Starting phenix.real_space_refine on Fri Feb 14 11:04:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbw_13307/02_2025/7pbw_13307.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbw_13307/02_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_13307/02_2025/7pbw_13307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbw_13307/02_2025/7pbw_13307.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbw_13307/02_2025/7pbw_13307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbw_13307/02_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-5592/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: 7.45, 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: 3.21 Conformation dependent library (CDL) restraints added in 836.2 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: 0.68 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: 2.59 Time building geometry restraints manager: 3.48 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.600 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.240 ------------------------------------------------------------------------------- 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 : 0.009 0.106 9603 Z= 0.434 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 *********************** 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 : 0.928 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: 1.9676 time to fit residues: 187.5218 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 : 0.966 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3168 r_free = 0.3168 target = 0.114477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.096331 restraints weight = 6610.524| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 0.56 r_work: 0.2777 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.2412 rms_B_bonded: 4.76 restraints_weight: 0.1250 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 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 : 0.006 0.045 9603 Z= 0.309 Angle : 0.874 9.402 13365 Z= 0.358 Chirality : 0.046 0.127 1359 Planarity : 0.007 0.038 1530 Dihedral : 14.177 67.709 2178 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.24), 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 TRP 0.026 0.003 TRPAA 40 HIS 0.007 0.002 HISBE 40 PHE 0.022 0.003 PHEAH 19 TYR 0.012 0.004 TYRAC 44 ARG 0.002 0.001 ARGBE 30 *********************** 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 : 0.870 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8349 (mt-10) REVERT: BE 7 LYS cc_start: 0.7732 (tttm) cc_final: 0.7511 (tttm) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 1.9793 time to fit residues: 163.7475 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 : 0.820 ------------------------------------------------------------------------------- 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: 1.9990 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3216 r_free = 0.3216 target = 0.118179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.100158 restraints weight = 6699.003| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 0.57 r_work: 0.2831 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.2476 rms_B_bonded: 4.99 restraints_weight: 0.1250 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9603 Z= 0.184 Angle : 0.708 7.418 13365 Z= 0.290 Chirality : 0.040 0.113 1359 Planarity : 0.006 0.039 1530 Dihedral : 13.590 69.645 2178 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.64 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 (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: 4.68 (0.24), residues: 828 helix: 4.07 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.80 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPAA 40 HIS 0.004 0.001 HISBE 40 PHE 0.019 0.003 PHEAI 19 TYR 0.007 0.002 TYRAB 44 ARG 0.001 0.000 ARGBE 30 *********************** 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 : 0.683 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8362 (mt-10) outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 1.9333 time to fit residues: 162.1298 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 : 0.894 ------------------------------------------------------------------------------- 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: 0.0770 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 = 0.118434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.100572 restraints weight = 6599.140| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 0.56 r_work: 0.2844 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.2489 rms_B_bonded: 4.98 restraints_weight: 0.1250 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9603 Z= 0.177 Angle : 0.695 7.085 13365 Z= 0.284 Chirality : 0.040 0.113 1359 Planarity : 0.006 0.038 1530 Dihedral : 13.215 68.890 2178 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.22 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: 4.79 (0.24), residues: 828 helix: 4.18 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.78 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAA 40 HIS 0.004 0.001 HISBH 40 PHE 0.019 0.002 PHEAI 19 TYR 0.007 0.001 TYRAC 44 ARG 0.001 0.000 ARGBE 30 *********************** 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 84 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.870 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8372 (mt-10) REVERT: BH 7 LYS cc_start: 0.7747 (tttp) cc_final: 0.7526 (tttp) outliers start: 3 outliers final: 1 residues processed: 81 average time/residue: 1.9787 time to fit residues: 167.8307 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 : 0.863 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.117650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.099768 restraints weight = 6643.979| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 0.56 r_work: 0.2828 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work: 0.2470 rms_B_bonded: 4.97 restraints_weight: 0.1250 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9603 Z= 0.188 Angle : 0.720 7.321 13365 Z= 0.293 Chirality : 0.041 0.113 1359 Planarity : 0.006 0.037 1530 Dihedral : 13.216 69.266 2178 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.69 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: 4.70 (0.25), residues: 828 helix: 4.13 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.70 (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 0.007 0.002 TYRAE 44 ARG 0.001 0.000 ARGBE 30 *********************** 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 83 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.827 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8359 (mt-10) REVERT: BH 7 LYS cc_start: 0.7715 (tttp) cc_final: 0.7474 (tttp) outliers start: 2 outliers final: 1 residues processed: 81 average time/residue: 2.0690 time to fit residues: 175.3108 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 : 0.880 ------------------------------------------------------------------------------- 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: 0.9990 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: 1.9990 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: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.118739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.100817 restraints weight = 6676.721| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 0.57 r_work: 0.2851 