Starting phenix.real_space_refine on Thu Mar 14 18:43:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/03_2024/7pbw_13307_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/03_2024/7pbw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/03_2024/7pbw_13307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/03_2024/7pbw_13307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/03_2024/7pbw_13307_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/03_2024/7pbw_13307_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.53, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 4.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 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... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'AA' and resid 4 through 9 Processing helix chain 'AA' and resid 12 through 37 Proline residue: AA 17 - end of helix Processing helix chain 'AA' and resid 39 through 49 removed outlier: 6.210A pdb=" N SERAA 48 " --> pdb=" O TYRAA 44 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALAAA 49 " --> pdb=" O TYRAA 45 " (cutoff:3.500A) Processing helix chain 'AB' and resid 4 through 9 Processing helix chain 'AB' and resid 12 through 37 Proline residue: AB 17 - end of helix Processing helix chain 'AB' and resid 40 through 49 removed outlier: 6.246A pdb=" N SERAB 48 " --> pdb=" O TYRAB 44 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALAAB 49 " --> pdb=" O TYRAB 45 " (cutoff:3.500A) Processing helix chain 'AC' and resid 4 through 9 Processing helix chain 'AC' and resid 12 through 37 Proline residue: AC 17 - end of helix Processing helix chain 'AC' and resid 40 through 49 removed outlier: 6.215A pdb=" N SERAC 48 " --> pdb=" O TYRAC 44 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALAAC 49 " --> pdb=" O TYRAC 45 " (cutoff:3.500A) Processing helix chain 'AD' and resid 4 through 9 Processing helix chain 'AD' and resid 12 through 37 Proline residue: AD 17 - end of helix Processing helix chain 'AD' and resid 40 through 49 removed outlier: 6.252A pdb=" N SERAD 48 " --> pdb=" O TYRAD 44 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALAAD 49 " --> pdb=" O TYRAD 45 " (cutoff:3.500A) Processing helix chain 'AE' and resid 4 through 9 Processing helix chain 'AE' and resid 12 through 37 Proline residue: AE 17 - end of helix Processing helix chain 'AE' and resid 40 through 49 removed outlier: 6.238A pdb=" N SERAE 48 " --> pdb=" O TYRAE 44 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALAAE 49 " --> pdb=" O TYRAE 45 " (cutoff:3.500A) Processing helix chain 'AF' and resid 4 through 9 Processing helix chain 'AF' and resid 12 through 37 Proline residue: AF 17 - end of helix Processing helix chain 'AF' and resid 40 through 49 removed outlier: 6.233A pdb=" N SERAF 48 " --> pdb=" O TYRAF 44 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALAAF 49 " --> pdb=" O TYRAF 45 " (cutoff:3.500A) Processing helix chain 'AG' and resid 4 through 9 Processing helix chain 'AG' and resid 12 through 37 Proline residue: AG 17 - end of helix Processing helix chain 'AG' and resid 40 through 49 removed outlier: 6.201A pdb=" N SERAG 48 " --> pdb=" O TYRAG 44 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALAAG 49 " --> pdb=" O TYRAG 45 " (cutoff:3.500A) Processing helix chain 'AH' and resid 4 through 9 Processing helix chain 'AH' and resid 12 through 37 Proline residue: AH 17 - end of helix Processing helix chain 'AH' and resid 40 through 49 removed outlier: 6.243A pdb=" N SERAH 48 " --> pdb=" O TYRAH 44 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALAAH 49 " --> pdb=" O TYRAH 45 " (cutoff:3.500A) Processing helix chain 'AI' and resid 4 through 9 Processing helix chain 'AI' and resid 12 through 37 Proline residue: AI 17 - end of helix Processing helix chain 'AI' and resid 40 through 49 removed outlier: 6.243A pdb=" N SERAI 48 " --> pdb=" O TYRAI 44 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALAAI 49 " --> pdb=" O TYRAI 45 " (cutoff:3.500A) Processing helix chain 'BA' and resid 15 through 46 Processing helix chain 'BB' and resid 15 through 46 Processing helix chain 'BC' and resid 15 through 46 Processing helix chain 'BD' and resid 15 through 46 Processing helix chain 'BE' and resid 15 through 46 Processing helix chain 'BF' and resid 15 through 46 Processing helix chain 'BG' and resid 15 through 46 Processing helix chain 'BH' and resid 15 through 46 Processing helix chain 'BI' and resid 15 through 46 487 hydrogen bonds defined for protein. 1380 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: 4.34 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: 84.93 - 99.93: 108 99.93 - 114.93: 6511 114.93 - 129.93: 6386 129.93 - 144.92: 279 144.92 - 159.92: 81 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: 8491 3.31 - 3.84: 18068 3.84 - 4.37: 22120 4.37 - 4.90: 35220 Nonbonded interactions: 85374 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 85369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.290 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: 11.160 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.140 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.130 ------------------------------------------------------------------------------- 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= 0.435 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 fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.877 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: 1.8846 time to fit residues: 179.9369 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 2.9990 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: 1.9990 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1207 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 : 0.859 9.480 13365 Z= 0.351 Chirality : 0.046 0.127 1359 Planarity : 0.007 0.038 1530 Dihedral : 14.383 67.738 2178 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.15 % Allowed : 2.93 % Favored : 96.91 % 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: 4.16 (0.25), residues: 828 helix: 3.68 (0.17), residues: 567 sheet: None (None), residues: 0 loop : 0.60 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRPAA 40 HIS 0.006 0.002 HISAC 31 PHE 0.021 0.003 PHEAG 19 TYR 0.014 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 fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.876 Fit side-chains REVERT: BD 17 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8138 (mt-10) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 1.8508 time to fit residues: 153.6723 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9603 Z= 0.264 Angle : 0.795 8.583 13365 Z= 0.323 Chirality : 0.044 0.120 1359 Planarity : 0.007 0.040 1530 Dihedral : 14.165 67.828 2178 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 3.55 % Favored : 95.99 % 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: 4.33 (0.24), residues: 828 helix: 3.89 (0.17), residues: 567 sheet: None (None), residues: 0 loop : 0.43 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRPAA 40 HIS 0.006 0.002 HISAC 31 PHE 0.021 0.003 PHEAI 19 TYR 0.012 0.003 TYRAC 44 ARG 0.002 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 81 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.882 