Starting phenix.real_space_refine on Sat Jul 4 20:23:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ddq_30656/07_2026/7ddq_30656.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ddq_30656/07_2026/7ddq_30656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ddq_30656/07_2026/7ddq_30656.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ddq_30656/07_2026/7ddq_30656.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ddq_30656/07_2026/7ddq_30656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ddq_30656/07_2026/7ddq_30656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ddq_30656/07_2026/7ddq_30656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ddq_30656/07_2026/7ddq_30656.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 34 5.21 5 S 84 5.16 5 C 15792 2.51 5 N 3246 2.21 5 O 3411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22571 Number of models: 1 Model: "" Number of chains: 64 Chain: "o" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "N" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "t" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "S" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "r" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "O" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "a" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "U" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "e" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "b" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "A" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "k" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "J" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "f" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "E" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "u" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 440 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "T" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "X" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "s" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "R" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "n" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "K" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "G" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "j" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "I" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "L" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2188 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 261} Chain: "M" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2420 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "H" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1907 Classifications: {'peptide': 250} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 230} Chain: "g" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "F" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "d" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "B" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "o" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 114 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "e" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 275 Unusual residues: {'BCL': 1, 'BPH': 2, 'U10': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'U10:plan-6': 2, 'U10:plan-7': 3, 'U10:plan-8': 3, 'U10:plan-9': 3, 'U10:plan-10': 3, 'U10:plan-11': 3, 'U10:plan-5': 1, 'BPH:plan-1': 1} Unresolved non-hydrogen planarities: 77 Chain: "M" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 372 Unusual residues: {' FE': 1, 'BCL': 3, 'BPH': 1, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1} Unresolved non-hydrogen planarities: 48 Chain: "H" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'3PE': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.55, per 1000 atoms: 0.20 Number of scatterers: 22571 At special positions: 0 Unit cell: (118.69, 132.8, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 84 16.00 P 3 15.00 Mg 34 11.99 O 3411 8.00 N 3246 7.00 C 15792 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 782.0 milliseconds 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4364 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 72.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'o' and resid 3 through 5 No H-bonds generated for 'chain 'o' and resid 3 through 5' Processing helix chain 'o' and resid 6 through 11 removed outlier: 3.619A pdb=" N ILE o 10 " --> pdb=" O LYS o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 38 Processing helix chain 'o' and resid 42 through 51 Processing helix chain 'N' and resid 12 through 45 Processing helix chain 't' and resid 3 through 10 Processing helix chain 't' and resid 12 through 38 Processing helix chain 't' and resid 42 through 51 Processing helix chain 'S' and resid 12 through 45 removed outlier: 3.502A pdb=" N ALA S 16 " --> pdb=" O THR S 12 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN S 17 " --> pdb=" O ASP S 13 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU S 18 " --> pdb=" O GLN S 14 " (cutoff:3.500A) Processing helix chain 'r' and resid 3 through 10 removed outlier: 3.824A pdb=" N LYS r 6 " --> pdb=" O LYS r 3 " (cutoff:3.500A) Processing helix chain 'r' and resid 12 through 38 Processing helix chain 'r' and resid 42 through 51 Processing helix chain 'O' and resid 12 through 45 Processing helix chain 'a' and resid 3 through 10 Processing helix chain 'a' and resid 12 through 38 Processing helix chain 'a' and resid 39 through 42 removed outlier: 3.741A pdb=" N ASN a 42 " --> pdb=" O PRO a 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 39 through 42' Processing helix chain 'U' and resid 12 through 44 Processing helix chain 'e' and resid 3 through 10 removed outlier: 3.580A pdb=" N LYS e 6 " --> pdb=" O LYS e 3 " (cutoff:3.500A) Processing helix chain 'e' and resid 12 through 38 Processing helix chain 'e' and resid 42 through 51 Processing helix chain 'D' and resid 12 through 45 Processing helix chain 'b' and resid 3 through 10 Processing helix chain 'b' and resid 12 through 38 Processing helix chain 'b' and resid 42 through 51 Processing helix chain 'A' and resid 12 through 45 Processing helix chain 'k' and resid 3 through 5 No H-bonds generated for 'chain 'k' and resid 3 through 5' Processing helix chain 'k' and resid 6 through 11 Processing helix chain 'k' and resid 12 through 38 Processing helix chain 'k' and resid 42 through 51 Processing helix chain 'J' and resid 12 through 45 removed outlier: 3.541A pdb=" N GLN J 17 " --> pdb=" O ASP J 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 3 through 10 removed outlier: 3.785A pdb=" N LYS f 6 " --> pdb=" O LYS f 3 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE f 7 " --> pdb=" O PHE f 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 38 Processing helix chain 'f' and resid 42 through 51 Processing helix chain 'E' and resid 12 through 45 Processing helix chain 'u' and resid 3 through 5 No H-bonds generated for 'chain 'u' and resid 3 through 5' Processing helix chain 'u' and resid 6 through 11 removed outlier: 3.657A pdb=" N ILE u 10 " --> pdb=" O LYS u 6 " (cutoff:3.500A) Processing helix chain 'u' and resid 12 through 38 Processing helix chain 'u' and resid 42 through 51 Processing helix chain 'T' and resid 12 through 45 removed outlier: 3.538A pdb=" N GLU T 18 " --> pdb=" O GLN T 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 49 Processing helix chain 'X' and resid 50 through 51 No H-bonds generated for 'chain 'X' and resid 50 through 51' Processing helix chain 'X' and resid 52 through 57 Processing helix chain 's' and resid 3 through 10 removed outlier: 3.548A pdb=" N LYS s 6 " --> pdb=" O LYS s 3 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 38 Processing helix chain 's' and resid 42 through 51 Processing helix chain 'R' and resid 12 through 45 removed outlier: 3.960A pdb=" N ALA R 16 " --> pdb=" O THR R 12 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN R 17 " --> pdb=" O ASP R 13 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU R 18 " --> pdb=" O GLN R 14 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 