Starting phenix.real_space_refine on Wed Mar 4 02:20:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbw_13307/03_2026/7pbw_13307.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbw_13307/03_2026/7pbw_13307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbw_13307/03_2026/7pbw_13307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbw_13307/03_2026/7pbw_13307.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbw_13307/03_2026/7pbw_13307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbw_13307/03_2026/7pbw_13307.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 9 9.91 5 Mg 27 5.21 5 S 18 5.16 5 C 6678 2.51 5 N 1206 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9500 Number of models: 1 Model: "" Number of chains: 54 Chain: "AA" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AC" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BB" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BC" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BD" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BE" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BF" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BG" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BH" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BI" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "AA" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 222 Unusual residues: {'7OT': 1, 'BCL': 2, 'LDA': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "AB" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'7OT': 1, 'BCL': 2, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AC" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'7OT': 1, 'BCL': 2, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AD" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 222 Unusual residues: {'7OT': 1, 'BCL': 2, 'LDA': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "AE" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'7OT': 1, 'BCL': 2, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AF" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'7OT': 1, 'BCL': 2, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AG" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'7OT': 1, 'BCL': 2, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AH" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'7OT': 1, 'BCL': 2, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AI" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'7OT': 1, 'BCL': 2, 'LDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BA" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'BCL': 1, 'LDA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BB" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'BCL': 1, 'LDA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BC" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'BCL': 1, 'LDA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BD" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {' CA': 1, 'BCL': 1, 'LDA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BE" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'BCL': 1, 'LDA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BF" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'BCL': 1, 'LDA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BG" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'BCL': 1, 'LDA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BH" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'BCL': 1, 'LDA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BI" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'BCL': 1, 'LDA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AA" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "AB" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "AC" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "AD" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "AE" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "AF" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "AG" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "AH" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "AI" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "BA" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "BB" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "BC" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "BD" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "BE" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "BF" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "BG" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "BH" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "BI" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 2.37, per 1000 atoms: 0.25 Number of scatterers: 9500 At special positions: 0 Unit cell: (87.12, 87.12, 77.88, 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 9 19.99 S 18 16.00 Mg 27 11.99 O 1562 8.00 N 1206 7.00 C 6678 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=27, symmetry=0 Number of additional bonds: simple=27, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 244.9 milliseconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 82.