Starting phenix.real_space_refine on Sat Jul 4 22:12:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jc9_36154/07_2026/8jc9_36154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jc9_36154/07_2026/8jc9_36154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jc9_36154/07_2026/8jc9_36154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jc9_36154/07_2026/8jc9_36154.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jc9_36154/07_2026/8jc9_36154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jc9_36154/07_2026/8jc9_36154.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13349 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Ca 14 9.91 5 Mg 28 5.21 5 S 42 5.16 5 C 9513 2.51 5 N 1821 2.21 5 O 1993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13411 Number of models: 1 Model: "" Number of chains: 56 Chain: "1" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "2" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 345 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "3" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "4" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "5" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "6" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "7" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "8" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "A" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "B" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "D" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "E" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "I" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "J" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "K" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "N" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "O" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "P" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Q" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "R" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "S" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "V" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Y" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 430 Classifications: {'peptide': 53} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 50} Chain: "Z" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 337 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "1" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 154 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Chain: "2" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'BCL': 1, 'CRT': 1, 'D12': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "4" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "6" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 149 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'BCL': 1, 'CRT': 1, 'D12': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "G" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "J" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 154 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Chain: "N" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "R" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 154 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Chain: "T" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "V" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "Z" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'BCL': 1, 'D12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.97, per 1000 atoms: 0.22 Number of scatterers: 13411 At special positions: 0 Unit cell: (120.15, 118.37, 74.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 14 19.99 S 42 16.00 Mg 28 11.99 O 1993 8.00 N 1821 7.00 C 9513 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=22, symmetry=0 Number of additional bonds: simple=22, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 487.7 milliseconds 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2530 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 73.