Starting phenix.real_space_refine on Fri May 23 06:05:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jc9_36154/05_2025/8jc9_36154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jc9_36154/05_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_36154/05_2025/8jc9_36154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jc9_36154/05_2025/8jc9_36154.map" model { file = "/net/cci-nas-00/data/ceres_data/8jc9_36154/05_2025/8jc9_36154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jc9_36154/05_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-5687/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: 7.82, per 1000 atoms: 0.58 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: 3.72 Conformation dependent library (CDL) restraints added in 1.3 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: 0.95 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: 4.17 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.430 Find NCS groups from input model: 0.760 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.430 ------------------------------------------------------------------------------- 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 : 1.381 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: 0.1795 time to fit residues: 31.4191 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 : 1.184 ------------------------------------------------------------------------------- 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 = 14432.107| |-----------------------------------------------------------------------------| 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 : 1.308 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.1775 time to fit residues: 32.7129 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 : 1.172 ------------------------------------------------------------------------------- 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: 0.7980 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.131285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111765 restraints weight = 14937.591| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.39 r_work: 0.3093 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13923 Z= 0.177 Angle : 0.700 18.225 19273 Z= 0.272 Chirality : 0.037 0.126 1997 Planarity : 0.003 0.038 2325 Dihedral : 13.867 179.919 2437 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.01 % 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: 3.57 (0.23), residues: 1251 helix: 3.78 (0.15), residues: 804 sheet: None (None), residues: 0 loop : -0.44 (0.33), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 45 HIS 0.004 0.001 HIS 6 36 PHE 0.008 0.001 PHE 4 17 TYR 0.008 0.001 TYR I 9 ARG 0.003 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.07060 ( 756) hydrogen bonds : angle 2.85866 ( 2148) covalent geometry : bond 0.00426 (13901) covalent geometry : angle 0.69978 (19273) Misc. bond : bond 0.00243 ( 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 106 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 1.193 Fit side-chains REVERT: N 9 LEU cc_start: 0.8437 (mp) cc_final: 0.8217 (mp) REVERT: O 37 MET cc_start: 0.7925 (mmt) cc_final: 0.7367 (mmt) outliers start: 4 outliers final: 1 residues processed: 103 average time/residue: 0.1914 time to fit residues: 32.5118 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 : 1.377 ------------------------------------------------------------------------------- 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: 5.9990 chunk 105 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.135938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116513 restraints weight = 14662.260| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.36 r_work: 0.3122 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1324 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= 0.144 Angle : 0.635 15.588 19273 Z= 0.247 Chirality : 0.036 0.123 1997 Planarity : 0.003 0.036 2325 Dihedral : 13.448 179.980 2437 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.43 % Allowed : 4.25 % Favored : 95.32 % 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: 3.94 (0.24), residues: 1251 helix: 3.99 (0.15), residues: 805 sheet: None (None), residues: 0 loop : -0.14 (0.34), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 8 45 HIS 0.003 0.001 HIS Z 36 PHE 0.007 0.001 PHE 2 21 TYR 0.007 0.001 TYR S 55 ARG 0.001 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.06249 ( 756) hydrogen bonds : angle 2.73036 ( 2148) covalent geometry : bond 0.00332 (13901) covalent geometry : angle 0.63470 (19273) Misc. bond : bond 0.00189 ( 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 109 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 1.192 Fit side-chains REVERT: N 9 LEU cc_start: 0.8436 (mp) cc_final: 0.8215 (mp) REVERT: O 37 MET cc_start: 0.7914 (mmt) cc_final: 0.7278 (mmt) outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 0.1991 time to fit residues: 34.3298 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 : 1.252 ------------------------------------------------------------------------------- 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 87 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.128501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109161 restraints weight = 15010.567| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.36 r_work: 0.3058 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13923 Z= 0.214 Angle : 0.758 16.292 19273 Z= 0.295 Chirality : 0.039 0.136 1997 Planarity : 0.003 0.034 2325 Dihedral : 14.366 179.970 2437 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.78 % Allowed : 5.55 % Favored : 93.67 % 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: 3.44 (0.23), residues: 1251 helix: 3.62 (0.14), residues: 812 sheet: None (None), residues: 0 loop : -0.45 (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 4 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 0.07838 ( 756) hydrogen bonds : angle 2.91370 ( 2148) covalent geometry : bond 0.00535 (13901) covalent geometry : angle 0.75807 (19273) Misc. bond : bond 0.00273 ( 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 112 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.233 Fit side-chains REVERT: O 37 MET cc_start: 0.7974 (mmt) cc_final: 0.7319 (mmt) outliers start: 9 outliers final: 0 residues processed: 110 average time/residue: 0.1842 time to fit residues: 33.7325 Evaluate side-chains 102 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.136162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116840 restraints weight = 14702.331| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.33 r_work: 0.3117 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1511 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= 0.143 Angle : 0.636 15.142 19273 Z= 0.249 Chirality : 0.036 0.126 1997 Planarity : 0.003 0.033 2325 Dihedral : 13.573 179.975 2437 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.52 % Allowed : 5.90 % 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 (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: 4.11 (0.23), residues: 1251 helix: 4.12 (0.14), residues: 795 sheet: None (None), residues: 0 loop : 0.05 (0.33), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 8 45 HIS 0.003 0.001 HIS Z 36 PHE 0.008 0.001 PHE E 21 TYR 0.007 0.001 TYR 1 55 ARG 0.001 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.06366 ( 756) hydrogen bonds : angle 2.71842 ( 2148) covalent geometry : bond 0.00326 (13901) covalent geometry : angle 0.63635 (19273) Misc. bond : bond 