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'AA' and resid 5 through 10 removed outlier: 3.995A pdb=" N VALAA 9 " --> pdb=" O LYSAA 5 " (cutoff:3.500A) Processing helix chain 'AA' and resid 11 through 38 Proline residue: AA 17 - end of helix Processing helix chain 'AA' and resid 39 through 47 Processing helix chain 'AA' and resid 48 through 50 No H-bonds generated for 'chain 'AA' and resid 48 through 50' Processing helix chain 'AB' and resid 5 through 10 removed outlier: 4.007A pdb=" N VALAB 9 " --> pdb=" O LYSAB 5 " (cutoff:3.500A) Processing helix chain 'AB' and resid 11 through 38 Proline residue: AB 17 - end of helix Processing helix chain 'AB' and resid 39 through 47 Processing helix chain 'AB' and resid 48 through 50 No H-bonds generated for 'chain 'AB' and resid 48 through 50' Processing helix chain 'AC' and resid 5 through 10 removed outlier: 4.017A pdb=" N VALAC 9 " --> pdb=" O LYSAC 5 " (cutoff:3.500A) Processing helix chain 'AC' and resid 11 through 38 Proline residue: AC 17 - end of helix Processing helix chain 'AC' and resid 39 through 47 Processing helix chain 'AC' and resid 48 through 50 No H-bonds generated for 'chain 'AC' and resid 48 through 50' Processing helix chain 'AD' and resid 5 through 10 removed outlier: 4.027A pdb=" N VALAD 9 " --> pdb=" O LYSAD 5 " (cutoff:3.500A) Processing helix chain 'AD' and resid 11 through 38 Proline residue: AD 17 - end of helix Processing helix chain 'AD' and resid 39 through 47 Processing helix chain 'AD' and resid 48 through 50 No H-bonds generated for 'chain 'AD' and resid 48 through 50' Processing helix chain 'AE' and resid 5 through 10 removed outlier: 4.024A pdb=" N VALAE 9 " --> pdb=" O LYSAE 5 " (cutoff:3.500A) Processing helix chain 'AE' and resid 11 through 38 Proline residue: AE 17 - end of helix Processing helix chain 'AE' and resid 39 through 47 Processing helix chain 'AE' and resid 48 through 50 No H-bonds generated for 'chain 'AE' and resid 48 through 50' Processing helix chain 'AF' and resid 5 through 10 removed outlier: 4.025A pdb=" N VALAF 9 " --> pdb=" O LYSAF 5 " (cutoff:3.500A) Processing helix chain 'AF' and resid 11 through 38 Proline residue: AF 17 - end of helix Processing helix chain 'AF' and resid 39 through 47 Processing helix chain 'AF' and resid 48 through 50 No H-bonds generated for 'chain 'AF' and resid 48 through 50' Processing helix chain 'AG' and resid 5 through 10 removed outlier: 4.030A pdb=" N VALAG 9 " --> pdb=" O LYSAG 5 " (cutoff:3.500A) Processing helix chain 'AG' and resid 11 through 38 Proline residue: AG 17 - end of helix Processing helix chain 'AG' and resid 39 through 47 Processing helix chain 'AG' and resid 48 through 50 No H-bonds generated for 'chain 'AG' and resid 48 through 50' Processing helix chain 'AH' and resid 5 through 10 removed outlier: 4.021A pdb=" N VALAH 9 " --> pdb=" O LYSAH 5 " (cutoff:3.500A) Processing helix chain 'AH' and resid 11 through 38 Proline residue: AH 17 - end of helix Processing helix chain 'AH' and resid 39 through 47 Processing helix chain 'AH' and resid 48 through 50 No H-bonds generated for 'chain 'AH' and resid 48 through 50' Processing helix chain 'AI' and resid 5 through 10 removed outlier: 4.009A pdb=" N VALAI 9 " --> pdb=" O LYSAI 5 " (cutoff:3.500A) Processing helix chain 'AI' and resid 11 through 38 Proline residue: AI 17 - end of helix Processing helix chain 'AI' and resid 39 through 47 Processing helix chain 'AI' and resid 48 through 50 No H-bonds generated for 'chain 'AI' and resid 48 through 50' Processing helix chain 'BA' and resid 14 through 47 Processing helix chain 'BB' and resid 14 through 47 Processing helix chain 'BC' and resid 14 through 47 Processing helix chain 'BD' and resid 14 through 47 Processing helix chain 'BE' and resid 14 through 47 Processing helix chain 'BF' and resid 14 through 47 Processing helix chain 'BG' and resid 14 through 47 Processing helix chain 'BH' and resid 14 through 47 Processing helix chain 'BI' and resid 14 through 47 513 hydrogen bonds defined for protein. 