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain '1' and resid 7 through 14 removed outlier: 3.687A pdb=" N LYS 1 10 " --> pdb=" O ASN 1 7 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP 1 12 " --> pdb=" O TYR 1 9 " (cutoff:3.500A) Processing helix chain '1' and resid 16 through 41 Processing helix chain '2' and resid 10 through 43 removed outlier: 3.679A pdb=" N ALA 2 14 " --> pdb=" O THR 2 10 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS 2 15 " --> pdb=" O ASP 2 11 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 14 removed outlier: 3.629A pdb=" N TRP 3 12 " --> pdb=" O TYR 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 41 removed outlier: 3.542A pdb=" N LEU 3 40 " --> pdb=" O HIS 3 36 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER 3 41 " --> pdb=" O MET 3 37 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 43 Processing helix chain '5' and resid 7 through 14 removed outlier: 3.514A pdb=" N LYS 5 10 " --> pdb=" O ASN 5 7 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP 5 12 " --> pdb=" O TYR 5 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE 5 14 " --> pdb=" O ILE 5 11 " (cutoff:3.500A) Processing helix chain '5' and resid 16 through 41 removed outlier: 3.535A pdb=" N SER 5 41 " --> pdb=" O MET 5 37 " (cutoff:3.500A) Processing helix chain '6' and resid 10 through 43 Processing helix chain '7' and resid 7 through 14 removed outlier: 3.718A pdb=" N LYS 7 10 " --> pdb=" O ASN 7 7 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP 7 12 " --> pdb=" O TYR 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 16 through 41 removed outlier: 3.579A pdb=" N SER 7 41 " --> pdb=" O MET 7 37 " (cutoff:3.500A) Processing helix chain '8' and resid 10 through 43 Processing helix chain 'A' and resid 7 through 14 removed outlier: 3.603A pdb=" N LYS A 10 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP A 12 " --> pdb=" O TYR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 41 removed outlier: 3.506A pdb=" N SER A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 43 Processing helix chain 'D' and resid 7 through 14 removed outlier: 3.507A pdb=" N LYS D 10 " --> pdb=" O ASN D 7 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP D 12 " --> pdb=" O TYR D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 42 removed outlier: 3.532A pdb=" N THR D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 43 Processing helix chain 'F' and resid 7 through 14 removed outlier: 3.507A pdb=" N LYS F 10 " --> pdb=" O ASN F 7 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TRP F 12 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 41 removed outlier: 3.571A pdb=" N SER F 41 " --> pdb=" O MET F 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 43 Processing helix chain 'I' and resid 7 through 14 removed outlier: 3.507A pdb=" N LYS I 10 " --> pdb=" O ASN I 7 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP I 12 " --> pdb=" O TYR I 9 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE I 14 " --> pdb=" O ILE I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 41 removed outlier: 3.510A pdb=" N SER I 41 " --> pdb=" O MET I 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 43 Processing helix chain 'K' and resid 7 through 14 removed outlier: 3.514A pdb=" N LYS K 10 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TRP K 12 " --> pdb=" O TYR K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 42 removed outlier: 3.930A pdb=" N THR K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 43 Processing helix chain 'O' and resid 7 through 14 removed outlier: 3.541A pdb=" N LYS O 10 " --> pdb=" O ASN O 7 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP O 12 " --> pdb=" O TYR O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 41 removed outlier: 3.507A pdb=" N SER O 41 " --> pdb=" O MET O 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 43 Processing helix chain 'Q' and resid 7 through 14 removed outlier: 3.530A pdb=" N LYS Q 10 " --> pdb=" O ASN Q 7 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP Q 12 " --> pdb=" O TYR Q 9 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE Q 14 " --> pdb=" O ILE Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 41 removed outlier: 3.565A pdb=" N SER Q 41 " --> pdb=" O MET Q 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 43 Processing helix chain 'S' and resid 7 through 14 removed outlier: 3.510A pdb=" N LYS S 10 " --> pdb=" O ASN S 7 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP S 12 " --> pdb=" O TYR S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 41 removed outlier: 3.587A pdb=" N SER S 41 " --> pdb=" O MET S 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 43 