10 removed outlier: 3.689A pdb=" N LYS n 6 " --> pdb=" O LYS n 3 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 38 Processing helix chain 'n' and resid 42 through 51 Processing helix chain 'K' and resid 12 through 45 Processing helix chain 'i' and resid 3 through 10 Processing helix chain 'i' and resid 12 through 38 Processing helix chain 'i' and resid 42 through 51 Processing helix chain 'G' and resid 12 through 45 Processing helix chain 'j' and resid 3 through 10 removed outlier: 3.681A pdb=" N LYS j 6 " --> pdb=" O LYS j 3 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 38 Processing helix chain 'j' and resid 42 through 51 Processing helix chain 'I' and resid 12 through 45 removed outlier: 3.504A pdb=" N GLN I 17 " --> pdb=" O ASP I 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.502A pdb=" N GLY L 57 " --> pdb=" O GLY L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 84 through 112 Processing helix chain 'L' and resid 116 through 134 Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'L' and resid 142 through 146 Processing helix chain 'L' and resid 152 through 165 removed outlier: 3.670A pdb=" N GLU L 156 " --> pdb=" O PHE L 152 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR L 165 " --> pdb=" O VAL L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 170 removed outlier: 6.168A pdb=" N HIS L 169 " --> pdb=" O GLY L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 200 Processing helix chain 'L' and resid 209 through 222 removed outlier: 3.571A pdb=" N GLU L 213 " --> pdb=" O THR L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 252 removed outlier: 3.848A pdb=" N HIS L 231 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER L 252 " --> pdb=" O CYS L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 263 Processing helix chain 'L' and resid 264 through 269 Processing helix chain 'M' and resid 26 through 30 Processing helix chain 'M' and resid 39 through 43 removed outlier: 3.763A pdb=" N TRP M 42 " --> pdb=" O ILE M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 109 through 112 Processing helix chain 'M' and resid 113 through 142 removed outlier: 3.503A pdb=" N ALA M 138 " --> pdb=" O THR M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 163 Processing helix chain 'M' and resid 163 through 170 Processing helix chain 'M' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLU M 174 " --> pdb=" O SER M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 194 removed outlier: 3.890A pdb=" N LEU M 184 " --> pdb=" O ILE M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 199 Processing helix chain 'M' and resid 200 through 227 Processing helix chain 'M' and resid 243 through 258 removed outlier: 3.547A pdb=" N TRP M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 262 through 288 removed outlier: 4.429A pdb=" N HIS M 267 " --> pdb=" O MET M 263 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG M 268 " --> pdb=" O GLU M 264 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR M 277 " --> pdb=" O PHE M 273 " (cutoff:3.500A) Proline residue: M 278 - end of helix Processing helix chain 'M' and resid 294 through 302 Processing helix chain 'H' and resid 11 through 35 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 134 through 138 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'H' and resid 226 through 244 removed outlier: 4.233A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 248 removed outlier: 3.516A pdb=" N LYS H 248 " --> pdb=" O ALA H 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 245 through 248' Processing helix chain 'g' and resid 3 through 10 removed outlier: 3.697A pdb=" N LYS g 6 " --> pdb=" O LYS g 3 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 38 Processing helix chain 'g' and resid 42 through 51 Processing helix chain 'F' and resid 12 through 45 Processing helix chain 'd' and resid 3 through 5 No H-bonds generated for 'chain 'd' and resid 3 through 5' Processing helix chain 'd' and resid 6 through 11 removed outlier: 3.614A pdb=" N ILE d 10 " --> pdb=" O LYS d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 38 Processing helix chain 'd' and resid 42 through 51 Processing helix chain 'B' and resid 12 through 45 Processing sheet with id=AA1, first strand: chain 'L' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'M' and resid 12 through 14 removed outlier: 6.588A pdb=" N GLN M 12 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'H' and resid 62 through 65 Processing sheet with id=AA5, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA6, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.565A pdb=" N GLY H 162 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU H 183 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL H 164 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL H 181 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU H 166 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU H 179 " --> pdb=" O GLU H 166 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP H 168 " --> pdb=" O ARG H 177 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET H 175 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.762A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) 1311 hydrogen bonds defined for protein. 3705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.32: 3417 1.32 - 1.53: 18460 1.53 - 1.74: 1290 1.74 - 1.96: 162 1.96 - 2.17: 136 Bond restraints: 23465 Sorted by residual: bond pdb=" C14 SPO E 201 " pdb=" C15 SPO E 201 " ideal model delta sigma weight residual 1.435 1.566 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C14 SPO M 406 " pdb=" C15 SPO M 406 " ideal model delta sigma weight residual 1.435 1.564 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C14 SPO g 102 " pdb=" C15 SPO g 102 " ideal model delta sigma weight residual 1.435 1.560 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C19 SPO E 201 " pdb=" C20 SPO E 201 " ideal model delta sigma weight residual 1.435 1.559 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C19 SPO g 102 " pdb=" C20 SPO g 102 " ideal model delta sigma weight residual 1.435 1.556 -0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 23460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.08: 32122 8.08 - 16.16: 116 16.16 - 24.24: 16 24.24 - 32.32: 48 32.32 - 40.41: 15 Bond angle restraints: 32317 Sorted by residual: angle pdb=" C4 SPO j 301 " pdb=" C1 SPO j 301 " pdb=" O1 SPO j 301 " ideal model delta sigma weight residual 104.58 144.99 -40.41 3.00e+00 1.11e-01 1.81e+02 angle pdb=" C4 SPO X 201 " pdb=" C1 SPO X 201 " pdb=" O1 SPO X 201 " ideal model delta sigma weight residual 104.58 143.97 -39.39 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C4 SPO F 102 " pdb=" C1 SPO F 102 " pdb=" O1 SPO F 102 " ideal model delta sigma weight residual 104.58 143.02 -38.44 3.00e+00 1.11e-01 1.64e+02 angle pdb=" C4 SPO t 102 " pdb=" C1 SPO t 102 " pdb=" O1 SPO t 102 " ideal model delta sigma weight residual 104.58 139.93 -35.35 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C3 SPO N 201 " pdb=" C1 SPO N 201 " pdb=" C4 SPO N 201 " ideal model delta sigma weight residual 108.79 74.66 34.13 3.00e+00 1.11e-01 1.29e+02 ... (remaining 32312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 11995 35.99 - 71.98: 315 71.98 - 107.96: 56 107.96 - 143.95: 7 143.95 - 179.94: 31 Dihedral angle restraints: 12404 sinusoidal: 5647 harmonic: 6757 Sorted by residual: dihedral pdb=" C1 BCL j 302 " pdb=" C2 BCL j 302 " pdb=" C3 BCL j 302 " pdb=" C5 BCL j 302 " ideal model delta sinusoidal sigma weight residual -180.00 -0.06 -179.94 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL r 101 " pdb=" C2 BCL r 101 " pdb=" C3 BCL r 101 " pdb=" C5 BCL r 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.07 -179.93 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL u 102 " pdb=" C2 BCL u 102 " pdb=" C3 BCL u 102 " pdb=" C5 BCL u 102 " ideal model delta sinusoidal sigma weight residual -180.00 -0.08 -179.92 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 12401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2826 0.075 - 0.150: 370 0.150 - 