Starting phenix.real_space_refine on Mon Jun 9 01:07:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbw_13307/06_2025/7pbw_13307.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbw_13307/06_2025/7pbw_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_13307/06_2025/7pbw_13307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbw_13307/06_2025/7pbw_13307.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbw_13307/06_2025/7pbw_13307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbw_13307/06_2025/7pbw_13307.cif" } resolution = 2.1 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= 0.004 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.39, per 1000 atoms: 0.78 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: 3.11 Conformation dependent library (CDL) restraints added in 795.5 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: 0.70 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: 2.23 Time building geometry restraints manager: 3.49 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 50 or resid 101 through 104)) selection = (chain 'AB' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AC' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AD' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AE' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AF' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AG' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AH' and (resid 1 through 50 or resid 101 through 104)) selection = chain 'AI' } ncs_group { reference = (chain 'BA' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BB' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BC' and (resid 5 through 51 or resid 101 through 103)) selection = chain 'BD' selection = (chain 'BE' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BF' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BG' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BH' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BI' and (resid 5 through 51 or resid 101 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.990 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.010 ------------------------------------------------------------------------------- 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 : 2.93 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 (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: 3.14 (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 TRP 0.033 0.004 TRPAA 40 HIS 0.008 0.003 HISAB 31 PHE 0.015 0.002 PHEAH 19 TYR 0.034 0.011 TYRAH 45 ARG 0.009 0.003 ARGBC 30 Details of bonding type rmsd hydrogen bonds : bond 0.12547 ( 513) hydrogen bonds : angle 4.80710 ( 1539) covalent geometry : bond 0.00878 ( 9603) covalent geometry : angle 0.99379 (13365) 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 : 0.826 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: 2.0484 time to fit residues: 194.8886 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 : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.115324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.097253 restraints weight = 6607.288| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 0.56 r_work: 0.2764 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.2396 rms_B_bonded: 4.76 restraints_weight: 0.1250 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.252 9630 Z= 0.208 Angle : 0.833 8.778 13365 Z= 0.342 Chirality : 0.045 0.123 1359 Planarity : 0.007 0.037 1530 Dihedral : 13.857 67.772 2178 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.15 % Allowed : 3.09 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.23 (0.24), residues: 828 helix: 3.72 (0.17), residues: 567 sheet: None (None), residues: 0 loop : 0.65 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRPAA 40 HIS 0.007 0.002 HISBE 40 PHE 0.022 0.003 PHEAH 19 TYR 0.011 0.003 TYRAC 44 ARG 0.002 0.001 ARGBE 30 Details of bonding type rmsd hydrogen bonds : bond 0.06159 ( 513) hydrogen bonds : angle 3.56592 ( 1539) covalent geometry : bond 0.00496 ( 9603) covalent geometry : angle 0.83312 (13365) Misc. bond : bond 0.13320 ( 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 : 0.936 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8305 (mt-10) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 2.0208 time to fit residues: 167.3773 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 : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.115883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.097823 restraints weight = 6685.923| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 0.56 r_work: 0.2769 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2402 rms_B_bonded: 4.79 restraints_weight: 0.1250 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.229 9630 Z= 0.184 Angle : 0.785 8.248 13365 Z= 0.322 Chirality : 0.043 0.117 1359 Planarity : 0.006 0.040 1530 Dihedral : 13.871 67.974 2178 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 4.17 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.41 (0.24), residues: 828 helix: 3.90 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.60 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPAA 40 HIS 0.006 0.002 HISBE 40 PHE 0.021 0.003 PHEAI 19 TYR 0.009 0.002 TYRAC 44 ARG 0.001 0.000 ARGBE 30 Details of bonding type rmsd hydrogen bonds : bond 0.05939 ( 513) hydrogen bonds : angle 3.45518 ( 1539) covalent geometry : bond 0.00431 ( 9603) covalent geometry : angle 0.78523 (13365) Misc. bond : bond 0.12268 ( 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 82 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.928 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8317 (mt-10) outliers start: 3 outliers final: 1 residues processed: 79 average time/residue: 1.9276 time to fit residues: 159.9592 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 : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 65 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3182 r_free = 0.3182 target = 0.115638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.097704 restraints weight = 6583.058| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 0.56 r_work: 0.2797 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.2436 rms_B_bonded: 4.89 restraints_weight: 