Processing helix chain 'U' and resid 7 through 14 removed outlier: 3.612A pdb=" N LYS U 10 " --> pdb=" O ASN U 7 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP U 12 " --> pdb=" O TYR U 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE U 14 " --> pdb=" O ILE U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 41 removed outlier: 3.558A pdb=" N SER U 41 " --> pdb=" O MET U 37 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 43 Processing helix chain 'Y' and resid 7 through 14 removed outlier: 3.860A pdb=" N TRP Y 12 " --> pdb=" O TYR Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 42 Processing helix chain 'Z' and resid 10 through 43 756 hydrogen bonds defined for protein. 2148 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: 1.76 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 3796 1.36 - 1.54: 9616 1.54 - 1.71: 293 1.71 - 1.88: 84 1.88 - 2.05: 112 Bond restraints: 13901 Sorted by residual: bond pdb=" NA BCL K 102 " pdb="MG BCL K 102 " ideal model delta sigma weight residual 2.170 1.994 0.176 2.40e-02 1.74e+03 5.38e+01 bond pdb=" NA BCL S 102 " pdb="MG BCL S 102 " ideal model delta sigma weight residual 2.170 1.995 0.175 2.40e-02 1.74e+03 5.32e+01 bond pdb=" NA BCL 1 101 " pdb="MG BCL 1 101 " ideal model delta sigma weight residual 2.170 1.995 0.175 2.40e-02 1.74e+03 5.29e+01 bond pdb=" NA BCL 7 102 " pdb="MG BCL 7 102 " ideal model delta sigma weight residual 2.170 1.996 0.174 2.40e-02 1.74e+03 5.26e+01 bond pdb=" NA BCL Y 102 " pdb="MG BCL Y 102 " ideal model delta sigma weight residual 2.170 1.996 0.174 2.40e-02 1.74e+03 5.24e+01 ... (remaining 13896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 17814 3.75 - 7.51: 1260 7.51 - 11.26: 145 11.26 - 15.02: 39 15.02 - 18.77: 15 Bond angle restraints: 19273 Sorted by residual: angle pdb=" NA BCL Q 101 " pdb="MG BCL Q 101 " pdb=" NC BCL Q 101 " ideal model delta sigma weight residual 160.52 179.29 -18.77 2.84e+00 1.24e-01 4.37e+01 angle pdb=" NA BCL F 101 " pdb="MG BCL F 101 " pdb=" NC BCL F 101 " ideal model delta sigma weight residual 160.52 179.16 -18.65 2.84e+00 1.24e-01 4.31e+01 angle pdb=" NA BCL Y 102 " pdb="MG BCL Y 102 " pdb=" NC BCL Y 102 " ideal model delta sigma weight residual 160.52 179.13 -18.61 2.84e+00 1.24e-01 4.29e+01 angle pdb=" NA BCL K 102 " pdb="MG BCL K 102 " pdb=" NC BCL K 102 " ideal model delta sigma weight residual 160.52 179.05 -18.53 2.84e+00 1.24e-01 4.25e+01 angle pdb=" NA BCL 1 101 " pdb="MG BCL 1 101 " pdb=" NC BCL 1 101 " ideal model delta sigma weight residual 160.52 179.02 -18.51 2.84e+00 1.24e-01 4.24e+01 ... (remaining 19268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 7048 35.94 - 71.88: 274 71.88 - 107.82: 26 107.82 - 143.76: 1 143.76 - 179.70: 4 Dihedral angle restraints: 7353 sinusoidal: 3488 harmonic: 3865 Sorted by residual: dihedral pdb=" CBD BCL R 101 " pdb=" CGD BCL R 101 " pdb=" O2D BCL R 101 " pdb=" CED BCL R 101 " ideal model delta sinusoidal sigma weight residual -180.00 -67.83 -112.17 1 5.00e+00 4.00e-02 5.29e+02 dihedral pdb=" C1 BCL 1 101 " pdb=" C2 BCL 1 101 " pdb=" C3 BCL 1 101 " pdb=" C5 BCL 1 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.30 -179.70 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL V 102 " pdb=" C2 BCL V 102 " pdb=" C3 BCL V 102 " pdb=" C5 BCL V 102 " ideal model delta sinusoidal sigma weight residual 180.00 0.48 179.52 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 7350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1782 0.070 - 0.140: 157 0.140 - 0.210: 44 0.210 - 0.281: 1 0.281 - 0.351: 13 Chirality restraints: 1997 Sorted by residual: chirality pdb=" CBD BCL P 101 " pdb=" CAD BCL P 101 " pdb=" CGD BCL P 101 " pdb=" CHA BCL P 101 " both_signs ideal model delta sigma weight residual False 2.62 2.27 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CBD BCL 2 101 " pdb=" CAD BCL 2 101 " pdb=" CGD BCL 2 101 " pdb=" CHA BCL 2 101 " both_signs ideal model delta sigma weight residual False 2.62 2.27 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CBD BCL 8 101 " pdb=" CAD BCL 8 101 " pdb=" CGD BCL 8 101 " pdb=" CHA BCL 8 101 " both_signs ideal model delta sigma weight residual False 2.62 2.28 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1994 not shown) Planarity restraints: 2325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 4 101 " 0.355 3.00e-02 1.11e+03 2.91e-01 4.72e+02 