1539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 2507 1.37 - 1.57: 6952 1.57 - 1.78: 9 1.78 - 1.98: 27 1.98 - 2.19: 108 Bond restraints: 9603 Sorted by residual: bond pdb=" N1 LDAAH 104 " pdb=" O1 LDAAH 104 " ideal model delta sigma weight residual 1.354 1.248 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" N1 LDAAA 105 " pdb=" O1 LDAAA 105 " ideal model delta sigma weight residual 1.354 1.249 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" N1 LDAAF 105 " pdb=" O1 LDAAF 105 " ideal model delta sigma weight residual 1.354 1.249 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" N1 LDAAC 105 " pdb=" O1 LDAAC 105 " ideal model delta sigma weight residual 1.354 1.250 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" N1 LDAAE 104 " pdb=" O1 LDAAE 104 " ideal model delta sigma weight residual 1.354 1.250 0.104 2.00e-02 2.50e+03 2.73e+01 ... (remaining 9598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 12352 1.69 - 3.39: 733 3.39 - 5.08: 234 5.08 - 6.77: 35 6.77 - 8.46: 11 Bond angle restraints: 13365 Sorted by residual: angle pdb=" C1 LDAAA 106 " pdb=" N1 LDAAA 106 " pdb=" CM1 LDAAA 106 " ideal model delta sigma weight residual 107.75 116.21 -8.46 3.00e+00 1.11e-01 7.96e+00 angle pdb=" C1 LDAAG 104 " pdb=" N1 LDAAG 104 " pdb=" CM1 LDAAG 104 " ideal model delta sigma weight residual 107.75 115.85 -8.10 3.00e+00 1.11e-01 7.29e+00 angle pdb=" CA TRPAA 40 " pdb=" CB TRPAA 40 " pdb=" CG TRPAA 40 " ideal model delta sigma weight residual 113.60 118.73 -5.13 1.90e+00 2.77e-01 7.29e+00 angle pdb=" C1 LDABC 103 " pdb=" C2 LDABC 103 " pdb=" C3 LDABC 103 " ideal model delta sigma weight residual 110.76 118.64 -7.88 3.00e+00 1.11e-01 6.90e+00 angle pdb=" C2 LDAAF 105 " pdb=" C1 LDAAF 105 " pdb=" N1 LDAAF 105 " ideal model delta sigma weight residual 114.17 106.32 7.85 3.00e+00 1.11e-01 6.85e+00 ... (remaining 13360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.06: 4352 14.06 - 28.13: 564 28.13 - 42.19: 91 42.19 - 56.26: 23 56.26 - 70.32: 10 Dihedral angle restraints: 5040 sinusoidal: 2565 harmonic: 2475 Sorted by residual: dihedral pdb=" C3 BCLAA 102 " pdb=" C5 BCLAA 102 " pdb=" C6 BCLAA 102 " pdb=" C7 BCLAA 102 " ideal model delta sinusoidal sigma weight residual -60.00 -97.58 37.58 3 9.00e+00 1.23e-02 1.83e+01 dihedral pdb=" CA LEUBE 13 " pdb=" C LEUBE 13 " pdb=" N THRBE 14 " pdb=" CA THRBE 14 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEUBC 13 " pdb=" C LEUBC 13 " pdb=" N THRBC 14 " pdb=" CA THRBC 14 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 750 0.028 - 0.056: 371 0.056 - 0.085: 96 0.085 - 0.113: 78 0.113 - 0.141: 64 Chirality restraints: 1359 Sorted by residual: chirality pdb=" CA LEUBB 50 " pdb=" N LEUBB 50 " pdb=" C LEUBB 50 " pdb=" CB LEUBB 50 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA LEUBF 50 " pdb=" N LEUBF 50 " pdb=" C LEUBF 50 " pdb=" CB LEUBF 50 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA LEUBH 50 " pdb=" N LEUBH 50 " pdb=" C LEUBH 50 " pdb=" CB LEUBH 50 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1356 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCLAH 102 " -0.038 1.50e-02 4.44e+03 3.38e-02 2.54e+01 pdb=" C2 BCLAH 102 " 0.039 1.50e-02 4.44e+03 pdb=" C3 BCLAH 102 " 0.036 1.50e-02 4.44e+03 pdb=" C4 BCLAH 102 " 0.001 1.50e-02 4.44e+03 pdb=" C5 BCLAH 102 " -0.038 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCLAF 102 " -0.038 1.50e-02 4.44e+03 3.30e-02 2.41e+01 pdb=" C2 BCLAF 102 " 0.045 1.50e-02 4.44e+03 pdb=" C3 BCLAF 102 " 0.028 1.50e-02 4.44e+03 pdb=" C4 BCLAF 102 " 0.001 1.50e-02 4.44e+03 pdb=" C5 BCLAF 102 " -0.035 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCLAH 102 " -0.061 3.00e-02 1.11e+03 5.32e-02 1.57e+01 pdb=" CBA BCLAH 102 " -0.059 3.00e-02 1.11e+03 pdb=" CGA BCLAH 102 " 0.057 3.00e-02 1.11e+03 pdb=" O1A BCLAH 102 " 0.001 3.00e-02 1.11e+03 pdb=" O2A BCLAH 102 " 0.062 3.00e-02 1.11e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1475 2.77 - 3.31: 8456 3.31 - 3.84: 18017 3.84 - 4.37: 22102 4.37 - 4.90: 35220 Nonbonded interactions: 85270 Sorted by model distance: nonbonded pdb=" O GLYBG 51 " pdb="CA CABG 102 " model vdw 2.243 2.510 nonbonded pdb=" O GLYBB 51 " pdb="CA CABB 102 " model vdw 2.247 2.510 nonbonded pdb=" O GLYBC 51 " pdb="CA CABC 102 " model vdw 2.251 2.510 nonbonded pdb=" O GLYBH 51 " pdb="CA CABH 102 " model vdw 2.254 2.510 nonbonded pdb=" OXT GLYBD 51 " pdb="CA CABD 102 " model vdw 2.255 2.510 ... (remaining 85265 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 'AA' and resid 1 through 104) selection = (chain 'AB' and resid 1 through 104) selection = (chain 'AC' and resid 1 through 104) selection = (chain 'AD' and resid 1 through 104) selection = (chain 'AE' and resid 1 through 104) selection = (chain 'AF' and resid 1 through 104) selection = (chain 'AG' and resid 1 through 104) selection = (chain 'AH' and resid 1 through 104) selection = chain 'AI' } ncs_group { reference = (chain 'BA' and resid 5 through 103) selection = (chain 'BB' and resid 5 through 103) selection = (chain 'BC' and resid 5 through 103) selection = chain 'BD' selection = (chain 'BE' and resid 5 through 103) selection = (chain 'BF' and resid 5 through 103) selection = (chain 'BG' and resid 5 through 103) selection = (chain 'BH' and resid 5 through 103) selection = (chain 'BI' and resid 5 through 103) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.410 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 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 : 0.020 0.401 9630 Z= 1.780 Angle : 0.994 8.464 13365 Z= 0.429 Chirality : 0.046 0.141 1359 Planarity : 0.009 0.053 