0.1250 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1408 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= 0.187 Angle : 0.796 8.190 13365 Z= 0.324 Chirality : 0.043 0.118 1359 Planarity : 0.007 0.040 1530 Dihedral : 14.022 68.033 2178 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.79 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 (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: 4.37 (0.24), residues: 828 helix: 3.91 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.48 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPAA 40 HIS 0.006 0.002 HISBH 40 PHE 0.021 0.003 PHEAI 19 TYR 0.009 0.002 TYRAC 44 ARG 0.001 0.000 ARGBE 30 Details of bonding type rmsd hydrogen bonds : bond 0.05952 ( 513) hydrogen bonds : angle 3.45198 ( 1539) covalent geometry : bond 0.00440 ( 9603) covalent geometry : angle 0.79587 (13365) Misc. bond : bond 0.12928 ( 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 : 0.831 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8349 (mt-10) outliers start: 3 outliers final: 1 residues processed: 79 average time/residue: 1.8846 time to fit residues: 156.3393 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 : 0.831 ------------------------------------------------------------------------------- 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 30 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.118341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.100569 restraints weight = 6636.317| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 0.56 r_work: 0.2803 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2441 rms_B_bonded: 4.86 restraints_weight: 0.1250 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1510 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= 0.149 Angle : 0.712 7.409 13365 Z= 0.291 Chirality : 0.040 0.113 1359 Planarity : 0.006 0.040 1530 Dihedral : 13.606 69.462 2178 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.63 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 (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: 4.66 (0.24), residues: 828 helix: 4.12 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.60 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPAA 40 HIS 0.004 0.001 HISBH 40 PHE 0.020 0.003 PHEAI 19 TYR 0.006 0.002 TYRAB 44 ARG 0.001 0.000 ARGBE 30 Details of bonding type rmsd hydrogen bonds : bond 0.05470 ( 513) hydrogen bonds : angle 3.30841 ( 1539) covalent geometry : bond 0.00333 ( 9603) covalent geometry : angle 0.71224 (13365) Misc. bond : bond 0.12756 ( 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: 2 poor density : 80 time to evaluate : 0.889 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8327 (mt-10) REVERT: BH 7 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7469 (tttp) outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 2.0058 time to fit residues: 168.1546 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 : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 41 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.117445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.099553 restraints weight = 6661.506| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 0.56 r_work: 0.2800 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2437 rms_B_bonded: 4.85 restraints_weight: 0.1250 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.238 9630 Z= 0.152 Angle : 0.722 7.283 13365 Z= 0.295 Chirality : 0.041 0.113 1359 Planarity : 0.006 0.039 1530 Dihedral : 13.451 69.103 2178 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.74 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 (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: 4.66 (0.25), residues: 828 helix: 4.10 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.68 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAI 40 HIS 0.005 0.002 HISBH 40 PHE 0.020 0.003 PHEAI 19 TYR 0.006 0.002 TYRAB 44 ARG 0.001 0.000 ARGBE 30 Details of bonding type rmsd hydrogen bonds : bond 0.05544 ( 513) hydrogen bonds : angle 3.33794 ( 1539) covalent geometry : bond 0.00343 ( 9603) covalent geometry : angle 0.72178 (13365) Misc. bond : bond 0.12814 ( 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 82 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 1.036 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8329 (mt-10) REVERT: BH 7 LYS cc_start: 0.7738 (ttpp) cc_final: 0.7474 (tttp) outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 2.6510 time to fit residues: 222.1351 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 : 0.918 ------------------------------------------------------------------------------- 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 10 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 69 optimal weight: 0.0030 chunk 78 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- 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 = 0.116899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.099021 restraints weight = 6632.435| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 0.56 r_work: 0.2786 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.2423 rms_B_bonded: 4.79 restraints_weight: 0.1250 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.238 9630 Z= 0.165 Angle : 0.751 7.584 13365 Z= 0.306 Chirality : 0.042 0.117 1359 Planarity : 0.006 0.038 1530 Dihedral : 13.483 68.791 2178 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.31 % Allowed : 5.09 % 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 (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: 4.61 (0.25), residues: 828 helix: 4.05 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.70 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAI 40 HIS 0.005 0.002 HISBH 40 PHE 0.021 0.003 PHEAI 19 TYR 0.007 0.002 TYRAC 44 ARG 0.001 0.000 ARGBE 30 Details of bonding type rmsd hydrogen bonds : bond 0.05705 ( 513) hydrogen bonds : angle 3.37589 ( 1539) covalent geometry : bond 0.00380 ( 9603) covalent geometry : angle 0.75072 (13365) Misc. bond : bond 0.12646 ( 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 : 0.988 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8308 (mt-10) outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 2.2344 time to fit residues: 