pdb=" CBA BCL 4 101 " 0.165 3.00e-02 1.11e+03 pdb=" CGA BCL 4 101 " -0.078 3.00e-02 1.11e+03 pdb=" O1A BCL 4 101 " 0.068 3.00e-02 1.11e+03 pdb=" O2A BCL 4 101 " -0.510 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL P 101 " 0.341 3.00e-02 1.11e+03 2.79e-01 4.33e+02 pdb=" CBA BCL P 101 " 0.172 3.00e-02 1.11e+03 pdb=" CGA BCL P 101 " -0.076 3.00e-02 1.11e+03 pdb=" O1A BCL P 101 " 0.048 3.00e-02 1.11e+03 pdb=" O2A BCL P 101 " -0.486 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL V 102 " -0.337 3.00e-02 1.11e+03 2.73e-01 4.15e+02 pdb=" CBA BCL V 102 " -0.186 3.00e-02 1.11e+03 pdb=" CGA BCL V 102 " 0.078 3.00e-02 1.11e+03 pdb=" O1A BCL V 102 " -0.022 3.00e-02 1.11e+03 pdb=" O2A BCL V 102 " 0.467 3.00e-02 1.11e+03 ... (remaining 2322 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3215 2.83 - 3.35: 11660 3.35 - 3.87: 22111 3.87 - 4.38: 25577 4.38 - 4.90: 45113 Nonbonded interactions: 107676 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 49 " pdb=" NH2 ARG Z 43 " model vdw 2.316 3.120 nonbonded pdb=" OH TYR 1 55 " pdb=" O PRO Z 44 " model vdw 2.328 3.040 nonbonded pdb=" OD2 ASP R 11 " pdb=" NZ LYS R 15 " model vdw 2.335 3.120 nonbonded pdb=" O PRO R 44 " pdb=" OH TYR S 55 " model vdw 2.362 3.040 nonbonded pdb=" O PRO P 44 " pdb=" OH TYR Q 55 " model vdw 2.376 3.040 ... (remaining 107671 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 '1' and resid 6 through 57) selection = (chain '3' and resid 6 through 57) selection = (chain '5' and resid 6 through 57) selection = (chain '7' and resid 6 through 57) selection = (chain 'A' and resid 6 through 57) selection = (chain 'D' and resid 6 through 57) selection = (chain 'F' and resid 6 through 57) selection = (chain 'I' and resid 6 through 57) selection = (chain 'K' and resid 6 through 57) selection = (chain 'O' and resid 6 through 57) selection = (chain 'Q' and resid 6 through 57) selection = (chain 'S' and resid 6 through 57) selection = (chain 'U' and resid 6 through 57) selection = (chain 'Y' and resid 6 through 57) } ncs_group { reference = (chain '2' and resid 7 through 46) selection = (chain '4' and resid 7 through 46) selection = (chain '6' and resid 7 through 46) selection = (chain '8' and resid 7 through 46) selection = (chain 'B' and resid 7 through 46) selection = (chain 'E' and resid 7 through 46) selection = (chain 'G' and resid 7 through 46) selection = (chain 'J' and resid 7 through 46) selection = (chain 'N' and resid 7 through 46) selection = (chain 'P' and resid 7 through 46) selection = (chain 'R' and resid 7 through 46) selection = (chain 'T' and resid 7 through 46) selection = (chain 'V' and resid 7 through 46) selection = (chain 'Z' and resid 7 through 46) } 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=1.00 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: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.060 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.010 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.025 0.682 13923 Z= 1.610 Angle : 1.916 18.774 19273 Z= 0.862 Chirality : 0.055 0.351 1997 Planarity : 0.026 0.291 2325 Dihedral : 18.371 179.703 4823 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.46 (0.25), residues: 1251 helix: 3.59 (0.16), residues: 833 sheet: None (None), residues: 0 loop : -0.56 (0.36), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 43 TYR 0.006 0.001 TYR O 55 PHE 0.007 0.001 PHE 4 17 TRP 0.010 0.001 TRP R 45 HIS 0.003 0.001 HIS S 36 Details of bonding type rmsd/Z covalent geometry : bond 0.02150 / 0.93 (13901) covalent geometry : angle 1.91560 / 0.86 (19273) hydrogen bonds : bond 0.12987 / 8.39 ( 756) hydrogen bonds : angle 3.73807 / 2.82 ( 2148) Misc. bond : bond 0.33058 / 20.63 ( 22) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.459 Fit side-chains REVERT: 8 25 MET cc_start: 0.8031 (ttp) cc_final: 0.7799 (ttp) REVERT: R 25 MET cc_start: 0.8047 (ttp) cc_final: 0.7818 (ttp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0798 time to fit residues: 14.2246 Evaluate side-chains 95 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 7 ASN 7 7 ASN D 7 ASN I 7 ASN K 7 ASN Q 7 ASN U 7 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.119907 restraints weight = 14715.629| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.38 r_work: 0.3159 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13923 Z= 0.154 Angle : 