1530 Dihedral : 12.270 70.321 3438 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.25), residues: 828 helix: 2.72 (0.17), residues: 567 sheet: None (None), residues: 0 loop : 0.69 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.003 ARGBC 30 TYR 0.034 0.011 TYRAH 45 PHE 0.015 0.002 PHEAH 19 TRP 0.033 0.004 TRPAA 40 HIS 0.008 0.003 HISAB 31 Details of bonding type rmsd covalent geometry : bond 0.00878 ( 9603) covalent geometry : angle 0.99379 (13365) hydrogen bonds : bond 0.12547 ( 513) hydrogen bonds : angle 4.80710 ( 1539) Misc. bond : bond 0.33127 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.303 Fit side-chains REVERT: BB 20 GLU cc_start: 0.8371 (tt0) cc_final: 0.8155 (tt0) REVERT: BD 20 GLU cc_start: 0.8313 (tt0) cc_final: 0.8031 (tt0) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.9335 time to fit residues: 88.6410 Evaluate side-chains 79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.114451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.096261 restraints weight = 6667.068| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 0.57 r_work: 0.2754 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.2388 rms_B_bonded: 4.71 restraints_weight: 0.1250 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.253 9630 Z= 0.234 Angle : 0.885 9.585 13365 Z= 0.361 Chirality : 0.046 0.127 1359 Planarity : 0.007 0.038 1530 Dihedral : 14.370 67.449 2178 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.15 % Allowed : 3.40 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.08 (0.24), residues: 828 helix: 3.62 (0.17), residues: 567 sheet: None (None), residues: 0 loop : 0.55 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARGBE 30 TYR 0.012 0.004 TYRAC 44 PHE 0.022 0.003 PHEAH 19 TRP 0.027 0.003 TRPAA 40 HIS 0.007 0.002 HISBF 40 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 9603) covalent geometry : angle 0.88476 (13365) hydrogen bonds : bond 0.06416 ( 513) hydrogen bonds : angle 3.63660 ( 1539) Misc. bond : bond 0.13075 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.257 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8357 (mt-10) REVERT: BE 7 LYS cc_start: 0.7733 (tttm) cc_final: 0.7517 (tttm) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.8738 time to fit residues: 72.2008 Evaluate side-chains 77 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.118467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.100590 restraints weight = 6628.477| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 0.56 r_work: 0.2841 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work: 0.2488 rms_B_bonded: 4.95 restraints_weight: 0.1250 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.240 9630 Z= 0.144 Angle : 0.701 7.486 13365 Z= 0.287 Chirality : 0.040 0.112 1359 Planarity : 0.006 0.038 1530 Dihedral : 13.636 69.715 2178 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 4.01 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.70 (0.24), residues: 828 helix: 4.08 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.82 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBE 30 TYR 0.007 0.002 TYRAC 44 PHE 0.019 0.002 PHEAI 19 TRP 0.019 0.002 TRPAA 40 HIS 0.004 0.001 HISBH 40 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9603) covalent geometry : angle 0.70091 (13365) hydrogen bonds : bond 0.05401 ( 513) hydrogen bonds : angle 3.30312 ( 1539) Misc. bond : bond 0.12874 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.245 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8356 (mt-10) outliers start: 3 outliers final: 2 residues processed: 80 average time/residue: 0.9168 time to fit residues: 76.5902 Evaluate side-chains 82 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 23 LYS Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.115649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.097823 restraints weight = 6710.413| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 0.56 r_work: 0.2789 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.2426 rms_B_bonded: 4.80 restraints_weight: 0.1250 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.240 9630 Z= 0.212 Angle : 0.844 9.280 13365 Z= 0.342 Chirality : 0.044 0.124 1359 Planarity : 0.007 0.041 1530 Dihedral : 14.282 67.717 2178 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 4.32 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.34 (0.24), residues: 828 helix: 3.90 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.44 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARGBE 30 TYR 0.011 0.003 TYRAC 44 PHE 0.021 0.003 PHEAI 19 TRP 0.020 0.003 TRPAI 40 HIS 0.007 0.002 HISBH 40 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 9603) covalent geometry : angle 0.84434 (13365) hydrogen bonds : bond 0.06182 ( 513) hydrogen bonds : angle 3.52031 ( 1539) Misc. bond : bond 0.12610 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.296 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8343 (mt-10) outliers start: 3 outliers final: 1 residues processed: 79 average time/residue: 0.8926 time to fit residues: 73.7815 Evaluate side-chains 79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.115500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.097398 restraints weight = 6703.111| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 0.57 r_work: 0.2777 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2413 rms_B_bonded: 4.82 restraints_weight: 0.1250 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.237 9630 Z= 0.190 Angle : 0.794 8.220 13365 Z= 0.325 Chirality : 0.043 0.121 1359 Planarity : 0.007 0.042 1530 Dihedral : 13.940 68.026 2178 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 4.63 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.42 (0.24), residues: 828 helix: 3.94 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.50 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBE 30 TYR 0.009 0.002 TYRAC 44 PHE 0.021 0.003 PHEAI 19 TRP 0.019 0.002 TRPAA 40 HIS 0.006 0.002 HISBH 40 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9603) covalent geometry : angle 0.79408 (13365) hydrogen bonds : bond 0.05943 ( 513) hydrogen bonds : angle 3.43436 ( 1539) Misc. bond : bond 0.12576 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.320 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8318 (mt-10) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.9026 time to fit residues: 74.5887 Evaluate side-chains 79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BB residue 23 LYS Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 28 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.116878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.098936 restraints weight = 6672.685| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 0.56 r_work: 0.2807 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2447 rms_B_bonded: 4.84 restraints_weight: 0.1250 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.237 9630 Z= 0.163 Angle : 0.743 7.697 13365 Z= 0.304 Chirality : 0.041 0.116 1359 Planarity : 0.006 0.040 1530 Dihedral : 13.731 69.408 2178 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.31 % Allowed : 4.78 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.57 (0.24), residues: 828 helix: 4.05 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.59 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBE 30 TYR 0.007 0.002 TYRAC 44 PHE 0.021 0.003 PHEAI 19 TRP 0.018 0.002 TRPAA 40 HIS 0.005 0.002 HISBH 40 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9603) covalent geometry : angle 0.74301 (13365) hydrogen bonds : bond 0.05651 ( 513) hydrogen bonds : angle 3.35728 ( 1539) Misc. bond : bond 0.12790 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.226 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8322 (mt-10) REVERT: BH 7 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7476 (tttp) outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 0.9063 time to fit residues: 74.9001 Evaluate side-chains 79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.115498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.097425 restraints weight = 6711.925| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 0.57 r_work: 0.2771 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2405 rms_B_bonded: 4.84 restraints_weight: 0.1250 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.239 9630 Z= 0.189 Angle : 0.796 8.171 13365 Z= 0.325 Chirality : 0.043 0.123 1359 Planarity : 0.007 0.040 1530 Dihedral : 13.854 67.772 2178 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.31 % Allowed : 4.94 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.45 (0.25), residues: 828 helix: 3.96 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.54 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBE 30 TYR 0.008 0.002 TYRAC 44 PHE 0.022 0.003 PHEAI 19 TRP 0.018 0.002 TRPAI 40 HIS 0.006 0.002 HISBH 40 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 9603) covalent geometry : angle 0.79556 (13365) hydrogen bonds : bond 0.05969 ( 513) hydrogen bonds : angle 3.44580 ( 1539) Misc. bond : bond 0.12472 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.267 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.9141 time to fit residues: 75.5178 Evaluate side-chains 80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BB residue 23 LYS Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.115899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.098155 restraints weight = 6614.649| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 0.55 r_work: 0.2768 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.2401 rms_B_bonded: 4.75 restraints_weight: 0.1250 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.236 9630 Z= 0.202 Angle : 0.822 8.275 13365 Z= 0.335 Chirality : 0.044 0.126 1359 Planarity : 0.007 0.041 1530 Dihedral : 13.967 67.870 2178 