Starting phenix.real_space_refine on Sun Aug 24 23:50:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jc9_36154/08_2025/8jc9_36154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jc9_36154/08_2025/8jc9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jc9_36154/08_2025/8jc9_36154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jc9_36154/08_2025/8jc9_36154.map" model { file = "/net/cci-nas-00/data/ceres_data/8jc9_36154/08_2025/8jc9_36154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jc9_36154/08_2025/8jc9_36154.cif" } 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-2.0-5787/lib/python3.9/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, 155 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 150 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 155 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 155 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 2.62, per 1000 atoms: 0.20 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: 0.84 Conformation dependent library (CDL) restraints added in 341.3 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 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: 0.20 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: 1.50 Time building geometry restraints manager: 1.09 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 10.150 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 aren 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 covalent geometry : bond 0.02150 (13901) covalent geometry : angle 1.91560 (19273) hydrogen bonds : bond 0.12987 ( 756) hydrogen bonds : angle 3.73807 ( 2148) Misc. bond : bond 0.33058 ( 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 : 0.476 Fit side-chains REVERT: 8 25 MET cc_start: 0.8031 (ttp) cc_final: 0.7798 (ttp) REVERT: R 25 MET cc_start: 0.8048 (ttp) cc_final: 0.7818 (ttp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0860 time to fit residues: 15.3080 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 : 0.474 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3568 r_free = 0.3568 target = 0.136937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117762 restraints weight = 14580.787| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.33 r_work: 0.3137 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13923 Z= 0.151 Angle : 0.682 12.749 19273 Z= 0.259 Chirality : 0.036 0.131 1997 Planarity : 0.004 0.041 2325 Dihedral : 14.155 179.985 2437 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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 aren not related in a simple way. whole: 3.74 (0.24), residues: 1251 helix: 3.94 (0.15), residues: 801 sheet: None (None), residues: 0 loop : -0.40 (0.34), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 43 TYR 0.008 0.001 TYR 7 55 PHE 0.008 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 covalent geometry : bond 0.00356 (13901) covalent geometry : angle 0.68185 (19273) hydrogen bonds : bond 0.06344 ( 756) hydrogen bonds : angle 2.84276 ( 2148) Misc. bond : bond 0.00168 ( 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 113 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.470 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 112 average time/residue: 0.0834 time to fit residues: 15.8072 Evaluate side-chains 107 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3588 r_free = 0.3588 target = 0.138732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119502 restraints weight = 14542.983| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.34 r_work: 0.3145 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1079 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= 0.140 Angle : 0.632 16.517 19273 Z= 0.243 Chirality : 0.035 0.135 1997 Planarity : 0.003 0.037 2325 Dihedral : 13.382 179.948 2437 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.35 % Allowed : 3.21 % Favored : 96.44 % 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 aren not related in a simple way. whole: 3.92 (0.24), residues: 1251 helix: 3.99 (0.15), residues: 805 sheet: None (None), residues: 0 loop : -0.18 (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 7 55 PHE 0.007 0.001 PHE Z 17 TRP 0.008 0.001 TRP R 45 HIS 0.003 0.001 HIS J 36 Details of bonding type rmsd covalent geometry : bond 0.00323 (13901) covalent geometry : angle 0.63169 (19273) hydrogen bonds : bond 0.06065 ( 756) hydrogen bonds : angle 2.73623 ( 2148) Misc. bond : bond 0.00181 ( 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: 4 poor density : 106 time to evaluate : 0.341 Fit side-chains REVERT: N 9 LEU cc_start: 0.8269 (mp) cc_final: 0.8068 (mp) outliers start: 4 outliers final: 1 residues processed: 107 average time/residue: 0.0768 time to fit residues: 13.5485 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 : 0.391 ------------------------------------------------------------------------------- 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: 0.9980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 93 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3554 r_free = 0.3554 target = 0.137047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117540 restraints weight = 14739.739| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.38 r_work: 0.3165 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1251 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= 0.123 Angle : 0.590 16.186 19273 Z= 0.228 Chirality : 0.035 0.122 1997 Planarity : 0.003 0.035 2325 Dihedral : 13.154 179.975 2437 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.43 % Allowed : 3.99 % Favored : 95.58 % 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 aren not related in a simple way. whole: 4.21 (0.24), residues: 1251 helix: 4.19 (0.14), residues: 805 sheet: None (None), residues: 0 loop : -0.00 (0.34), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 43 TYR 0.006 0.001 TYR S 55 PHE 0.006 0.001 PHE J 17 TRP 0.007 0.001 TRP 8 45 HIS 0.003 0.001 HIS Z 36 Details of bonding type rmsd covalent geometry : bond 0.00271 (13901) covalent geometry : angle 0.59032 (19273) hydrogen bonds : bond 0.05559 ( 756) hydrogen bonds : angle 2.63984 ( 2148) Misc. bond : bond 0.00145 ( 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 : 0.385 Fit side-chains REVERT: N 9 LEU cc_start: 0.8256 (mp) cc_final: 0.8048 (mp) REVERT: O 37 MET cc_start: 0.7811 (mmt) cc_final: 0.7225 (mmt) outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 0.0795 time to fit residues: 14.3929 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 : 0.416 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3478 r_free = 0.3478 target = 0.130386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111149 restraints weight = 14928.825| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.36 r_work: 0.3051 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13923 Z= 0.243 Angle : 0.790 17.036 19273 Z= 0.309 Chirality : 0.040 0.145 1997 Planarity : 0.003 0.034 2325 Dihedral : 14.516 179.961 2437 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.43 % Allowed : 5.38 % Favored : 94.19 % 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 aren not related in a simple way. whole: 3.42 (0.23), residues: 1251 helix: 3.61 (0.14), residues: 810 sheet: None (None), residues: 0 loop : -0.45 (0.34), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 43 TYR 0.013 0.002 TYR I 9 PHE 0.010 0.001 PHE 4 17 TRP 0.010 0.002 TRP 8 45 HIS 0.004 0.001 HIS 6 36 Details of bonding type rmsd covalent geometry : bond 0.00616 (13901) covalent geometry : angle 0.79003 (19273) hydrogen bonds : bond 0.08206 ( 756) hydrogen bonds : angle 2.95005 ( 2148) Misc. bond : bond 0.00285 ( 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 111 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.452 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 108 average time/residue: 0.0763 time to fit residues: 13.6368 Evaluate side-chains 103 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 83 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3504 r_free = 0.3504 target = 0.133007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113527 restraints weight = 14719.562| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.38 r_work: 0.3100 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1452 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= 0.141 Angle : 0.637 15.123 19273 Z= 0.249 Chirality : 0.036 0.125 1997 Planarity : 0.003 0.032 2325 Dihedral : 13.565 179.987 2437 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.61 % Allowed : 5.81 % Favored : 93.58 % 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 aren not related in a simple way. whole: 4.08 (0.23), residues: 1251 helix: 4.11 (0.14), residues: 806 sheet: None (None), residues: 0 loop : -0.11 (0.33), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 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 covalent geometry : bond 0.00321 (13901) covalent geometry : angle 0.63679 (19273) hydrogen bonds : bond 0.06339 ( 756) hydrogen bonds : angle 2.71675 ( 2148) Misc. bond : bond 0.00193 ( 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 110 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.363 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 109 average time/residue: 0.0713 time to fit residues: 13.1250 Evaluate side-chains 101 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain R residue 41 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3468 r_free = 0.3468 target = 0.130087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110615 restraints weight = 14837.372| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.36 r_work: 0.3076 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13923 Z= 0.185 Angle : 0.713 15.770 19273 Z= 0.278 Chirality : 0.038 0.139 1997 Planarity : 0.003 0.033 2325 Dihedral : 13.972 179.991 2437 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.35 % Allowed : 6.50 % Favored : 93.15 % 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 aren not related in a simple way. whole: 3.79 (0.23), residues: 1251 helix: 3.85 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.26 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 43 TYR 0.010 0.001 TYR I 9 PHE 0.007 0.001 PHE 8 21 TRP 0.009 0.001 TRP 8 45 HIS 0.004 0.001 HIS P 36 Details of bonding type rmsd covalent geometry : bond 0.00454 (13901) covalent geometry : angle 0.71263 (19273) hydrogen bonds : bond 0.07200 ( 756) hydrogen bonds : angle 2.81787 ( 2148) Misc. bond : bond 0.00234 ( 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 106 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.359 Fit side-chains REVERT: P 41 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7792 (mp) outliers start: 4 outliers final: 0 residues processed: 105 average time/residue: 0.0798 time to fit residues: 14.0407 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 : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P 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: 2.9990 chunk 46 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3498 r_free = 0.3498 target = 