0.686 12.743 19273 Z= 0.263 Chirality : 0.036 0.121 1997 Planarity : 0.004 0.041 2325 Dihedral : 14.161 179.960 2437 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.17 % Allowed : 2.08 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.70 (0.24), residues: 1251 helix: 3.93 (0.15), residues: 801 sheet: None (None), residues: 0 loop : -0.47 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 43 TYR 0.008 0.001 TYR Q 55 PHE 0.008 0.001 PHE 4 17 TRP 0.010 0.001 TRP R 45 HIS 0.003 0.001 HIS P 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (13901) covalent geometry : angle 0.68638 / 0.26 (19273) hydrogen bonds : bond 0.06417 / 4.35 ( 756) hydrogen bonds : angle 2.86089 / 2.09 ( 2148) Misc. bond : bond 0.00254 / 0.17 ( 22) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.555 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.0790 time to fit residues: 14.7942 Evaluate side-chains 106 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 7 ASN D 7 ASN I 7 ASN K 7 ASN Q 7 ASN U 7 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121267 restraints weight = 14561.291| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.33 r_work: 0.3174 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13923 Z= 0.143 Angle : 0.637 17.250 19273 Z= 0.246 Chirality : 0.035 0.125 1997 Planarity : 0.003 0.037 2325 Dihedral : 13.396 179.932 2437 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.43 % Allowed : 3.30 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.88 (0.24), residues: 1251 helix: 3.98 (0.15), residues: 805 sheet: None (None), residues: 0 loop : -0.23 (0.34), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 43 TYR 0.007 0.001 TYR 1 55 PHE 0.007 0.001 PHE 4 17 TRP 0.008 0.001 TRP R 45 HIS 0.003 0.001 HIS 6 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (13901) covalent geometry : angle 0.63745 / 0.25 (19273) hydrogen bonds : bond 0.06145 / 4.17 ( 756) hydrogen bonds : angle 2.74443 / 2.00 ( 2148) Misc. bond : bond 0.00210 / 0.14 ( 22) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.427 Fit side-chains REVERT: N 9 LEU cc_start: 0.8288 (mp) cc_final: 0.8087 (mp) outliers start: 5 outliers final: 1 residues processed: 107 average time/residue: 0.0780 time to fit residues: 14.0156 Evaluate side-chains 105 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.0170 chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 7 ASN D 7 ASN I 7 ASN K 7 ASN Q 7 ASN U 7 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121292 restraints weight = 14593.882| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.33 r_work: 0.3188 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13923 Z= 0.138 Angle : 0.620 15.974 19273 Z= 0.241 Chirality : 0.035 0.126 1997 Planarity : 0.003 0.034 2325 Dihedral : 13.354 179.982 2437 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.43 % Allowed : 4.08 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.05 (0.23), residues: 1251 helix: 4.07 (0.14), residues: 805 sheet: None (None), residues: 0 loop : -0.09 (0.34), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 43 TYR 0.007 0.001 TYR S 55 PHE 0.006 0.001 PHE 8 21 TRP 0.008 0.001 TRP 8 45 HIS 0.003 0.001 HIS 6 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13901) covalent geometry : angle 0.62019 / 0.24 (19273) hydrogen bonds : bond 0.06047 / 4.10 ( 756) hydrogen bonds : angle 2.69383 / 1.96 ( 2148) Misc. bond : bond 0.00178 / 0.12 ( 22) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.479 Fit side-chains REVERT: N 9 LEU cc_start: 0.8273 (mp) cc_final: 0.8063 (mp) REVERT: O 37 MET cc_start: 0.7844 (mmt) cc_final: 0.7256 (mmt) outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 0.0794 time to fit residues: 14.2768 Evaluate side-chains 105 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain R residue 41 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 7 ASN D 7 ASN I 7 ASN K 7 ASN Q 7 ASN U 7 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119999 restraints weight = 14578.639| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.32 r_work: 0.3165 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13923 Z= 0.142 Angle : 0.628 15.602 19273 Z= 0.245 Chirality : 0.036 0.125 1997 Planarity : 0.003 0.032 2325 Dihedral : 13.355 179.994 2437 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.61 % Allowed : 4.34 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.23), residues: 