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9603 Z= 0.173 Angle : 0.692 7.426 13365 Z= 0.282 Chirality : 0.040 0.113 1359 Planarity : 0.006 0.036 1530 Dihedral : 13.072 69.179 2178 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.58 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: 4.83 (0.25), residues: 828 helix: 4.21 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.79 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPAI 40 HIS 0.004 0.001 HISBG 40 PHE 0.019 0.002 PHEAI 19 TYR 0.006 0.001 TYRAB 44 ARG 0.001 0.000 ARGBE 30 *********************** 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 80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.902 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8130 (mt-10) REVERT: BH 7 LYS cc_start: 0.7689 (tttp) cc_final: 0.7481 (tttp) outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 1.9887 time to fit residues: 164.7132 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 : 0.820 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.116488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.098536 restraints weight = 6642.083| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 0.57 r_work: 0.2789 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2425 rms_B_bonded: 4.85 restraints_weight: 0.1250 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9603 Z= 0.222 Angle : 0.764 7.685 13365 Z= 0.310 Chirality : 0.042 0.119 1359 Planarity : 0.006 0.037 1530 Dihedral : 13.398 68.457 2178 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.74 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: 4.62 (0.25), residues: 828 helix: 4.04 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.72 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAI 40 HIS 0.006 0.002 HISBH 40 PHE 0.021 0.003 PHEAI 19 TYR 0.008 0.002 TYRAC 44 ARG 0.001 0.000 ARGBE 30 *********************** 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 82 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.873 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8332 (mt-10) outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 1.9844 time to fit residues: 166.3307 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 : 0.892 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.116852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.098817 restraints weight = 6719.109| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 0.57 r_work: 0.2794 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.2431 rms_B_bonded: 4.88 restraints_weight: 0.1250 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9603 Z= 0.210 Angle : 0.749 7.578 13365 Z= 0.305 Chirality : 0.042 0.117 1359 Planarity : 0.006 0.038 1530 Dihedral : 13.432 69.256 2178 Min Nonbonded Distance : 2.225 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: 4.67 (0.25), residues: 828 helix: 4.06 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.79 (0.37), 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 *********************** 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 81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.872 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8335 (mt-10) REVERT: BH 7 LYS cc_start: 0.7710 (tttp) cc_final: 0.7461 (tttp) outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 1.9630 time to fit residues: 162.5775 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 : 0.887 ------------------------------------------------------------------------------- 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: 10.0000 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3194 r_free = 0.3194 target = 0.116552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.098599 restraints weight = 6688.105| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 0.57 r_work: 0.2780 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.2416 rms_B_bonded: 4.82 restraints_weight: 0.1250 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 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 : 0.004 0.031 9603 Z= 0.231 Angle : 0.779 7.906 13365 Z= 0.316 Chirality : 0.042 0.121 1359 Planarity : 0.006 0.038 1530 Dihedral : 13.521 68.088 2178 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.31 % Allowed : 5.40 % Favored : 94.29 % 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: 4.56 (0.25), residues: 828 helix: 4.00 (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 0.006 0.002 HISBH 40 PHE 0.021 0.003 PHEAI 19 TYR 0.008 0.002 TYRAC 44 ARG 0.001 0.000 ARGBE 30 *********************** 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: 2 poor density : 79 time to evaluate : 0.775 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8318 (mt-10) outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 1.9731 time to fit residues: 163.4006 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 : 0.870 ------------------------------------------------------------------------------- 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: 0.9980 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3201 r_free = 0.3201 target = 0.117129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.099127 restraints weight = 6731.049| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 0.57 r_work: 0.2805 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.2443 rms_B_bonded: 4.89 restraints_weight: 0.1250 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9603 Z= 0.208 Angle : 0.744 7.855 13365 Z= 0.303 Chirality : 0.041 0.117 1359 Planarity : 0.006 0.038 1530 Dihedral : 13.345 69.483 2178 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.31 % Allowed : 5.56 % 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: 4.66 (0.25), residues: 828 helix: 4.06 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.78 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 ********************** 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: 2 poor density : 79 time to evaluate : 0.880 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8332 (mt-10) outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 1.9694 time to fit residues: 162.9937 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 : 0.901 ------------------------------------------------------------------------------- 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: 5.9990 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 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 = 0.3219 r_free = 0.3219 target = 0.118468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.100540 restraints weight = 6678.508| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 0.57 r_work: 0.2816 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.2456 rms_B_bonded: 4.87 restraints_weight: 0.1250 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9603 Z= 0.177 Angle : 0.697 7.248 13365 Z= 0.285 Chirality : 0.040 0.114 1359 Planarity : 0.006 0.037 1530 Dihedral : 13.140 69.143 2178 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.63 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: 4.78 (0.25), residues: 828 helix: 4.15 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.84 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPAA 40 HIS 0.004 0.001 HISBG 40 PHE 0.019 0.003 PHEAI 19 TYR 0.006 0.001 TYRAB 44 ARG 0.001 0.000 ARGBE 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7818.77 seconds wall clock time: 138 minutes 50.90 seconds (8330.90 seconds total)