185.0245 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 : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.117369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.099390 restraints weight = 6730.248| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 0.57 r_work: 0.2803 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.2442 rms_B_bonded: 4.87 restraints_weight: 0.1250 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.238 9630 Z= 0.156 Angle : 0.728 7.390 13365 Z= 0.297 Chirality : 0.041 0.115 1359 Planarity : 0.006 0.038 1530 Dihedral : 13.406 69.418 2178 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.31 % Allowed : 5.25 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.69 (0.25), residues: 828 helix: 4.10 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.75 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPAA 40 HIS 0.004 0.002 HISBH 40 PHE 0.020 0.003 PHEAI 19 TYR 0.006 0.002 TYRAB 44 ARG 0.001 0.000 ARGBE 30 Details of bonding type rmsd hydrogen bonds : bond 0.05552 ( 513) hydrogen bonds : angle 3.33487 ( 1539) covalent geometry : bond 0.00353 ( 9603) covalent geometry : angle 0.72814 (13365) Misc. bond : bond 0.12831 ( 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: 2 poor density : 80 time to evaluate : 0.824 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8324 (mt-10) outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 2.0032 time to fit residues: 167.9782 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 : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 28 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.115712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.097975 restraints weight = 6664.457| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 0.56 r_work: 0.2781 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work: 0.2420 rms_B_bonded: 4.73 restraints_weight: 0.1250 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.231 9630 Z= 0.239 Angle : 0.890 9.062 13365 Z= 0.360 Chirality : 0.046 0.131 1359 Planarity : 0.007 0.040 1530 Dihedral : 14.214 67.555 2178 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.15 % Allowed : 5.40 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.29 (0.25), residues: 828 helix: 3.83 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.51 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRPAI 40 HIS 0.008 0.003 HISBE 40 PHE 0.022 0.003 PHEAI 19 TYR 0.011 0.003 TYRAC 44 ARG 0.002 0.001 ARGBA 30 Details of bonding type rmsd hydrogen bonds : bond 0.06341 ( 513) hydrogen bonds : angle 3.55443 ( 1539) covalent geometry : bond 0.00583 ( 9603) covalent geometry : angle 0.88988 (13365) Misc. bond : bond 0.12181 ( 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 80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.934 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 1.9452 time to fit residues: 161.1544 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 : 0.820 ------------------------------------------------------------------------------- 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 2 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.0970 chunk 8 optimal weight: 10.0000 chunk 65 optimal weight: 0.0000 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.117274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.099300 restraints weight = 6734.075| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 0.57 r_work: 0.2798 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2437 rms_B_bonded: 4.85 restraints_weight: 0.1250 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1556 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= 0.159 Angle : 0.738 7.613 13365 Z= 0.301 Chirality : 0.041 0.115 1359 Planarity : 0.006 0.039 1530 Dihedral : 13.658 69.441 2178 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.95 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 (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: 4.60 (0.25), residues: 828 helix: 4.04 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.69 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAA 40 HIS 0.005 0.002 HISBH 40 PHE 0.020 0.003 PHEAI 19 TYR 0.006 0.002 TYRAD 44 ARG 0.001 0.000 ARGBA 30 Details of bonding type rmsd hydrogen bonds : bond 0.05613 ( 513) hydrogen bonds : angle 3.34087 ( 1539) covalent geometry : bond 0.00361 ( 9603) covalent geometry : angle 0.73816 (13365) Misc. bond : bond 0.12774 ( 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 80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.822 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8330 (mt-10) outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 1.9417 time to fit residues: 160.6467 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 : 0.936 ------------------------------------------------------------------------------- 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 10 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 79 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.119406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.101539 restraints weight = 6699.057| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 0.57 r_work: 0.2826 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.2468 rms_B_bonded: 4.90 restraints_weight: 0.1250 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.237 9630 Z= 0.137 Angle : 0.685 7.285 13365 Z= 0.280 Chirality : 0.040 0.114 1359 Planarity : 0.006 0.038 1530 Dihedral : 13.216 69.371 2178 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.37 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 (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: 4.83 (0.25), residues: 828 helix: 4.19 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.85 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAA 40 HIS 0.003 0.001 HISBG 40 PHE 0.019 0.002 PHEAI 19 TYR 0.006 0.001 TYRAD 44 ARG 0.001 0.000 ARGBH 30 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 513) hydrogen bonds : angle 3.25423 ( 1539) covalent geometry : bond 0.00301 ( 9603) covalent geometry : angle 0.68482 (13365) Misc. bond : bond 0.12749 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8666.67 seconds wall clock time: 152 minutes 25.02 seconds (9145.02 seconds total)