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 4.94 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.38 (0.25), residues: 828 helix: 3.91 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.50 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBE 30 TYR 0.009 0.003 TYRAC 44 PHE 0.022 0.003 PHEAI 19 TRP 0.019 0.002 TRPAA 40 HIS 0.006 0.002 HISBH 40 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 9603) covalent geometry : angle 0.82157 (13365) hydrogen bonds : bond 0.06074 ( 513) hydrogen bonds : angle 3.47044 ( 1539) Misc. bond : bond 0.12397 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.307 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8348 (mt-10) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.9206 time to fit residues: 76.0978 Evaluate side-chains 80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BB residue 23 LYS Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.118935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.101079 restraints weight = 6698.246| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 0.56 r_work: 0.2821 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2465 rms_B_bonded: 4.86 restraints_weight: 0.1250 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.239 9630 Z= 0.137 Angle : 0.688 7.347 13365 Z= 0.281 Chirality : 0.040 0.114 1359 Planarity : 0.006 0.039 1530 Dihedral : 13.497 69.939 2178 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.15 % Allowed : 5.25 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.79 (0.25), residues: 828 helix: 4.19 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.74 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBE 30 TYR 0.005 0.001 TYRAD 44 PHE 0.019 0.002 PHEAI 19 TRP 0.017 0.002 TRPAA 40 HIS 0.003 0.001 HISBH 40 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9603) covalent geometry : angle 0.68825 (13365) hydrogen bonds : bond 0.05288 ( 513) hydrogen bonds : angle 3.26068 ( 1539) Misc. bond : bond 0.12905 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.313 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8324 (mt-10) REVERT: BH 7 LYS cc_start: 0.7739 (ttpp) cc_final: 0.7483 (tttp) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.9124 time to fit residues: 76.3346 Evaluate side-chains 81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 chunk 77 optimal weight: 0.0030 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.119807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.101939 restraints weight = 6633.222| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 0.57 r_work: 0.2834 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.2477 rms_B_bonded: 4.89 restraints_weight: 0.1250 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 9630 Z= 0.132 Angle : 0.670 7.162 13365 Z= 0.274 Chirality : 0.039 0.113 1359 Planarity : 0.006 0.038 1530 Dihedral : 12.981 68.970 2178 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.15 % Allowed : 5.71 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.92 (0.25), residues: 828 helix: 4.24 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.94 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBH 30 TYR 0.005 0.001 TYRAD 44 PHE 0.018 0.002 PHEAI 19 TRP 0.017 0.002 TRPAA 40 HIS 0.003 0.001 HISBG 40 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9603) covalent geometry : angle 0.67010 (13365) hydrogen bonds : bond 0.05184 ( 513) hydrogen bonds : angle 3.23078 ( 1539) Misc. bond : bond 0.12863 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.336 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8329 (mt-10) REVERT: BH 7 LYS cc_start: 0.7709 (ttpp) cc_final: 0.7460 (tttp) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.9299 time to fit residues: 77.8303 Evaluate side-chains 81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.118569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.100678 restraints weight = 6653.073| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 0.56 r_work: 0.2815 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2455 rms_B_bonded: 4.86 restraints_weight: 0.1250 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 9630 Z= 0.143 Angle : 0.698 7.228 13365 Z= 0.285 Chirality : 0.040 0.113 1359 Planarity : 0.006 0.037 1530 Dihedral : 13.017 69.207 2178 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.82 (0.25), residues: 828 helix: 4.15 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.91 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGBE 30 TYR 0.006 0.001 TYRAB 44 PHE 0.020 0.003 PHEAI 19 TRP 0.017 0.002 TRPAA 40 HIS 0.004 0.001 HISBG 40 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9603) covalent geometry : angle 0.69778 (13365) hydrogen bonds : bond 0.05384 ( 513) hydrogen bonds : angle 3.30039 ( 1539) Misc. bond : bond 0.13081 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3900.88 seconds wall clock time: 67 minutes 0.20 seconds (4020.20 seconds total)