528 Fit side-chains REVERT: G 47 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.6961 (pp20) REVERT: G 83 GLN cc_start: 0.9024 (tp-100) cc_final: 0.8801 (tp-100) REVERT: H 74 ASP cc_start: 0.8985 (t0) cc_final: 0.8286 (t0) REVERT: H 77 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8728 (mtmm) REVERT: I 2 GLN cc_start: 0.8039 (pm20) cc_final: 0.7816 (pm20) outliers start: 46 outliers final: 32 residues processed: 312 average time/residue: 1.5581 time to fit residues: 522.2631 Evaluate side-chains 302 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 191 LYS Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 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 12 LEU Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 H 4 GLN I 4 GLN I 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13880 Z= 0.221 Angle : 0.651 9.565 18875 Z= 0.325 Chirality : 0.048 0.273 2015 Planarity : 0.004 0.043 2395 Dihedral : 8.335 59.571 2240 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.89 % Allowed : 26.76 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.60 (0.71), residues: 45 sheet: -0.12 (0.19), residues: 680 loop : -0.92 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 133 HIS 0.001 0.000 HIS A 140 PHE 0.010 0.001 PHE H 38 TYR 0.017 0.001 TYR I 96 ARG 0.009 0.001 ARG D 204 *********************** 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 317 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 1.443 Fit side-chains REVERT: G 47 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.6918 (pp20) REVERT: G 83 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8768 (tp-100) REVERT: H 74 ASP cc_start: 0.8982 (t0) cc_final: 0.8279 (t0) REVERT: H 77 LYS cc_start: 0.9177 (mtmm) cc_final: 0.8721 (mtmm) outliers start: 41 outliers final: 33 residues processed: 305 average time/residue: 1.5100 time to fit residues: 497.7494 Evaluate side-chains 300 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 191 LYS Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 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 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 94 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 GLN F 4 GLN H 4 GLN I 2 GLN I 4 GLN I 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13880 Z= 0.241 Angle : 0.661 9.580 18875 Z= 0.331 Chirality : 0.048 0.273 2015 Planarity : 0.004 0.044 2395 Dihedral : 8.315 57.595 2240 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.38 % Allowed : 26.69 % 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: -0.80 (0.20), residues: 1620 helix: 0.49 (0.71), residues: 45 sheet: -0.09 (0.19), residues: 680 loop : -0.90 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 133 HIS 0.001 0.000 HIS A 140 PHE 0.009 0.001 PHE H 38 TYR 0.017 0.001 TYR G 60 ARG 0.010 0.001 ARG D 204 *********************** 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 322 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 274 time to evaluate : 1.574 Fit side-chains REVERT: G 47 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.6936 (pp20) REVERT: G 83 GLN cc_start: 0.8980 (tp-100) cc_final: 0.8749 (tp-100) REVERT: H 74 ASP cc_start: 0.8981 (t0) cc_final: 0.8273 (t0) REVERT: H 77 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8716 (mtmm) outliers start: 48 outliers final: 36 residues processed: 307 average time/residue: 1.5014 time to fit residues: 498.9339 Evaluate side-chains 306 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 269 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 191 LYS Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 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 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain G residue 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 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 0.0970 chunk 112 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN C 65 GLN E 116 GLN F 4 GLN H 4 GLN I 2 GLN I 115 GLN J 2 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13880 Z= 0.247 Angle : 0.676 9.580 18875 Z= 0.338 Chirality : 0.048 0.273 2015 Planarity : 0.004 0.043 2395 Dihedral : 8.301 56.738 2240 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.17 % Allowed : 26.97 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1620 helix: 0.44 (0.71), residues: 45 sheet: -0.08 (0.19), residues: 680 loop : -0.89 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 133 HIS 0.001 0.000 HIS A 140 PHE 0.009 0.001 PHE H 38 TYR 0.017 0.001 TYR G 60 ARG 0.009 0.001 ARG D 204 *********************** 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 318 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 1.600 Fit side-chains REVERT: G 47 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.6916 (pp20) REVERT: H 74 ASP cc_start: 0.8983 (t0) cc_final: 0.8270 (t0) REVERT: H 77 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8715 (mtmm) outliers start: 45 outliers final: 38 residues processed: 305 average time/residue: 1.4998 time to fit residues: 492.7184 Evaluate side-chains 307 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 191 LYS Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 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 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain G residue 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 2 GLN Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 2 GLN Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 98 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN E 65 GLN E 116 GLN F 2 GLN F 4 GLN H 2 GLN H 4 GLN I 2 GLN I 115 GLN J 2 GLN J 85 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13880 Z= 0.345 Angle : 0.710 9.610 18875 Z= 0.356 Chirality : 0.049 0.282 2015 Planarity : 0.004 0.052 2395 Dihedral : 8.402 56.749 2240 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.96 % Allowed : 27.25 % 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: -0.81 (0.20), residues: 1620 helix: 0.11 (0.70), residues: 45 sheet: -0.10 (0.19), residues: 680 loop : -0.88 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 133 HIS 0.002 0.000 HIS A 140 PHE 0.010 0.001 PHE G 48 TYR 0.017 0.002 TYR G 60 ARG 0.011 0.001 ARG C 204 ********************** 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 308 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 1.564 Fit side-chains REVERT: G 47 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7028 (pp20) REVERT: H 74 ASP cc_start: 0.8988 (t0) cc_final: 0.8288 (t0) REVERT: H 77 LYS cc_start: 0.9211 (mtmm) cc_final: 0.8728 (mtmm) outliers start: 42 outliers final: 37 residues processed: 298 average time/residue: 1.4848 time to fit residues: 476.8127 Evaluate side-chains 299 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 261 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 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 22 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain G residue 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 2 GLN 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 Chi-restraints excluded: chain J residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 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 47 GLN C 47 GLN E 116 GLN F 2 GLN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN H 4 GLN I 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.078594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.051208 restraints weight = 56925.645| |-----------------------------------------------------------------------------| r_work (start): 0.2506 rms_B_bonded: 3.86 r_work: 0.2354 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2353 r_free = 0.2353 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2353 r_free = 0.2353 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.164 13880 Z= 0.369 Angle : 1.062 59.194 18875 Z= 0.606 Chirality : 0.055 0.811 2015 Planarity : 0.004 0.050 2395 Dihedral : 8.406 56.752 2240 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.96 % Allowed : 27.39 % Favored : 69.65 % Cbeta Deviations : 0.13 % 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: -0.81 (0.20), residues: 1620 helix: 0.12 (0.70), residues: 45 sheet: -0.10 (0.19), residues: 680 loop : -0.89 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 133 HIS 0.002 0.000 HIS A 140 PHE 0.009 0.001 PHE G 48 TYR 0.016 0.001 TYR G 60 ARG 0.010 0.001 ARG C 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7608.49 seconds wall clock time: 136 minutes 49.76 seconds (8209.76 seconds total)