Starting phenix.real_space_refine on Fri Jun 20 15:03:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jc9_36154/06_2025/8jc9_36154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jc9_36154/06_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_36154/06_2025/8jc9_36154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jc9_36154/06_2025/8jc9_36154.map" model { file = "/net/cci-nas-00/data/ceres_data/8jc9_36154/06_2025/8jc9_36154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jc9_36154/06_2025/8jc9_36154.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.91, per 1000 atoms: 0.59 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: 3.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.91 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: 3.21 Time building geometry restraints manager: 4.50 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.310 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.680 ------------------------------------------------------------------------------- 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 : 5.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.010 0.001 TRP R 45 HIS 0.003 0.001 HIS S 36 PHE 0.007 0.001 PHE 4 17 TYR 0.006 0.001 TYR O 55 ARG 0.003 0.000 ARG Z 43 Details of bonding type rmsd hydrogen bonds : bond 0.12987 ( 756) hydrogen bonds : angle 3.73807 ( 2148) covalent geometry : bond 0.02150 (13901) covalent geometry : angle 1.91560 (19273) 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 : 1.213 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: 0.1752 time to fit residues: 30.6044 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 : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3575 r_free = 0.3575 target = 0.137452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118247 restraints weight = 14432.114| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.33 r_work: 0.3143 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13923 Z= 0.158 Angle : 0.700 12.865 19273 Z= 0.265 Chirality : 0.037 0.150 1997 Planarity : 0.004 0.040 2325 Dihedral : 14.188 179.997 2437 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.17 % Allowed : 2.17 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.24), residues: 1251 helix: 3.89 (0.15), residues: 801 sheet: None (None), residues: 0 loop : -0.42 (0.34), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 45 HIS 0.003 0.001 HIS 6 36 PHE 0.008 0.001 PHE 4 17 TYR 0.008 0.001 TYR 7 55 ARG 0.003 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.06532 ( 756) hydrogen bonds : angle 2.87117 ( 2148) covalent geometry : bond 0.00379 (13901) covalent geometry : angle 0.70001 (19273) Misc. bond : bond 0.00226 ( 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 : 1.136 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.1763 time to fit residues: 32.4312 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 : 1.138 ------------------------------------------------------------------------------- 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 87 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 102 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 = 0.138817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119648 restraints weight = 14583.856| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.33 r_work: 0.3157 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1148 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= 0.136 Angle : 0.627 18.320 19273 Z= 0.241 Chirality : 0.035 0.127 1997 Planarity : 0.003 0.039 2325 Dihedral : 13.259 179.968 2437 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.43 % Allowed : 3.38 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.24), residues: 1251 helix: 4.04 (0.15), residues: 805 sheet: None (None), residues: 0 loop : -0.20 (0.34), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 45 HIS 0.003 0.001 HIS J 36 PHE 0.006 0.001 PHE J 17 TYR 0.007 0.001 TYR O 55 ARG 0.002 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.05913 ( 756) hydrogen bonds : angle 2.71200 ( 2148) covalent geometry : bond 0.00311 (13901) covalent geometry : angle 0.62726 (19273) Misc. bond : bond 0.00195 ( 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 111 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 1.185 Fit side-chains REVERT: N 9 LEU cc_start: 0.8303 (mp) cc_final: 0.8103 (mp) outliers start: 5 outliers final: 1 residues processed: 108 average time/residue: 0.1920 time to fit residues: 35.1479 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 : 1.164 ------------------------------------------------------------------------------- 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 86 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.130742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111475 restraints weight = 14876.224| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.36 r_work: 0.3036 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1533 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= 0.220 Angle : 0.771 16.232 19273 Z= 0.301 Chirality : 0.039 0.136 1997 Planarity : 0.004 0.035 2325 Dihedral : 14.483 179.999 2437 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.35 % Allowed : 4.68 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.23), residues: 1251 helix: 3.82 (0.14), residues: 782 sheet: None (None), residues: 0 loop : -0.62 (0.32), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 8 45 HIS 0.004 0.001 HIS 6 36 PHE 0.009 0.001 PHE 4 17 TYR 0.012 0.002 TYR I 9 ARG 0.003 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.08035 ( 756) hydrogen bonds : angle 2.95917 ( 2148) covalent geometry : bond 0.00553 (13901) covalent geometry : angle 0.77071 (19273) Misc. bond : bond 0.00264 ( 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: 4 poor density : 106 time to evaluate : 1.209 Fit side-chains REVERT: O 37 MET cc_start: 0.7953 (mmt) cc_final: 0.7383 (mmt) outliers start: 4 outliers final: 1 residues processed: 108 average time/residue: 0.1866 time to fit residues: 33.3392 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 : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.127183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107832 restraints weight = 15064.888| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.36 r_work: 0.3037 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13923 Z= 0.247 Angle : 0.807 16.358 19273 Z= 0.317 Chirality : 0.041 0.143 1997 Planarity : 0.004 0.035 2325 Dihedral : 14.844 180.000 2437 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.04 % Allowed : 4.94 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.23), residues: 1251 helix: 3.38 (0.15), residues: 812 sheet: None (None), residues: 0 loop : -0.59 (0.33), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 8 45 HIS 0.004 0.001 HIS P 36 PHE 0.009 0.001 PHE T 17 TYR 0.012 0.002 TYR I 9 ARG 0.002 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.08383 ( 756) hydrogen bonds : angle 2.98697 ( 2148) covalent geometry : bond 0.00629 (13901) covalent geometry : angle 0.80713 (19273) Misc. bond : bond 0.00305 ( 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 117 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.193 Fit side-chains REVERT: 3 37 MET cc_start: 0.8045 (mmt) cc_final: 0.7817 (mmm) REVERT: Y 43 ASP cc_start: 0.8668 (t0) cc_final: 0.8393 (t0) outliers start: 12 outliers final: 2 residues processed: 115 average time/residue: 0.1756 time to fit residues: 33.6360 Evaluate side-chains 107 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 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 = 0.3505 r_free = 0.3505 target = 0.132665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113239 restraints weight = 14929.465| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.36 r_work: 0.3059 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1642 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= 0.172 Angle : 0.686 14.903 19273 Z= 0.270 Chirality : 0.037 0.129 1997 Planarity : 0.003 0.034 2325 Dihedral : 14.076 179.989 2437 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.78 % Allowed : 5.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.72 (0.23), residues: 1251 helix: 3.83 (0.14), residues: 805 sheet: None (None), residues: 0 loop : -0.25 (0.33), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 8 45 HIS 0.003 0.001 HIS 6 36 PHE 0.007 0.001 PHE 8 21 TYR 0.008 0.001 TYR 1 55 ARG 0.001 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.07009 ( 756) hydrogen bonds : angle 2.81137 ( 2148) covalent geometry : bond 0.00413 (13901) covalent geometry : angle 0.68623 (19273) Misc. bond : bond 0.00238 ( 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 111 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 1.292 Fit side-chains REVERT: E 22 MET cc_start: 0.8217 (mmt) cc_final: 0.7930 (mmm) REVERT: P 41 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7785 (mp) outliers start: 9 outliers final: 2 residues processed: 111 average time/residue: 0.1894 time to fit residues: 34.3790 Evaluate side-chains 101 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain P 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 13 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 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 = 0.3575 r_free = 0.3575 target = 0.138101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118808 restraints weight = 14491.833| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.32 r_work: 0.3155 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1610 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= 0.130 Angle : 0.609 14.914 19273 Z= 0.238 Chirality : 0.035 0.127 1997 Planarity : 0.003 0.033 2325 Dihedral : 13.375 179.998 2437 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.43 % Allowed : 6.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.23), residues: 1251 helix: 4.16 (0.14), residues: 815 sheet: None (None), residues: 0 loop : -0.23 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 28 HIS 0.003 0.001 HIS Z 36 PHE 0.007 0.001 PHE J 17 TYR 0.007 0.001 TYR 1 55 ARG 0.001 0.000 ARG F 19 Details of bonding type rmsd hydrogen bonds : bond 0.05831 ( 756) hydrogen bonds : angle 2.64985 ( 2148) covalent geometry : bond 0.00288 (13901) covalent geometry : angle 0.60880 (19273) Misc. bond : bond 0.00166 ( 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 109 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 1.154 Fit side-chains REVERT: N 22 MET cc_start: 0.8186 (mmt) cc_final: 0.7956 (mmm) outliers start: 5 outliers final: 2 residues processed: 109 average time/residue: 0.1880 time to fit residues: 33.4618 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 : 1.198 ------------------------------------------------------------------------------- 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 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 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 = 0.3571 r_free = 0.3571 target = 0.137780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118444 restraints weight = 14520.498| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.32 r_work: 0.3133 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1629 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= 0.134 Angle : 0.621 15.085 19273 Z= 0.243 Chirality : 0.036 0.131 1997 Planarity : 0.003 0.033 2325 Dihedral : 13.388 179.983 2437 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.17 % Allowed : 6.