0.225: 30 0.225 - 0.300: 13 0.300 - 0.375: 3 Chirality restraints: 3242 Sorted by residual: chirality pdb=" CBD BCL b 101 " pdb=" CAD BCL b 101 " pdb=" CGD BCL b 101 " pdb=" CHA BCL b 101 " both_signs ideal model delta sigma weight residual False 2.62 2.25 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB VAL M 160 " pdb=" CA VAL M 160 " pdb=" CG1 VAL M 160 " pdb=" CG2 VAL M 160 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C2C BPH L 302 " pdb=" C1C BPH L 302 " pdb=" C3C BPH L 302 " pdb=" CMC BPH L 302 " both_signs ideal model delta sigma weight residual False -2.81 -2.49 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 3239 not shown) Planarity restraints: 3934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BPH L 306 " 0.014 2.00e-02 2.50e+03 6.17e-02 8.55e+01 pdb=" C1D BPH L 306 " 0.017 2.00e-02 2.50e+03 pdb=" C2D BPH L 306 " -0.031 2.00e-02 2.50e+03 pdb=" C3D BPH L 306 " -0.048 2.00e-02 2.50e+03 pdb=" C4D BPH L 306 " -0.030 2.00e-02 2.50e+03 pdb=" CAD BPH L 306 " 0.137 2.00e-02 2.50e+03 pdb=" CHA BPH L 306 " -0.060 2.00e-02 2.50e+03 pdb=" CHD BPH L 306 " 0.060 2.00e-02 2.50e+03 pdb=" CMD BPH L 306 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 273 " 0.052 2.00e-02 2.50e+03 5.60e-02 7.85e+01 pdb=" CG TRP L 273 " -0.144 2.00e-02 2.50e+03 pdb=" CD1 TRP L 273 " 0.086 2.00e-02 2.50e+03 pdb=" CD2 TRP L 273 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP L 273 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP L 273 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP L 273 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 273 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 273 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP L 273 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 217 " -0.067 2.00e-02 2.50e+03 5.88e-02 6.05e+01 pdb=" CG PHE M 217 " 0.132 2.00e-02 2.50e+03 pdb=" CD1 PHE M 217 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE M 217 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE M 217 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE M 217 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE M 217 " -0.014 2.00e-02 2.50e+03 ... (remaining 3931 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.34: 51 2.34 - 2.98: 10795 2.98 - 3.62: 34892 3.62 - 4.26: 57007 4.26 - 4.90: 91893 Nonbonded interactions: 194638 Sorted by model distance: nonbonded pdb=" OE2 GLU M 235 " pdb="FE FE M 404 " model vdw 1.706 2.260 nonbonded pdb=" OG1 THR O 12 " pdb=" OE1 GLN O 15 " model vdw 2.019 3.040 nonbonded pdb=" NE2 HIS L 191 " pdb="FE FE M 404 " model vdw 2.083 2.340 nonbonded pdb=" OE1 GLN N 25 " pdb=" OG SER k 2 " model vdw 2.135 3.040 nonbonded pdb=" OD1 ASP T 13 " pdb=" NE2 GLN T 17 " model vdw 2.177 3.120 ... (remaining 194633 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 'A' and resid 5 through 47) selection = (chain 'B' and resid 5 through 47) selection = (chain 'D' and resid 5 through 47) selection = (chain 'E' and resid 5 through 47) selection = (chain 'F' and resid 5 through 47) selection = (chain 'G' and resid 5 through 47) selection = (chain 'I' and resid 5 through 47) selection = (chain 'J' and resid 5 through 47) selection = (chain 'K' and resid 5 through 47) selection = (chain 'N' and resid 5 through 47) selection = (chain 'O' and resid 5 through 47) selection = (chain 'R' and resid 5 through 47) selection = (chain 'S' and resid 5 through 47) selection = chain 'T' selection = chain 'U' } ncs_group { reference = (chain 'a' and resid 3 through 45) selection = (chain 'e' and resid 3 through 45) selection = (chain 'f' and resid 3 through 45) selection = (chain 'i' and resid 3 through 45) selection = (chain 'n' and resid 3 through 45) selection = (chain 'o' and resid 3 through 45) selection = (chain 'u' and resid 3 through 45) } ncs_group { reference = (chain 'b' and resid 2 through 54) selection = (chain 'd' and resid 2 through 54) selection = (chain 'g' and resid 2 through 54) selection = (chain 'j' and resid 2 through 54) selection = (chain 'k' and resid 2 through 54) selection = (chain 'r' and resid 2 through 54) selection = (chain 's' and resid 2 through 54) selection = (chain 't' and resid 2 through 54) } 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.700 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.692 23497 Z= 1.698 Angle : 1.916 40.405 32317 Z= 0.692 Chirality : 0.055 0.375 3242 Planarity : 0.005 0.062 3934 Dihedral : 20.420 179.938 8040 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2286 helix: 1.64 (0.12), residues: 1519 sheet: 1.24 (1.04), residues: 22 loop : -1.33 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG b 53 TYR 0.023 0.003 TYR k 51 PHE 0.132 0.003 PHE M 217 TRP 0.144 0.004 TRP L 273 HIS 0.023 0.002 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.01240 / 0.58 (23465) covalent geometry : angle 1.91574 / 0.69 (32317) hydrogen bonds : bond 0.12958 / 8.62 ( 1309) hydrogen bonds : angle 4.72254 / 3.49 ( 3705) Misc. bond : bond 0.43271 / 27.13 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 5 TYR cc_start: 0.6159 (p90) cc_final: 0.5605 (p90) REVERT: k 5 TYR cc_start: 0.6886 (p90) cc_final: 0.6610 (p90) REVERT: j 42 ASN cc_start: 0.7183 (t0) cc_final: 0.6435 (t0) outliers start: 0 outliers final: 3 residues processed: 637 average time/residue: 0.5205 time to fit residues: 386.3671 Evaluate side-chains 477 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 474 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain g residue 10 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... t 20 GLN r 42 ASN O 25 GLN e 20 GLN k 20 GLN k 42 ASN J 17 GLN f 20 GLN i 42 ASN j 20 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN M 78 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN F 17 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.084784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.065784 restraints weight = 57559.041| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.20 r_work: 0.2824 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23497 Z= 0.170 Angle : 1.405 37.892 32317 Z= 0.515 Chirality : 0.041 0.347 3242 Planarity : 0.004 0.050 3934 Dihedral : 23.093 179.979 3827 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.00 % Allowed : 11.89 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.17), residues: 2286 helix: 2.04 (0.13), residues: 1557 sheet: 1.67 (1.08), residues: 22 loop : -0.89 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG u 53 TYR 0.015 0.002 TYR M 304 PHE 0.040 0.001 PHE M 217 TRP 0.041 0.001 TRP L 273 HIS 0.008 0.001 HIS O 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (23465) covalent geometry : angle 1.40510 / 0.52 (32317) hydrogen bonds : bond 0.05500 / 3.60 ( 1309) hydrogen bonds : angle 4.02554 / 2.97 ( 3705) Misc. bond : bond 0.00183 / 0.12 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 549 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 5 TYR cc_start: 0.8242 (p90) cc_final: 0.7033 (p90) REVERT: N 14 GLN cc_start: 0.9247 (pm20) cc_final: 0.9009 (pm20) REVERT: N 15 GLN cc_start: 0.8801 (pt0) cc_final: 0.8517 (pm20) REVERT: N 18 GLU cc_start: 0.9276 (mp0) cc_final: 0.9050 (pm20) REVERT: t 5 TYR cc_start: 0.8511 (p90) cc_final: 0.8061 (p90) REVERT: t 14 ARG cc_start: 0.8760 (mtm180) cc_final: 0.8495 (mpp80) REVERT: S 14 GLN cc_start: 0.9177 (pp30) cc_final: 0.8485 (pp30) REVERT: S 15 GLN cc_start: 0.8865 (mt0) cc_final: 0.8601 (mp10) REVERT: S 27 MET cc_start: 0.9364 (ttm) cc_final: 0.8948 (mtp) REVERT: r 6 LYS cc_start: 0.9718 (tppp) cc_final: 0.9517 (tppt) REVERT: r 14 ARG cc_start: 0.8684 (mtm180) cc_final: 0.8381 (mpp80) REVERT: r 26 LEU cc_start: 0.9578 (mm) cc_final: 0.9325 (mm) REVERT: U 13 ASP cc_start: 0.9243 (p0) cc_final: 0.8852 (p0) REVERT: D 14 GLN cc_start: 0.9178 (mp10) cc_final: 0.8963 (mp10) REVERT: b 3 LYS cc_start: 0.9025 (ptpp) cc_final: 0.8773 (mmpt) REVERT: b 30 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8967 (tmm) REVERT: b 45 ASP cc_start: 0.8674 (t0) cc_final: 0.8469 (t0) REVERT: k 45 ASP cc_start: 0.8804 (m-30) cc_final: 0.8601 (m-30) REVERT: J 11 LEU cc_start: 0.9117 (mp) cc_final: 0.8915 (mp) REVERT: J 