1251 helix: 4.06 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.24 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 43 TYR 0.007 0.001 TYR 1 55 PHE 0.007 0.001 PHE 8 21 TRP 0.008 0.001 TRP 8 45 HIS 0.003 0.001 HIS 6 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (13901) covalent geometry : angle 0.62845 / 0.24 (19273) hydrogen bonds : bond 0.06189 / 4.20 ( 756) hydrogen bonds : angle 2.69397 / 1.96 ( 2148) Misc. bond : bond 0.00181 / 0.12 ( 22) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.914 Fit side-chains REVERT: N 9 LEU cc_start: 0.8255 (mp) cc_final: 0.8039 (mp) outliers start: 7 outliers final: 2 residues processed: 111 average time/residue: 0.0889 time to fit residues: 16.4840 Evaluate side-chains 104 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain R residue 41 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 83 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 7 ASN D 7 ASN I 7 ASN K 7 ASN Q 7 ASN U 7 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115046 restraints weight = 14680.264| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.30 r_work: 0.3095 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13923 Z= 0.221 Angle : 0.766 16.460 19273 Z= 0.299 Chirality : 0.039 0.143 1997 Planarity : 0.003 0.033 2325 Dihedral : 14.340 179.954 2437 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.78 % Allowed : 5.81 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.23), residues: 1251 helix: 3.64 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.33 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 43 TYR 0.012 0.002 TYR I 9 PHE 0.009 0.001 PHE T 17 TRP 0.010 0.002 TRP 8 45 HIS 0.004 0.001 HIS 6 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.22 (13901) covalent geometry : angle 0.76643 / 0.30 (19273) hydrogen bonds : bond 0.07880 / 5.34 ( 756) hydrogen bonds : angle 2.90636 / 2.12 ( 2148) Misc. bond : bond 0.00273 / 0.18 ( 22) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.322 Fit side-chains REVERT: P 41 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7889 (mp) outliers start: 9 outliers final: 0 residues processed: 108 average time/residue: 0.0748 time to fit residues: 13.6732 Evaluate side-chains 104 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 41 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 0.0060 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 7 ASN D 7 ASN I 7 ASN K 7 ASN Q 7 ASN U 7 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122655 restraints weight = 14412.807| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.32 r_work: 0.3203 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13923 Z= 0.120 Angle : 0.594 14.551 19273 Z= 0.233 Chirality : 0.035 0.132 1997 Planarity : 0.003 0.032 2325 Dihedral : 13.071 180.000 2437 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.52 % Allowed : 6.07 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.35 (0.23), residues: 1251 helix: 4.30 (0.14), residues: 805 sheet: None (None), residues: 0 loop : 0.04 (0.34), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 19 TYR 0.006 0.001 TYR O 55 PHE 0.007 0.001 PHE V 21 TRP 0.007 0.001 TRP 4 28 HIS 0.003 0.001 HIS Z 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (13901) covalent geometry : angle 0.59434 / 0.23 (19273) hydrogen bonds : bond 0.05566 / 3.77 ( 756) hydrogen bonds : angle 2.61704 / 1.89 ( 2148) Misc. bond : bond 0.00154 / 0.10 ( 22) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.409 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 110 average time/residue: 0.0791 time to fit residues: 14.7195 Evaluate side-chains 104 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain R residue 41 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 7 ASN D 7 ASN I 7 ASN K 7 ASN Q 7 ASN U 7 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119076 restraints weight = 14454.925| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.30 r_work: 0.3150 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13923 Z= 0.158 Angle : 0.665 15.462 19273 Z= 0.258 Chirality : 0.037 0.135 1997 Planarity : 0.003 0.032 2325 Dihedral : 13.500 179.984 2437 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.43 % Allowed : 6.33 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.06 (0.23), residues: 1251 helix: 4.07 