0.132711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.113170 restraints weight = 14669.209| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.36 r_work: 0.3108 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1571 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= 0.150 Angle : 0.652 15.050 19273 Z= 0.255 Chirality : 0.036 0.132 1997 Planarity : 0.003 0.032 2325 Dihedral : 13.508 179.997 2437 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.43 % Allowed : 6.07 % Favored : 93.50 % 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 aren not related in a simple way. whole: 4.04 (0.23), residues: 1251 helix: 4.06 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.21 (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 0.008 0.001 TRP 8 45 HIS 0.003 0.001 HIS 6 36 Details of bonding type rmsd covalent geometry : bond 0.00347 (13901) covalent geometry : angle 0.65168 (19273) hydrogen bonds : bond 0.06399 ( 756) hydrogen bonds : angle 2.71755 ( 2148) Misc. bond : bond 0.00195 ( 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 : 0.358 Fit side-chains REVERT: P 41 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7769 (mp) outliers start: 5 outliers final: 0 residues processed: 105 average time/residue: 0.0742 time to fit residues: 13.1119 Evaluate side-chains 101 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P 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: 3.9990 chunk 93 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 98 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3571 r_free = 0.3571 target = 0.137942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118675 restraints weight = 14611.878| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.32 r_work: 0.3139 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1585 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= 0.129 Angle : 0.613 15.025 19273 Z= 0.239 Chirality : 0.035 0.133 1997 Planarity : 0.003 0.032 2325 Dihedral : 13.126 180.000 2437 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.17 % Allowed : 6.76 % 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 aren not related in a simple way. whole: 4.29 (0.23), residues: 1251 helix: 4.27 (0.14), residues: 815 sheet: None (None), residues: 0 loop : -0.13 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 19 TYR 0.007 0.001 TYR 1 55 PHE 0.007 0.001 PHE G 21 TRP 0.008 0.001 TRP T 28 HIS 0.003 0.001 HIS Z 36 Details of bonding type rmsd covalent geometry : bond 0.00288 (13901) covalent geometry : angle 0.61345 (19273) hydrogen bonds : bond 0.05669 ( 756) hydrogen bonds : angle 2.63086 ( 2148) Misc. bond : bond 0.00164 ( 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 103 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.391 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 103 average time/residue: 0.0804 time to fit residues: 13.8564 Evaluate side-chains 100 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3544 r_free = 0.3544 target = 0.135505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116348 restraints weight = 14615.972| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.31 r_work: 0.3126 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13923 Z= 0.144 Angle : 0.646 15.220 19273 Z= 0.252 Chirality : 0.036 0.134 1997 Planarity : 0.003 0.032 2325 Dihedral : 13.313 179.964 2437 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.09 % Allowed : 7.03 % Favored : 92.89 % 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 aren not related in a simple way. whole: 4.15 (0.23), residues: 1251 helix: 4.15 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.15 (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 8 21 TRP 0.008 0.001 TRP D 12 HIS 0.003 0.001 HIS 6 36 Details of bonding type rmsd covalent geometry : bond 0.00333 (13901) covalent geometry : angle 0.64642 (19273) hydrogen bonds : bond 0.06176 ( 756) hydrogen bonds : angle 2.68897 ( 2148) Misc. bond : bond 0.00184 ( 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 101 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.444 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 101 average time/residue: 0.0864 time to fit residues: 14.7014 Evaluate side-chains 101 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 0.7980 chunk 79 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3481 r_free = 0.3481 target = 0.131176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111610 restraints weight = 14912.708| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.37 r_work: 0.3092 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1679 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= 0.173 Angle : 0.702 15.630 19273 Z= 0.273 Chirality : 0.037 0.140 1997 Planarity : 0.003 0.032 2325 Dihedral : 13.638 179.956 2437 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.09 % Allowed : 7.20 % Favored : 92.71 % 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 aren not related in a simple way. whole: 3.95 (0.23), residues: 1251 helix: 3.98 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.22 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 43 TYR 0.009 0.001 TYR 1 55 PHE 0.008 0.001 PHE 8 21 TRP 0.009 0.001 TRP D 12 HIS 0.003 0.001 HIS 6 36 Details of bonding type rmsd covalent geometry : bond 0.00417 (13901) covalent geometry : angle 0.70170 (19273) hydrogen bonds : bond 0.06856 ( 756) hydrogen bonds : angle 2.76927 ( 2148) Misc. bond : bond 0.00219 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2462.56 seconds wall clock time: 43 minutes 0.89 seconds (2580.89 seconds total)