18 GLU cc_start: 0.8730 (pp20) cc_final: 0.8495 (pp20) REVERT: J 25 GLN cc_start: 0.9448 (mt0) cc_final: 0.9028 (mm110) REVERT: f 38 ASN cc_start: 0.9207 (t0) cc_final: 0.8984 (t0) REVERT: E 18 GLU cc_start: 0.9038 (mp0) cc_final: 0.8777 (mm-30) REVERT: u 45 ASP cc_start: 0.8659 (m-30) cc_final: 0.8443 (m-30) REVERT: u 53 ARG cc_start: 0.7954 (mmt-90) cc_final: 0.7565 (mmt-90) REVERT: T 27 MET cc_start: 0.8992 (ptm) cc_final: 0.8781 (ptp) REVERT: s 6 LYS cc_start: 0.9499 (mmmm) cc_final: 0.9235 (mmmt) REVERT: s 20 GLN cc_start: 0.8683 (mt0) cc_final: 0.8454 (pt0) REVERT: s 25 PHE cc_start: 0.9502 (t80) cc_final: 0.9109 (t80) REVERT: i 3 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8307 (tmmm) REVERT: G 18 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8881 (mt-10) REVERT: j 26 LEU cc_start: 0.9488 (mt) cc_final: 0.9218 (mm) REVERT: j 45 ASP cc_start: 0.8713 (m-30) cc_final: 0.8401 (m-30) REVERT: I 15 GLN cc_start: 0.8497 (mt0) cc_final: 0.7872 (mt0) REVERT: I 18 GLU cc_start: 0.8402 (pp20) cc_final: 0.8115 (pp20) REVERT: I 19 LEU cc_start: 0.9275 (mp) cc_final: 0.8946 (mp) REVERT: L 217 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.9014 (t80) REVERT: L 272 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8347 (p90) REVERT: g 3 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8699 (tmmm) REVERT: g 38 ASN cc_start: 0.9314 (t0) cc_final: 0.9097 (t0) outliers start: 60 outliers final: 11 residues processed: 564 average time/residue: 0.5044 time to fit residues: 333.3830 Evaluate side-chains 503 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 487 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain b residue 30 MET Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain u residue 30 MET Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain g residue 3 LYS Chi-restraints excluded: chain g residue 10 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 215 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 189 optimal weight: 0.0570 chunk 191 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... t 20 GLN a 42 ASN e 20 GLN f 20 GLN j 20 GLN I 17 GLN L 61 ASN L 148 GLN M 188 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.083541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.064396 restraints weight = 58323.696| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.22 r_work: 0.2775 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 23497 Z= 0.183 Angle : 1.330 40.496 32317 Z= 0.490 Chirality : 0.040 0.288 3242 Planarity : 0.004 0.052 3934 Dihedral : 22.636 179.961 3823 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.50 % Allowed : 13.19 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.18), residues: 2286 helix: 2.09 (0.13), residues: 1574 sheet: 2.01 (1.10), residues: 26 loop : -0.73 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 45 TYR 0.014 0.001 TYR M 304 PHE 0.024 0.001 PHE M 217 TRP 0.024 0.001 TRP L 273 HIS 0.006 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (23465) covalent geometry : angle 1.32961 / 0.49 (32317) hydrogen bonds : bond 0.05169 / 3.38 ( 1309) hydrogen bonds : angle 3.98792 / 2.93 ( 3705) Misc. bond : bond 0.00121 / 0.07 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 534 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 5 TYR cc_start: 0.8184 (p90) cc_final: 0.7280 (p90) REVERT: o 6 LYS cc_start: 0.9489 (mmtm) cc_final: 0.9110 (mmpt) REVERT: N 7 SER cc_start: 0.7872 (OUTLIER) cc_final: 0.7526 (p) REVERT: N 15 GLN cc_start: 0.8778 (pt0) cc_final: 0.8454 (pm20) REVERT: N 18 GLU cc_start: 0.9268 (mp0) cc_final: 0.8958 (pm20) REVERT: t 5 TYR cc_start: 0.8395 (p90) cc_final: 0.7948 (p90) REVERT: t 42 ASN cc_start: 0.8970 (t0) cc_final: 0.8659 (t0) REVERT: S 15 GLN cc_start: 0.8792 (mt0) cc_final: 0.8540 (mp10) REVERT: S 18 GLU cc_start: 0.8919 (pm20) cc_final: 0.8673 (pm20) REVERT: S 27 MET cc_start: 0.9291 (ttm) cc_final: 0.8998 (mtp) REVERT: r 14 ARG cc_start: 0.8731 (mtm180) cc_final: 0.8295 (mpp80) REVERT: r 23 PHE cc_start: 0.9438 (t80) cc_final: 0.8992 (t80) REVERT: r 46 ILE cc_start: 0.9421 (mt) cc_final: 0.9175 (mp) REVERT: U 13 ASP cc_start: 0.9228 (p0) cc_final: 0.8929 (p0) REVERT: e 20 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.9014 (mt0) REVERT: e 38 ASN cc_start: 0.9242 (t0) cc_final: 0.8998 (t0) REVERT: b 3 LYS cc_start: 0.9028 (ptpp) cc_final: 0.8618 (mmpt) REVERT: k 9 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8814 (mm) REVERT: k 14 ARG cc_start: 0.9080 (mtt90) cc_final: 0.8786 (mtt90) REVERT: J 11 LEU cc_start: 0.9170 (mp) cc_final: 0.8928 (mp) REVERT: J 13 ASP cc_start: 0.9515 (t0) cc_final: 0.9064 (t0) REVERT: J 17 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8868 (mp10) REVERT: J 18 GLU cc_start: 0.8763 (pp20) cc_final: 0.8553 (pp20) REVERT: J 25 GLN cc_start: 0.9475 (mt0) cc_final: 0.9100 (mp10) REVERT: f 15 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6312 (ttt-90) REVERT: f 38 ASN cc_start: 0.9232 (t0) cc_final: 0.9007 (t0) REVERT: E 14 GLN cc_start: 0.8778 (pm20) cc_final: 0.8533 (pm20) REVERT: E 18 GLU cc_start: 0.9089 (mp0) cc_final: 0.8822 (mm-30) REVERT: u 45 ASP cc_start: 0.8669 (m-30) cc_final: 0.8391 (m-30) REVERT: u 53 ARG cc_start: 0.7940 (mmt-90) cc_final: 0.7710 (mmt-90) REVERT: T 27 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8767 (ptp) REVERT: s 6 LYS cc_start: 0.9518 (mmmm) cc_final: 0.9306 (mmmt) REVERT: s 20 GLN cc_start: 0.8698 (mt0) cc_final: 0.8452 (pt0) REVERT: s 25 PHE cc_start: 0.9504 (t80) cc_final: 0.9032 (t80) REVERT: n 6 LYS cc_start: 0.9514 (mmtp) cc_final: 0.9259 (mmtt) REVERT: n 38 ASN cc_start: 0.9299 (t0) cc_final: 0.9080 (t0) REVERT: i 3 LYS cc_start: 0.8701 (tmmm) cc_final: 0.8460 (tmmm) REVERT: G 18 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8872 (mt-10) REVERT: j 3 LYS cc_start: 0.8952 (mmpt) cc_final: 0.8546 (ptpp) REVERT: j 14 ARG cc_start: 0.8913 (mtm-85) cc_final: 0.8705 (mtm-85) REVERT: j 45 ASP cc_start: 0.8819 (m-30) cc_final: 0.8318 (m-30) REVERT: I 15 GLN cc_start: 0.8500 (mt0) cc_final: 0.7868 (mt0) REVERT: I 18 GLU cc_start: 0.8471 (pp20) cc_final: 0.8145 (pp20) REVERT: I 19 LEU cc_start: 0.9252 (mp) cc_final: 0.8931 (mp) REVERT: L 217 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.9029 (t80) REVERT: L 272 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8193 (p90) REVERT: g 3 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8723 (tmmm) REVERT: g 38 ASN cc_start: 0.9295 (t0) cc_final: 0.9021 (t0) outliers start: 70 outliers final: 18 residues processed: 556 average time/residue: 0.5175 time to fit residues: 335.2424 Evaluate side-chains 518 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 492 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain O residue 29 LEU Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain e residue 20 GLN Chi-restraints excluded: chain e residue 34 MET Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain g residue 3 LYS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 55 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... o 20 GLN o 38 ASN t 20 GLN ** U 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 20 GLN j 20 GLN L 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.064281 restraints weight = 58462.104| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.18 r_work: 0.2790 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 23497 Z= 0.196 Angle : 1.267 37.311 32317 Z= 0.473 Chirality : 0.042 0.409 3242 Planarity : 0.004 0.052 3934 Dihedral : 22.426 179.994 3821 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.50 % Allowed : 14.74 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.18), residues: 2286 helix: 2.09 (0.13), residues: 1582 sheet: 1.99 (1.08), residues: 26 loop : -0.77 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 45 TYR 0.013 0.001 TYR M 304 PHE 0.021 0.001 PHE L 217 TRP 0.019 0.001 TRP L 273 HIS 0.007 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (23465) covalent geometry : angle 1.26656 / 0.47 (32317) hydrogen bonds : bond 0.05111 / 3.34 ( 1309) hydrogen bonds : angle 3.97751 / 2.93 ( 3705) Misc. bond : bond 0.00178 / 0.10 