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 78 average time/residue: 1.8146 time to fit residues: 148.9861 Evaluate side-chains 78 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 55 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9603 Z= 0.268 Angle : 0.804 8.411 13365 Z= 0.324 Chirality : 0.044 0.120 1359 Planarity : 0.007 0.041 1530 Dihedral : 14.220 67.842 2178 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 4.01 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.26 (0.24), residues: 828 helix: 3.89 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.27 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRPAA 40 HIS 0.006 0.002 HISAI 31 PHE 0.021 0.003 PHEAI 19 TYR 0.011 0.003 TYRAB 44 ARG 0.002 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 82 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.841 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 79 average time/residue: 1.8494 time to fit residues: 153.4390 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9603 Z= 0.186 Angle : 0.697 7.605 13365 Z= 0.281 Chirality : 0.040 0.114 1359 Planarity : 0.006 0.040 1530 Dihedral : 13.633 69.666 2178 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 3.86 % Favored : 95.68 % 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: 4.65 (0.25), residues: 828 helix: 4.20 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.38 (0.32), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPAA 40 HIS 0.005 0.002 HISAH 31 PHE 0.019 0.002 PHEAI 19 TYR 0.008 0.002 TYRAB 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 82 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.832 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 1.8583 time to fit residues: 154.1331 Evaluate side-chains 80 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BB residue 23 LYS Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.0000 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9603 Z= 0.215 Angle : 0.734 7.747 13365 Z= 0.296 Chirality : 0.041 0.117 1359 Planarity : 0.006 0.038 1530 Dihedral : 13.615 68.529 2178 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 4.01 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.51 (0.25), residues: 828 helix: 4.10 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.31 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAA 40 HIS 0.005 0.002 HISAC 31 PHE 0.020 0.003 PHEAI 19 TYR 0.009 0.002 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 82 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.922 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 1.8156 time to fit residues: 150.9430 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BB residue 23 LYS Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9603 Z= 0.226 Angle : 0.750 7.854 13365 Z= 0.302 Chirality : 0.042 0.118 1359 Planarity : 0.006 0.039 1530 Dihedral : 13.658 68.468 2178 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 4.01 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.44 (0.25), residues: 828 helix: 4.05 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.28 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAA 40 HIS 0.006 0.002 HISAC 31 PHE 0.021 0.003 PHEAI 19 TYR 0.010 0.002 TYRAB 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 81 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.933 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 78 average time/residue: 1.8434 time to fit residues: 150.9954 Evaluate side-chains 80 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BB residue 23 LYS Chi-restraints excluded: chain BC residue 23 LYS Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9603 Z= 0.191 Angle : 0.703 7.527 13365 Z= 0.283 Chirality : 0.040 0.115 1359 Planarity : 0.006 0.038 1530 Dihedral : 13.394 69.643 2178 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.04 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: 4.60 (0.25), residues: 828 helix: 4.17 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.36 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAA 40 HIS 0.005 0.002 HISAC 31 PHE 0.020 0.003 PHEAI 19 TYR 0.008 0.002 TYRAB 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 fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.926 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 1.9098 time to fit residues: 156.8940 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BB residue 23 LYS Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9603 Z= 0.158 Angle : 0.653 7.655 13365 Z= 0.262 Chirality : 0.038 0.112 1359 Planarity : 0.005 0.038 1530 Dihedral : 12.958 69.939 2178 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.31 % Allowed : 4.48 % 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: 4.81 (0.25), residues: 828 helix: 4.30 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.51 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPAA 40 HIS 0.004 0.001 HISAC 31 PHE 0.017 0.002 PHEAI 19 TYR 0.006 0.002 TYRAE 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 fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.918 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 1.8556 time to fit residues: 154.0445 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BB residue 23 LYS Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9603 Z= 0.226 Angle : 0.748 7.641 13365 Z= 0.301 Chirality : 0.042 0.118 1359 Planarity : 0.006 0.037 1530 Dihedral : 13.334 68.214 2178 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.31 % Allowed : 4.78 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.50 (0.24), residues: 828 helix: 4.08 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.35 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAI 40 HIS 0.006 0.002 HISAC 31 PHE 0.021 0.003 PHEAI 19 TYR 0.010 0.002 TYRAB 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 80 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.884 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 78 average time/residue: 1.7920 time to fit residues: 147.1123 Evaluate side-chains 80 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BB residue 23 LYS Chi-restraints excluded: chain BD residue 23 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3173 r_free = 0.3173 target = 0.115202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.097419 restraints weight = 6644.273| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 0.56 r_work: 0.2764 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.2403 rms_B_bonded: 4.90 restraints_weight: 0.1250 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9603 Z= 0.224 Angle : 0.748 7.721 13365 Z= 0.302 Chirality : 0.042 0.118 1359 Planarity : 0.006 0.038 1530 Dihedral : 13.401 68.829 2178 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 4.94 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.48 (0.25), residues: 828 helix: 4.04 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.38 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAI 40 HIS 0.006 0.002 HISAC 31 PHE 0.021 0.003 PHEAI 19 TYR 0.010 0.002 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: 3290.16 seconds wall clock time: 58 minutes 42.24 seconds (3522.24 seconds total)