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.18 (0.23), residues: 1251 helix: 4.18 (0.14), residues: 815 sheet: None (None), residues: 0 loop : -0.17 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 8 45 HIS 0.003 0.001 HIS 6 36 PHE 0.007 0.001 PHE 8 21 TYR 0.007 0.001 TYR 1 55 ARG 0.001 0.000 ARG O 18 Details of bonding type rmsd hydrogen bonds : bond 0.05907 ( 756) hydrogen bonds : angle 2.65710 ( 2148) covalent geometry : bond 0.00304 (13901) covalent geometry : angle 0.62057 (19273) Misc. bond : bond 0.00171 ( 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 103 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 1.070 Fit side-chains REVERT: E 22 MET cc_start: 0.8190 (mmt) cc_final: 0.7918 (mmm) REVERT: N 22 MET cc_start: 0.8170 (mmt) cc_final: 0.7943 (mmm) outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.1885 time to fit residues: 32.4936 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 : 1.189 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 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 = 0.3532 r_free = 0.3532 target = 0.134196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115032 restraints weight = 14464.352| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.30 r_work: 0.3090 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1714 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= 0.174 Angle : 0.697 15.967 19273 Z= 0.272 Chirality : 0.038 0.139 1997 Planarity : 0.003 0.033 2325 Dihedral : 13.833 179.963 2437 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.35 % Allowed : 6.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.23), residues: 1251 helix: 3.95 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.25 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 8 45 HIS 0.003 0.001 HIS 6 36 PHE 0.008 0.001 PHE 8 21 TYR 0.009 0.001 TYR 1 55 ARG 0.001 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.06932 ( 756) hydrogen bonds : angle 2.77139 ( 2148) covalent geometry : bond 0.00421 (13901) covalent geometry : angle 0.69701 (19273) Misc. bond : bond 0.00224 ( 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 107 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 1.495 Fit side-chains REVERT: E 22 MET cc_start: 0.8220 (mmt) cc_final: 0.7959 (mmm) outliers start: 4 outliers final: 1 residues processed: 107 average time/residue: 0.2067 time to fit residues: 37.8160 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 : 1.515 ------------------------------------------------------------------------------- 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 41 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 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 = 0.3507 r_free = 0.3507 target = 0.132137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.112871 restraints weight = 14675.868| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.30 r_work: 0.3060 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13923 Z= 0.216 Angle : 0.774 16.275 19273 Z= 0.301 Chirality : 0.040 0.148 1997 Planarity : 0.003 0.032 2325 Dihedral : 14.257 179.947 2437 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.26 % Allowed : 7.11 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.23), residues: 1251 helix: 3.70 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.34 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 8 45 HIS 0.003 0.001 HIS N 18 PHE 0.008 0.001 PHE T 17 TYR 0.011 0.002 TYR I 9 ARG 0.002 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.07765 ( 756) hydrogen bonds : angle 2.87640 ( 2148) covalent geometry : bond 0.00541 (13901) covalent geometry : angle 0.77389 (19273) Misc. bond : bond 0.00266 ( 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 107 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 1.206 Fit side-chains REVERT: 7 37 MET cc_start: 0.8187 (mmp) cc_final: 0.7905 (mmt) REVERT: E 22 MET cc_start: 0.8267 (mmt) cc_final: 0.8003 (mmm) outliers start: 3 outliers final: 2 residues processed: 107 average time/residue: 0.1868 time to fit residues: 33.2373 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 : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain R residue 41 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 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 = 0.3539 r_free = 0.3539 target = 0.135157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115832 restraints weight = 14615.996| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.31 r_work: 0.3119 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1735 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= 0.142 Angle : 0.648 14.273 19273 Z= 0.256 Chirality : 0.036 0.132 1997 Planarity : 0.003 0.033 2325 Dihedral : 13.412 179.960 2437 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.26 % Allowed : 7.11 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.02 (0.23), residues: 1251 helix: 4.07 (0.14), residues: 815 sheet: None (None), residues: 0 loop : -0.25 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 8 45 HIS 0.003 0.001 HIS P 36 PHE 0.007 0.001 PHE 8 21 TYR 0.008 0.001 TYR 1 55 ARG 0.001 0.000 ARG O 18 Details of bonding type rmsd hydrogen bonds : bond 0.06194 ( 756) hydrogen bonds : angle 2.69587 ( 2148) covalent geometry : bond 0.00322 (13901) covalent geometry : angle 0.64846 (19273) Misc. bond : bond 0.00189 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5488.94 seconds wall clock time: 94 minutes 56.21 seconds (5696.21 seconds total)