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 533 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 5 TYR cc_start: 0.8328 (p90) cc_final: 0.8103 (p90) REVERT: o 6 LYS cc_start: 0.9458 (mmtm) cc_final: 0.9211 (mmpt) REVERT: N 7 SER cc_start: 0.7929 (OUTLIER) cc_final: 0.7598 (p) REVERT: N 14 GLN cc_start: 0.9206 (pm20) cc_final: 0.8647 (pm20) REVERT: N 15 GLN cc_start: 0.8832 (pt0) cc_final: 0.8237 (pm20) REVERT: N 18 GLU cc_start: 0.9285 (mp0) cc_final: 0.8968 (pm20) REVERT: t 5 TYR cc_start: 0.8440 (p90) cc_final: 0.8180 (p90) REVERT: t 6 LYS cc_start: 0.9416 (mmtp) cc_final: 0.9065 (mmpt) REVERT: t 14 ARG cc_start: 0.8695 (mpp80) cc_final: 0.8395 (mpp80) REVERT: t 42 ASN cc_start: 0.8877 (t0) cc_final: 0.8650 (t0) REVERT: S 15 GLN cc_start: 0.8762 (mt0) cc_final: 0.8433 (mp10) REVERT: S 18 GLU cc_start: 0.8960 (pm20) cc_final: 0.8755 (pm20) REVERT: r 14 ARG cc_start: 0.8785 (mtm180) cc_final: 0.8258 (mpp80) REVERT: r 23 PHE cc_start: 0.9411 (t80) cc_final: 0.8907 (t80) REVERT: r 46 ILE cc_start: 0.9459 (mt) cc_final: 0.9217 (mp) REVERT: e 38 ASN cc_start: 0.9277 (t0) cc_final: 0.9067 (t0) REVERT: b 3 LYS cc_start: 0.9164 (ptpp) cc_final: 0.8732 (mmpt) REVERT: k 9 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8971 (mm) REVERT: J 11 LEU cc_start: 0.9200 (mp) cc_final: 0.8911 (mp) REVERT: J 25 GLN cc_start: 0.9484 (mt0) cc_final: 0.9124 (mp10) REVERT: J 27 MET cc_start: 0.9093 (ttp) cc_final: 0.8827 (ttp) REVERT: f 15 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6399 (ttt-90) REVERT: f 38 ASN cc_start: 0.9290 (t0) cc_final: 0.9081 (t0) REVERT: u 45 ASP cc_start: 0.8650 (m-30) cc_final: 0.8297 (m-30) REVERT: T 15 GLN cc_start: 0.8782 (mt0) cc_final: 0.8442 (mt0) REVERT: s 6 LYS cc_start: 0.9542 (mmmm) cc_final: 0.9294 (mmmm) REVERT: s 20 GLN cc_start: 0.8712 (mt0) cc_final: 0.8485 (pt0) REVERT: s 25 PHE cc_start: 0.9470 (t80) cc_final: 0.8987 (t80) REVERT: n 5 TYR cc_start: 0.8124 (p90) cc_final: 0.7751 (p90) REVERT: n 6 LYS cc_start: 0.9506 (mmtp) cc_final: 0.9292 (mmtt) REVERT: i 3 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8440 (tmmm) REVERT: G 14 GLN cc_start: 0.9059 (pm20) cc_final: 0.8840 (pm20) REVERT: G 15 GLN cc_start: 0.8949 (mt0) cc_final: 0.8737 (mt0) REVERT: G 18 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8843 (mt-10) REVERT: j 14 ARG cc_start: 0.8997 (mtm-85) cc_final: 0.8772 (mpp80) REVERT: j 42 ASN cc_start: 0.9146 (t0) cc_final: 0.8293 (t0) REVERT: j 45 ASP cc_start: 0.8821 (m-30) cc_final: 0.8163 (m-30) REVERT: I 15 GLN cc_start: 0.8565 (mt0) cc_final: 0.7881 (mt0) REVERT: I 18 GLU cc_start: 0.8486 (pp20) cc_final: 0.8153 (pp20) REVERT: I 19 LEU cc_start: 0.9287 (mp) cc_final: 0.8931 (mp) REVERT: L 217 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.9168 (t80) REVERT: L 272 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8164 (p90) REVERT: H 206 GLN cc_start: 0.9096 (mt0) cc_final: 0.8763 (pt0) REVERT: g 38 ASN cc_start: 0.9339 (t0) cc_final: 0.9059 (t0) REVERT: F 48 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8686 (mt) REVERT: d 52 GLU cc_start: 0.9162 (mp0) cc_final: 0.8943 (mp0) outliers start: 70 outliers final: 19 residues processed: 560 average time/residue: 0.5336 time to fit residues: 349.4151 Evaluate side-chains 519 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 493 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain a residue 14 ARG Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain u residue 54 VAL Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 86 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... o 20 GLN t 20 GLN e 20 GLN b 42 ASN ** k 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN L 61 ASN L 160 ASN M 78 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.082510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.063682 restraints weight = 58216.954| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.17 r_work: 0.2779 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 23497 Z= 0.203 Angle : 1.265 40.485 32317 Z= 0.477 Chirality : 0.042 0.424 3242 Planarity : 0.004 0.053 3934 Dihedral : 22.259 179.976 3821 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.50 % Allowed : 14.54 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.18), residues: 2286 helix: 2.10 (0.13), residues: 1582 sheet: 2.02 (1.08), residues: 26 loop : -0.74 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 45 TYR 0.019 0.002 TYR K 23 PHE 0.022 0.001 PHE L 217 TRP 0.017 0.001 TRP L 273 HIS 0.007 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.20 (23465) covalent geometry : angle 1.26519 / 0.48 (32317) hydrogen bonds : bond 0.05123 / 3.34 ( 1309) hydrogen bonds : angle 4.02518 / 2.95 ( 3705) Misc. bond : bond 0.00173 / 0.10 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 525 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 5 TYR cc_start: 0.8411 (p90) cc_final: 0.7864 (p90) REVERT: o 6 LYS cc_start: 0.9440 (mmtm) cc_final: 0.9108 (mmpt) REVERT: o 34 MET cc_start: 0.9183 (ptp) cc_final: 0.8854 (ptm) REVERT: N 7 SER cc_start: 0.8000 (OUTLIER) cc_final: 0.7701 (p) REVERT: N 14 GLN cc_start: 0.9192 (pm20) cc_final: 0.8821 (pm20) REVERT: N 15 GLN cc_start: 0.8852 (pt0) cc_final: 0.8422 (pm20) REVERT: N 18 GLU cc_start: 0.9298 (mt-10) cc_final: 0.9029 (pt0) REVERT: t 5 TYR cc_start: 0.8425 (p90) cc_final: 0.8194 (p90) REVERT: t 6 LYS cc_start: 0.9418 (mmtp) cc_final: 0.9068 (mmpt) REVERT: t 14 ARG cc_start: 0.8743 (mpp80) cc_final: 0.8434 (mpp80) REVERT: t 42 ASN cc_start: 0.8858 (t0) cc_final: 0.8629 (t0) REVERT: S 15 GLN cc_start: 0.8694 (mt0) cc_final: 0.8381 (mp10) REVERT: S 18 GLU cc_start: 0.9054 (pm20) cc_final: 0.8797 (pm20) REVERT: S 27 MET cc_start: 0.9359 (ttm) cc_final: 0.9145 (mtm) REVERT: r 14 ARG cc_start: 0.8768 (mtm180) cc_final: 0.8490 (mpp80) REVERT: r 23 PHE cc_start: 0.9404 (t80) cc_final: 0.8892 (t80) REVERT: r 46 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9227 (mp) REVERT: e 38 ASN cc_start: 0.9306 (t0) cc_final: 0.9094 (t0) REVERT: k 9 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9012 (mm) REVERT: J 25 GLN cc_start: 0.9480 (mt0) cc_final: 0.9141 (mp10) REVERT: J 27 MET cc_start: 0.9063 (ttp) cc_final: 0.8818 (ttp) REVERT: f 15 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6396 (ttt-90) REVERT: f 38 ASN cc_start: 0.9307 (t0) cc_final: 0.9094 (t0) REVERT: E 14 GLN cc_start: 0.8786 (pm20) cc_final: 0.8553 (pm20) REVERT: E 18 GLU cc_start: 0.9026 (mp0) cc_final: 0.8760 (mm-30) REVERT: u 45 ASP cc_start: 0.8629 (m-30) cc_final: 0.8290 (m-30) REVERT: T 15 GLN cc_start: 0.8778 (mt0) cc_final: 0.8441 (mt0) REVERT: s 6 LYS cc_start: 0.9534 (mmmm) cc_final: 0.9304 (mmmm) REVERT: s 25 PHE cc_start: 0.9481 (t80) cc_final: 0.9043 (t80) REVERT: n 5 TYR cc_start: 0.8181 (p90) cc_final: 0.7579 (p90) REVERT: K 15 GLN cc_start: 0.9110 (mt0) cc_final: 0.8754 (mp10) REVERT: i 3 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8357 (tmmm) REVERT: G 14 GLN cc_start: 0.9075 (pm20) cc_final: 0.8872 (pm20) REVERT: G 15 GLN cc_start: 0.8949 (mt0) cc_final: 0.8678 (mt0) REVERT: G 18 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8888 (mt-10) REVERT: j 14 ARG cc_start: 0.9024 (mtm-85) cc_final: 0.8804 (mpp80) REVERT: j 42 ASN cc_start: 0.9178 (t0) cc_final: 0.8454 (t0) REVERT: j 45 ASP cc_start: 0.8851 (m-30) cc_final: 0.8246 (m-30) REVERT: I 15 GLN cc_start: 0.8595 (mt0) cc_final: 0.7870 (mt0) REVERT: I 18 GLU cc_start: 0.8490 (pp20) cc_final: 0.8079 (pp20) REVERT: I 19 LEU cc_start: 0.9296 (mp) cc_final: 0.8920 (mp) REVERT: L 272 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.7956 (p90) REVERT: H 206 GLN cc_start: 0.9082 (mt0) cc_final: 0.8784 (pt0) REVERT: g 3 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8214 (tmmm) REVERT: g 38 ASN cc_start: 0.9337 (t0) cc_final: 0.9023 (t0) REVERT: F 48 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8624 (mt) outliers start: 70 outliers final: 24 residues processed: 556 average time/residue: 0.5420 time to fit residues: 352.1171 Evaluate side-chains 515 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 483 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain r residue 34 MET Chi-restraints excluded: chain r residue 46 ILE Chi-restraints excluded: chain a residue 14 ARG Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain e residue 54 VAL Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain u residue 54 VAL Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain g residue 3 LYS Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain B residue 7 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 126 optimal weight: 6.9990 chunk 220 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... o 20 GLN t 20 GLN e 20 GLN e 42 ASN b 42 ASN ** k 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 20 GLN j 20 GLN M 78 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.083105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.064415 restraints weight = 58289.071| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.18 r_work: 0.2798 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23497 Z= 0.171 Angle : 1.201 37.911 32317 Z= 0.461 Chirality : 0.042 0.447 3242 Planarity : 0.003 0.053 3934 Dihedral : 22.137 179.985 3821 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.90 % Allowed : 16.24 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.18), residues: 2286 helix: 2.11 (0.13), residues: 1583 sheet: 2.05 (1.08), residues: 26 loop : -0.70 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 45 TYR 0.017 0.001 TYR M 304 PHE 0.019 0.001 PHE L 217 TRP 0.016 0.001 TRP k 43 HIS 0.005 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (23465) covalent geometry : angle 1.20058 / 0.46 (32317) hydrogen bonds : bond 0.04943 / 3.23 ( 1309) hydrogen bonds : angle 4.07358 / 3.00 ( 3705) Misc. bond : bond 0.00133 / 0.08 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 532 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 5 TYR cc_start: 0.8409 (p90) cc_final: 0.7815 (p90) REVERT: o 6 LYS cc_start: 0.9448 (mmtm) cc_final: 0.9196 (mmpt) REVERT: N 7 SER cc_start: 0.7950 (OUTLIER) cc_final: 0.7678 (p) REVERT: N 14 GLN cc_start: 0.9187 (pm20) cc_final: 0.8854 (pm20) REVERT: N 15 GLN cc_start: 0.8840 (pt0) cc_final: 0.8391 (pm20) REVERT: N 18 GLU cc_start: 0.9311 (mt-10) cc_final: 0.9031 (pt0) REVERT: t 6 LYS cc_start: 0.9413 (mmtp) cc_final: 0.9108 (mmpt) REVERT: t 14 ARG cc_start: 0.8732 (mpp80) cc_final: 0.8417 (mpp80) REVERT: t 45 ASP cc_start: 0.8868 (t0) cc_final: 0.8596 (t0) REVERT: S 15 GLN cc_start: 0.8673 (mt0) cc_final: 0.8259 (mp10) REVERT: S 27 MET cc_start: 0.9276 (ttm) cc_final: 0.8974 (mtp) REVERT: r 14 ARG cc_start: 0.8734 (mtm180) cc_final: 0.8315 (mpp80) REVERT: r 23 PHE cc_start: 0.9394 (t80) cc_final: 0.8916 (t80) REVERT: r 46 ILE cc_start: 0.9475 (OUTLIER) cc_final: 0.9232 (mp) REVERT: e 42 ASN cc_start: 0.8929 (t0) cc_final: 0.8719 (t0) REVERT: k 9 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8981 (mm) REVERT: k 42 ASN cc_start: 0.8905 (t0) cc_final: 0.8506 (t0) REVERT: k 45 ASP cc_start: 0.8813 (m-30) cc_final: 0.8472 (m-30) REVERT: J 25 GLN cc_start: 0.9476 (mt0) cc_final: 0.9139 (mp10) REVERT: J 27 MET cc_start: 0.9059 (ttp) cc_final: 0.8843 (ttp) REVERT: f 38 ASN cc_start: 0.9293 (t0) cc_final: 0.9063 (t0) REVERT: E 14 GLN cc_start: 0.8840 (pm20) cc_final: 0.8553 (pm20) REVERT: E 18 GLU cc_start: 0.9053 (mp0) cc_final: 0.8780 (mm-30) REVERT: u 45 ASP cc_start: 0.8617 (m-30) cc_final: 0.8268 (m-30) REVERT: T 15 GLN cc_start: 0.8761 (mt0) cc_final: 0.8513 (mt0) REVERT: s 6 LYS cc_start: 0.9529 (mmmm) cc_final: 0.9288 (mmmm) REVERT: s 25 PHE cc_start: 0.9489 (t80) cc_final: 0.9072 (t80) REVERT: R 13 ASP cc_start: 0.9394 (t0) cc_final: 0.9179 (t0) REVERT: n 5 TYR cc_start: 0.8207 (p90) cc_final: 0.7384 (p90) REVERT: K 14 GLN cc_start: 0.8911 (pm20) cc_final: 0.8623 (pm20) REVERT: K 15 GLN cc_start: 0.9141 (mt0) cc_final: 0.8757 (mp10) REVERT: i 6 LYS cc_start: 0.9392 (tppt) cc_final: 0.9140 (tptp) REVERT: G 14 GLN cc_start: 0.9087 (pm20) cc_final: 0.8869 (pm20) REVERT: G 15 GLN cc_start: 0.8948 (mt0) cc_final: 0.8654 (mt0) REVERT: G 18 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8867 (mt-10) REVERT: j 3 LYS cc_start: 0.8943 (mmpt) cc_final: 0.8639 (ttpp) REVERT: j 14 ARG cc_start: 0.9017 (mtm-85) cc_final: 0.8801 (mpp80) REVERT: j 42 ASN cc_start: 0.9219 (t0) cc_final: 0.8066 (t0) REVERT: j 45 ASP cc_start: 0.8880 (m-30) cc_final: 0.8077 (m-30) REVERT: I 15 GLN cc_start: 0.8647 (mt0) cc_final: 0.7888 (mt0) REVERT: I 18 GLU cc_start: 0.8506 (pp20) cc_final: 0.8197 (pp20) REVERT: I 19 LEU cc_start: 0.9300 (mp) cc_final: 0.8908 (mp) REVERT: L 202 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8726 (mt-10) REVERT: L 272 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.7958 (p90) REVERT: H 206 GLN cc_start: 0.9029 (mt0) cc_final: 0.8742 (pt0) REVERT: g 38 ASN cc_start: 0.9341 (t0) cc_final: 0.9016 (t0) outliers start: 58 outliers final: 22 residues processed: 560 average time/residue: 0.4948 time to fit residues: 324.5235 Evaluate side-chains 515 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 489 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 46 ILE Chi-restraints excluded: chain a residue 14 ARG Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain u residue 54 VAL Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 54 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain M residue 207 ILE Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain B residue 7 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 96 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... o 20 GLN t 20 GLN e 20 GLN b 42 ASN ** k 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 20 GLN ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 GLN M 238 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.062742 restraints weight = 58780.436| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.17 r_work: 0.2757 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 23497 Z= 0.250 Angle : 1.201 38.079 32317 Z= 0.473 Chirality : 0.044 0.411 3242 Planarity : 0.004 0.054 3934 Dihedral : 22.096 179.982 3821 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.25 % Allowed : 16.79 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.18), residues: 2286 helix: 1.99 (0.13), residues: 1579 sheet: 1.59 (1.41), residues: 16 loop : -0.77 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG U 45 TYR 0.019 0.002 TYR M 304 PHE 0.020 0.002 PHE H 20 TRP 0.016 0.001 TRP L 273 HIS 0.009 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.25 (23465) covalent geometry : angle 1.20114 / 0.47 (32317) hydrogen bonds : bond 0.05318 / 3.46 ( 1309) hydrogen bonds : angle 4.19438 / 3.09 ( 3705) Misc. bond : bond 0.00206 / 0.12 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 502 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 5 TYR cc_start: 0.8381 (p90) cc_final: 0.8031 (p90) REVERT: o 6 LYS cc_start: 0.9449 (mmtm) cc_final: 0.9159 (mmpt) REVERT: o 34 MET cc_start: 0.9258 (ptp) cc_final: 0.8914 (ptm) REVERT: N 7 SER cc_start: 0.7917 (OUTLIER) cc_final: 0.7683 (p) REVERT: t 6 LYS cc_start: 0.9413 (mmtp) cc_final: 0.9099 (mmpt) REVERT: t 14 ARG cc_start: 0.8765 (mpp80) cc_final: 0.8436 (mpp80) REVERT: t 45 ASP cc_start: 0.8822 (t0) cc_final: 0.8540 (t0) REVERT: S 15 GLN cc_start: 0.8578 (mt0) cc_final: 0.8149 (mp10) REVERT: S 27 MET cc_start: 0.9269 (ttm) cc_final: 0.8934 (mtm) REVERT: r 14 ARG cc_start: 0.8693 (mtm180) cc_final: 0.8270 (mpp80) REVERT: r 23 PHE cc_start: 0.9379 (t80) cc_final: 0.8898 (t80) REVERT: r 46 ILE cc_start: 0.9477 (mt) cc_final: 0.9235 (mp) REVERT: O 19 LEU cc_start: 0.9600 (tm) cc_final: 0.9381 (pp) REVERT: e 45 ASP cc_start: 0.9047 (m-30) cc_final: 0.8844 (m-30) REVERT: b 3 LYS cc_start: 0.9249 (ptpp) cc_final: 0.8788 (mmpt) REVERT: k 9 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8998 (mm) REVERT: k 14 ARG cc_start: 0.9208 (mtt90) cc_final: 0.8882 (mtt90) REVERT: k 42 ASN cc_start: 0.8981 (t0) cc_final: 0.8635 (t0) REVERT: J 25 GLN cc_start: 0.9480 (mt0) cc_final: 0.9134 (mp10) REVERT: J 27 MET cc_start: 0.9066 (ttp) cc_final: 0.8828 (ttp) REVERT: f 15 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6678 (ttt-90) REVERT: f 