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.18 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 43 TYR 0.008 0.001 TYR 1 55 PHE 0.007 0.001 PHE G 21 TRP 0.009 0.001 TRP 8 45 HIS 0.003 0.001 HIS 6 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (13901) covalent geometry : angle 0.66537 / 0.26 (19273) hydrogen bonds : bond 0.06476 / 4.40 ( 756) hydrogen bonds : angle 2.72053 / 1.97 ( 2148) Misc. bond : bond 0.00202 / 0.13 ( 22) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.676 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 104 average time/residue: 0.0767 time to fit residues: 13.4186 Evaluate side-chains 102 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 76 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 7 ASN D 7 ASN I 7 ASN K 7 ASN Q 7 ASN U 7 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121389 restraints weight = 14601.642| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.32 r_work: 0.3181 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13923 Z= 0.133 Angle : 0.621 15.006 19273 Z= 0.242 Chirality : 0.035 0.131 1997 Planarity : 0.003 0.031 2325 Dihedral : 13.164 179.987 2437 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.09 % Allowed : 6.68 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.26 (0.23), residues: 1251 helix: 4.26 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.17 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG O 18 TYR 0.007 0.001 TYR 1 55 PHE 0.007 0.001 PHE 8 21 TRP 0.007 0.001 TRP T 28 HIS 0.003 0.001 HIS Z 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (13901) covalent geometry : angle 0.62083 / 0.24 (19273) hydrogen bonds : bond 0.05876 / 3.99 ( 756) hydrogen bonds : angle 2.64747 / 1.92 ( 2148) Misc. bond : bond 0.00167 / 0.11 ( 22) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.503 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.0837 time to fit residues: 14.6988 Evaluate side-chains 102 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 7 ASN D 7 ASN I 7 ASN K 7 ASN Q 7 ASN U 7 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118035 restraints weight = 14604.641| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.31 r_work: 0.3146 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13923 Z= 0.171 Angle : 0.692 15.836 19273 Z= 0.270 Chirality : 0.037 0.143 1997 Planarity : 0.003 0.031 2325 Dihedral : 13.595 179.983 2437 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.09 % Allowed : 6.85 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.00 (0.23), residues: 1251 helix: 4.03 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.22 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 43 TYR 0.008 0.001 TYR 1 55 PHE 0.008 0.001 PHE 8 21 TRP 0.009 0.001 TRP 8 45 HIS 0.003 0.001 HIS 6 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (13901) covalent geometry : angle 0.69185 / 0.27 (19273) hydrogen bonds : bond 0.06791 / 4.61 ( 756) hydrogen bonds : angle 2.75514 / 2.00 ( 2148) Misc. bond : bond 0.00208 / 0.14 ( 22) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.325 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.0726 time to fit residues: 12.6011 Evaluate side-chains 103 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 7 ASN D 7 ASN I 7 ASN K 7 ASN Q 7 ASN U 7 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120887 restraints weight = 14562.614| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.31 r_work: 0.3178 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13923 Z= 0.135 Angle : 0.632 14.668 19273 Z= 0.246 Chirality : 0.036 0.133 1997 Planarity : 0.003 0.031 2325 Dihedral : 13.163 179.998 2437 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.17 % Allowed : 7.03 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.21 (0.23), residues: 1251 helix: 4.22 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.19 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG O 18 TYR 0.008 0.001 TYR 1 55 PHE 0.007 0.001 PHE 8 21 TRP 0.007 0.001 TRP 8 45 HIS 0.003 0.001 HIS Z 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13901) covalent geometry : angle 0.63152 / 0.25 (19273) hydrogen bonds : bond 0.05982 / 4.06 ( 756) hydrogen bonds : angle 2.66254 / 1.93 ( 2148) Misc. bond : bond 0.00171 / 0.11 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2541.57 seconds wall clock time: 44 minutes 10.28 seconds (2650.28 seconds total)