0.00187 ( 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 106 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: P 41 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7871 (mp) outliers start: 6 outliers final: 2 residues processed: 105 average time/residue: 0.1882 time to fit residues: 32.9192 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 : 1.371 ------------------------------------------------------------------------------- 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: 0.9990 chunk 125 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.135146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115942 restraints weight = 14613.366| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.32 r_work: 0.3120 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1558 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= 0.144 Angle : 0.637 15.189 19273 Z= 0.248 Chirality : 0.036 0.128 1997 Planarity : 0.003 0.033 2325 Dihedral : 13.423 179.987 2437 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.52 % Allowed : 6.24 % 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: 4.10 (0.23), residues: 1251 helix: 4.10 (0.14), residues: 815 sheet: None (None), residues: 0 loop : -0.16 (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 2 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 0.06199 ( 756) hydrogen bonds : angle 2.69200 ( 2148) covalent geometry : bond 0.00332 (13901) covalent geometry : angle 0.63653 (19273) Misc. bond : bond 0.00184 ( 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 108 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 1.143 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 107 average time/residue: 0.1753 time to fit residues: 31.1036 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 : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B 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: 0.9990 chunk 40 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 117 optimal weight: 0.4980 chunk 76 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.138385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119166 restraints weight = 14501.269| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.32 r_work: 0.3162 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1592 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= 0.122 Angle : 0.594 15.061 19273 Z= 0.231 Chirality : 0.035 0.124 1997 Planarity : 0.003 0.032 2325 Dihedral : 13.014 179.987 2437 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.43 % Allowed : 6.33 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.34 (0.23), residues: 1251 helix: 4.31 (0.14), residues: 815 sheet: None (None), residues: 0 loop : -0.12 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 28 HIS 0.002 0.001 HIS Z 36 PHE 0.008 0.001 PHE G 21 TYR 0.007 0.001 TYR 1 55 ARG 0.001 0.000 ARG F 19 Details of bonding type rmsd hydrogen bonds : bond 0.05535 ( 756) hydrogen bonds : angle 2.60583 ( 2148) covalent geometry : bond 0.00268 (13901) covalent geometry : angle 0.59383 (19273) Misc. bond : bond 0.00150 ( 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 107 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 1.152 Fit side-chains REVERT: O 37 MET cc_start: 0.7942 (mmt) cc_final: 0.7332 (mmt) outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 0.1879 time to fit residues: 33.2916 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 : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain R residue 41 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 0.8980 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: 4.9990 chunk 63 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 F 56 GLN 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 = 0.3499 r_free = 0.3499 target = 0.131447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112313 restraints weight = 14617.689| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.29 r_work: 0.3070 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1812 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= 0.246 Angle : 0.810 16.943 19273 Z= 0.314 Chirality : 0.041 0.152 1997 Planarity : 0.003 0.032 2325 Dihedral : 14.280 179.987 2437 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 (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: 3.61 (0.23), residues: 1251 helix: 3.69 (0.14), residues: 816 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 8 45 HIS 0.004 0.001 HIS B 36 PHE 0.009 0.001 PHE T 17 TYR 0.013 0.002 TYR I 9 ARG 0.003 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.07982 ( 756) hydrogen bonds : angle 2.88654 ( 2148) covalent geometry : bond 0.00627 (13901) covalent geometry : angle 0.80994 (19273) Misc. bond : bond 0.00288 ( 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 105 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 1.269 Fit side-chains REVERT: 7 37 MET cc_start: 0.8248 (mmp) cc_final: 0.7934 (mmt) outliers start: 2 outliers final: 1 residues processed: 104 average time/residue: 0.1823 time to fit residues: 31.5579 Evaluate side-chains 103 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 41 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 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 = 0.3558 r_free = 0.3558 target = 0.136597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117290 restraints weight = 14490.844| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.31 r_work: 0.3140 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1676 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= 0.140 Angle : 0.641 14.744 19273 Z= 0.251 Chirality : 0.036 0.131 1997 Planarity : 0.003 0.032 2325 Dihedral : 13.355 179.975 2437 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.17 % Allowed : 6.85 % Favored : 92.97 % 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: 4.11 (0.23), residues: 1251 helix: 4.13 (0.14), residues: 815 sheet: None (None), residues: 0 loop : -0.20 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 28 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 3 19 Details of bonding type rmsd hydrogen bonds : bond 0.06216 ( 756) hydrogen bonds : angle 2.69023 ( 2148) covalent geometry : bond 0.00315 (13901) covalent geometry : angle 0.64063 (19273) Misc. bond : bond 0.00175 ( 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 104 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 1.298 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 104 average time/residue: 0.2022 time to fit residues: 34.6490 Evaluate side-chains 103 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 88 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.135804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116513 restraints weight = 14610.768| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.32 r_work: 0.3111 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13923 Z= 0.153 Angle : 0.669 15.153 19273 Z= 0.261 Chirality : 0.037 0.137 1997 Planarity : 0.003 0.032 2325 Dihedral : 13.417 179.966 2437 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % 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: 4.08 (0.23), residues: 1251 helix: 4.09 (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 B 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 0.06408 ( 756) hydrogen bonds : angle 2.71493 ( 2148) covalent geometry : bond 0.00359 (13901) covalent geometry : angle 0.66873 (19273) Misc. bond : bond 0.00194 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5393.03 seconds wall clock time: 94 minutes 15.81 seconds (5655.81 seconds total)