38 ASN cc_start: 0.9298 (t0) cc_final: 0.9066 (t0) REVERT: E 14 GLN cc_start: 0.8890 (pm20) cc_final: 0.8596 (pm20) REVERT: E 18 GLU cc_start: 0.9134 (mp0) cc_final: 0.8888 (mm-30) REVERT: u 53 ARG cc_start: 0.8047 (mmt-90) cc_final: 0.7503 (mpp-170) REVERT: T 13 ASP cc_start: 0.9326 (t0) cc_final: 0.8934 (t0) REVERT: T 15 GLN cc_start: 0.8826 (mt0) cc_final: 0.8605 (mt0) REVERT: T 17 GLN cc_start: 0.9369 (mt0) cc_final: 0.9149 (mp10) REVERT: s 6 LYS cc_start: 0.9564 (mmmm) cc_final: 0.9291 (mmmt) REVERT: s 25 PHE cc_start: 0.9486 (t80) cc_final: 0.9064 (t80) REVERT: s 42 ASN cc_start: 0.9035 (t0) cc_final: 0.8552 (t0) REVERT: s 45 ASP cc_start: 0.8921 (m-30) cc_final: 0.8191 (m-30) REVERT: R 19 LEU cc_start: 0.9537 (tt) cc_final: 0.9259 (pp) REVERT: R 27 MET cc_start: 0.8871 (ttp) cc_final: 0.8613 (ttp) REVERT: n 5 TYR cc_start: 0.8302 (p90) cc_final: 0.7851 (p90) REVERT: K 14 GLN cc_start: 0.8968 (pm20) cc_final: 0.8658 (pm20) REVERT: K 15 GLN cc_start: 0.9146 (mt0) cc_final: 0.8799 (mp10) REVERT: i 3 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8122 (tmmm) REVERT: i 14 ARG cc_start: 0.8292 (mtm180) cc_final: 0.7822 (mtm-85) REVERT: i 15 ARG cc_start: 0.7773 (ptm160) cc_final: 0.7217 (tpt170) REVERT: G 14 GLN cc_start: 0.9108 (pm20) cc_final: 0.8902 (pm20) REVERT: G 15 GLN cc_start: 0.8949 (mt0) cc_final: 0.8652 (mt0) REVERT: G 18 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8883 (mt-10) REVERT: j 14 ARG cc_start: 0.9018 (mtm-85) cc_final: 0.8783 (mpp80) REVERT: j 42 ASN cc_start: 0.9233 (t0) cc_final: 0.8402 (t0) REVERT: j 45 ASP cc_start: 0.8887 (m-30) cc_final: 0.8194 (m-30) REVERT: I 15 GLN cc_start: 0.8651 (mt0) cc_final: 0.7937 (mt0) REVERT: I 18 GLU cc_start: 0.8492 (pp20) cc_final: 0.8174 (pp20) REVERT: I 19 LEU cc_start: 0.9290 (mp) cc_final: 0.8918 (mp) REVERT: L 272 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8172 (p90) REVERT: H 206 GLN cc_start: 0.9100 (mt0) cc_final: 0.8854 (pt0) REVERT: g 3 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8679 (tmmm) REVERT: g 38 ASN cc_start: 0.9363 (t0) cc_final: 0.9004 (t0) outliers start: 65 outliers final: 29 residues processed: 532 average time/residue: 0.5452 time to fit residues: 336.2647 Evaluate side-chains 517 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 482 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain a residue 14 ARG Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain e residue 54 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain u residue 54 VAL Chi-restraints excluded: chain X residue 18 MET Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain j residue 54 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain g residue 3 LYS Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 48 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 165 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 58 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... o 20 GLN N 15 GLN t 20 GLN e 20 GLN e 42 ASN b 42 ASN A 25 GLN ** k 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 20 GLN ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN M 78 GLN H 5 ASN ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.083301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.064511 restraints weight = 57909.049| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.19 r_work: 0.2807 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 23497 Z= 0.166 Angle : 1.168 38.112 32317 Z= 0.465 Chirality : 0.043 0.442 3242 Planarity : 0.003 0.053 3934 Dihedral : 22.026 179.992 3821 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.80 % Allowed : 19.14 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.18), residues: 2286 helix: 1.99 (0.13), residues: 1585 sheet: 1.66 (1.41), residues: 16 loop : -0.66 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG U 45 TYR 0.028 0.001 TYR M 304 PHE 0.018 0.001 PHE H 20 TRP 0.016 0.001 TRP k 43 HIS 0.004 0.001 HIS I 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (23465) covalent geometry : angle 1.16789 / 0.46 (32317) hydrogen bonds : bond 0.04960 / 3.23 ( 1309) hydrogen bonds : angle 4.18482 / 3.08 ( 3705) Misc. bond : bond 0.00104 / 0.06 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 513 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 5 TYR cc_start: 0.8321 (p90) cc_final: 0.7744 (p90) REVERT: o 6 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9179 (mmpt) REVERT: N 7 SER cc_start: 0.7869 (OUTLIER) cc_final: 0.7660 (p) REVERT: N 15 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8094 (pm20) REVERT: N 18 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8995 (pt0) REVERT: t 6 LYS cc_start: 0.9394 (mmtp) cc_final: 0.9118 (mmpt) REVERT: t 14 ARG cc_start: 0.8735 (mpp80) cc_final: 0.8417 (mpp80) REVERT: t 45 ASP cc_start: 0.8817 (t0) cc_final: 0.8533 (t0) REVERT: S 11 LEU cc_start: 0.9423 (tp) cc_final: 0.8664 (tt) REVERT: S 14 GLN cc_start: 0.8989 (pm20) cc_final: 0.8499 (pm20) REVERT: S 27 MET cc_start: 0.9258 (ttm) cc_final: 0.8954 (mtm) REVERT: r 14 ARG cc_start: 0.8634 (mtm180) cc_final: 0.8276 (mpp80) REVERT: r 23 PHE cc_start: 0.9330 (t80) cc_final: 0.8889 (t80) REVERT: r 46 ILE cc_start: 0.9484 (mt) cc_final: 0.9238 (mp) REVERT: U 18 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8794 (mt-10) REVERT: b 3 LYS cc_start: 0.9203 (ptpp) cc_final: 0.8742 (mmpt) REVERT: k 14 ARG cc_start: 0.9202 (mtt90) cc_final: 0.8885 (mtt90) REVERT: k 42 ASN cc_start: 0.8952 (t0) cc_final: 0.8568 (t0) REVERT: k 45 ASP cc_start: 0.8816 (m-30) cc_final: 0.8489 (m-30) REVERT: J 25 GLN cc_start: 0.9468 (mt0) cc_final: 0.9133 (mp10) REVERT: J 27 MET cc_start: 0.9018 (ttp) cc_final: 0.8786 (ttp) REVERT: f 15 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6689 (ttt-90) REVERT: f 38 ASN cc_start: 0.9287 (t0) cc_final: 0.9063 (t0) REVERT: E 14 GLN cc_start: 0.8883 (pm20) cc_final: 0.8545 (pm20) REVERT: E 18 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8890 (mm-30) REVERT: u 20 GLN cc_start: 0.9068 (mt0) cc_final: 0.8840 (mt0) REVERT: u 53 ARG cc_start: 0.8029 (mmt-90) cc_final: 0.7209 (mmp80) REVERT: T 15 GLN cc_start: 0.8793 (mt0) cc_final: 0.8545 (mt0) REVERT: X 63 THR cc_start: 0.8811 (m) cc_final: 0.8603 (p) REVERT: s 6 LYS cc_start: 0.9543 (mmmm) cc_final: 0.9256 (mmmt) REVERT: s 25 PHE cc_start: 0.9457 (t80) cc_final: 0.9099 (t80) REVERT: s 42 ASN cc_start: 0.9015 (t0) cc_final: 0.8390 (t0) REVERT: s 45 ASP cc_start: 0.8889 (m-30) cc_final: 0.8150 (m-30) REVERT: R 15 GLN cc_start: 0.8932 (mp10) cc_final: 0.8709 (OUTLIER) REVERT: R 19 LEU cc_start: 0.9531 (tt) cc_final: 0.9266 (pp) REVERT: R 27 MET cc_start: 0.8823 (ttp) cc_final: 0.8535 (ttp) REVERT: K 14 GLN cc_start: 0.8965 (pm20) cc_final: 0.8729 (pm20) REVERT: K 15 GLN cc_start: 0.9123 (mt0) cc_final: 0.8742 (mp10) REVERT: K 18 GLU cc_start: 0.8960 (mp0) cc_final: 0.8712 (mp0) REVERT: i 3 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8168 (tmmm) REVERT: G 14 GLN cc_start: 0.9103 (pm20) cc_final: 0.8878 (pm20) REVERT: G 15 GLN cc_start: 0.8975 (mt0) cc_final: 0.8622 (mt0) REVERT: G 18 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8845 (mt-10) REVERT: j 3 LYS cc_start: 0.8996 (mmpt) cc_final: 0.8739 (ttpp) REVERT: j 42 ASN cc_start: 0.9241 (t0) cc_final: 0.8313 (t0) REVERT: j 45 ASP cc_start: 0.8908 (m-30) cc_final: 0.8485 (m-30) REVERT: I 15 GLN cc_start: 0.8658 (mt0) cc_final: 0.7912 (mt0) REVERT: I 18 GLU cc_start: 0.8478 (pp20) cc_final: 0.8185 (pp20) REVERT: I 19 LEU cc_start: 0.9313 (mp) cc_final: 0.8944 (mp) REVERT: L 272 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8324 (p90) REVERT: H 206 GLN cc_start: 0.8977 (mt0) cc_final: 0.8692 (pt0) REVERT: g 38 ASN cc_start: 0.9366 (t0) cc_final: 0.9014 (t0) outliers start: 56 outliers final: 27 residues processed: 540 average time/residue: 0.5082 time to fit residues: 320.0674 Evaluate side-chains 520 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 487 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 6 LYS Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain a residue 14 ARG Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain e residue 54 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain u residue 54 VAL Chi-restraints excluded: chain X residue 18 MET Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 54 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain M residue 207 ILE Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain B residue 7 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 119 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... o 20 GLN N 15 GLN t 20 GLN e 20 GLN b 42 ASN A 25 GLN ** k 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 20 GLN ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 GLN M 78 GLN H 93 ASN g 20 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.083162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.064324 restraints weight = 58178.587| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.21 r_work: 0.2783 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 23497 Z= 0.180 Angle : 1.174 38.161 32317 Z= 0.471 Chirality : 0.044 0.436 3242 Planarity : 0.004 0.053 3934 Dihedral : 21.935 179.972 3821 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.40 % Allowed : 19.89 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.18), residues: 2286 helix: 1.96 (0.13), residues: 1583 sheet: 2.87 (1.62), residues: 10 loop : -0.62 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG U 45 TYR 0.030 0.001 TYR M 304 PHE 0.018 0.001 PHE H 20 TRP 0.016 0.001 TRP U 44 HIS 0.006 0.001 HIS X 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (23465) covalent geometry : angle 1.17356 / 0.47 (32317) hydrogen bonds : bond 0.05007 / 3.26 ( 1309) hydrogen bonds : angle 4.24366 / 3.11 ( 3705) Misc. bond : bond 0.00129 / 0.07 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 510 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 5 TYR cc_start: 0.8268 (p90) cc_final: 0.7612 (p90) REVERT: o 6 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.9190 (mmpt) REVERT: N 15 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8347 (pm20) REVERT: N 18 GLU cc_start: 0.9332 (mt-10) cc_final: 0.9014 (mp0) REVERT: t 6 LYS cc_start: 0.9368 (mmtp) cc_final: 0.9054 (mmpt) REVERT: t 14 ARG cc_start: 0.8662 (mpp80) cc_final: 0.8355 (mpp80) REVERT: t 33 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9320 (mm) REVERT: t 45 ASP cc_start: 0.8807 (t0) cc_final: 0.8520 (t0) REVERT: S 11 LEU cc_start: 0.9201 (tp) cc_final: 0.8638 (tp) REVERT: S 27 MET cc_start: 0.9265 (ttm) cc_final: 0.8965 (mtp) REVERT: r 14 ARG cc_start: 0.8549 (mtm180) cc_final: 0.8263 (mpp80) REVERT: r 23 PHE cc_start: 0.9305 (t80) cc_final: 0.8952 (t80) REVERT: r 26 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9349 (mm) REVERT: r 46 ILE cc_start: 0.9456 (mt) cc_final: 0.9204 (mp) REVERT: O 18 GLU cc_start: 0.9312 (pt0) cc_final: 0.9060 (pt0) REVERT: U 18 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8779 (mt-10) REVERT: b 3 LYS cc_start: 0.9168 (ptpp) cc_final: 0.8706 (mmpt) REVERT: k 14 ARG cc_start: 0.9125 (mtt90) cc_final: 0.8818 (mtt90) REVERT: k 42 ASN cc_start: 0.8975 (t0) cc_final: 0.8562 (t0) REVERT: J 25 GLN cc_start: 0.9459 (mt0) cc_final: 0.9116 (mp10) REVERT: J 27 MET cc_start: 0.9023 (ttp) cc_final: 0.8797 (ttp) REVERT: f 15 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6534 (ttt-90) REVERT: f 38 ASN cc_start: 0.9262 (t0) cc_final: 0.8999 (t0) REVERT: E 14 GLN cc_start: 0.8921 (pm20) cc_final: 0.8618 (pm20) REVERT: E 18 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8848 (mm-30) REVERT: u 53 ARG cc_start: 0.8024 (mmt-90) cc_final: 0.7522 (mpp-170) REVERT: X 63 THR cc_start: 0.8799 (m) cc_final: 0.8576 (p) REVERT: s 6 LYS cc_start: 0.9554 (mmmm) cc_final: 0.9240 (mmmt) REVERT: s 25 PHE cc_start: 0.9444 (t80) cc_final: 0.9108 (t80) REVERT: s 42 ASN cc_start: 0.9082 (t0) cc_final: 0.8493 (t0) REVERT: s 45 ASP cc_start: 0.8932 (m-30) cc_final: 0.8211 (m-30) REVERT: R 27 MET cc_start: 0.8836 (ttp) cc_final: 0.8541 (ttp) REVERT: n 5 TYR cc_start: 0.8042 (p90) cc_final: 0.7806 (p90) REVERT: n 45 ASP cc_start: 0.8696 (m-30) cc_final: 0.8381 (m-30) REVERT: K 14 GLN cc_start: 0.9019 (pm20) cc_final: 0.8781 (pm20) REVERT: K 15 GLN cc_start: 0.9058 (mt0) cc_final: 0.8504 (mp10) REVERT: i 6 LYS cc_start: 0.9404 (tppp) cc_final: 0.9053 (mmmt) REVERT: G 14 GLN cc_start: 0.9115 (pm20) cc_final: 0.8889 (pm20) REVERT: G 15 GLN cc_start: 0.8931 (mt0) cc_final: 0.8573 (mt0) REVERT: G 18 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8835 (mt-10) REVERT: j 3 LYS cc_start: 0.9008 (mmpt) cc_final: 0.8727 (ttpp) REVERT: j 42 ASN cc_start: 0.9257 (t0) cc_final: 0.8372 (t0) REVERT: j 45 ASP cc_start: 0.8920 (m-30) cc_final: 0.8482 (m-30) REVERT: I 15 GLN cc_start: 0.8626 (mt0) cc_final: 0.7872 (mt0) REVERT: I 18 GLU cc_start: 0.8480 (pp20) cc_final: 0.8085 (pp20) REVERT: I 19 LEU cc_start: 0.9253 (mp) cc_final: 0.8893 (mp) REVERT: L 112 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7903 (mt) REVERT: L 272 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8330 (p90) REVERT: H 206 GLN cc_start: 0.9067 (mt0) cc_final: 0.8818 (pt0) REVERT: g 3 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8021 (tmmm) REVERT: g 38 ASN cc_start: 0.9355 (t0) cc_final: 0.9115 (t0) outliers start: 48 outliers final: 27 residues processed: 534 average time/residue: 0.5042 time to fit residues: 314.5593 Evaluate side-chains 521 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 485 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 6 LYS Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain t residue 33 LEU Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 34 MET Chi-restraints excluded: chain a residue 14 ARG Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain e residue 54 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain u residue 54 VAL Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 54 VAL Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain M residue 207 ILE Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain g residue 3 LYS Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain B residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 161 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 158 optimal weight: 0.0070 chunk 89 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... o 20 GLN N 15 GLN t 20 GLN e 42 ASN b 42 ASN A 25 GLN ** k 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 20 GLN ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 GLN H 93 ASN g 20 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.063810 restraints weight = 58678.792| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.21 r_work: 0.2775 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 23497 Z= 0.195 Angle : 1.194 38.115 32317 Z= 0.485 Chirality : 0.044 0.424 3242 Planarity : 0.004 0.054 3934 Dihedral : 21.878 179.986 3821 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.25 % Allowed : 20.84 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.18), residues: 2286 helix: 1.88 (0.13), residues: 1586 sheet: 2.72 (1.68), residues: 10 loop : -0.63 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG U 45 TYR 0.030 0.002 TYR M 304 PHE 0.018 0.001 PHE H 20 TRP 0.015 0.001 TRP U 44 HIS 0.006 0.001 HIS J 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.19 (23465) covalent geometry : angle 1.19368 / 0.48 (32317) hydrogen bonds : bond 0.05071 / 3.31 ( 1309) hydrogen bonds : angle 4.33003 / 3.17 ( 3705) Misc. bond : bond 0.00144 / 0.08 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 497 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 5 TYR cc_start: 0.8318 (p90) cc_final: 0.7671 (p90) REVERT: N 15 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8362 (pm20) REVERT: N 18 GLU cc_start: 0.9332 (mt-10) cc_final: 0.9032 (mp0) REVERT: t 6 LYS cc_start: 0.9364 (mmtp) cc_final: 0.9057 (mmpt) REVERT: t 14 ARG cc_start: 0.8666 (mpp80) cc_final: 0.8358 (mpp80) REVERT: t 33 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9335 (mm) REVERT: t 45 ASP cc_start: 0.8808 (t0) cc_final: 0.8526 (t0) REVERT: S 27 MET cc_start: 0.9267 (ttm) cc_final: 0.8950 (mtm) REVERT: r 14 ARG cc_start: 0.8540 (mtm180) cc_final: 0.8263 (mpp80) REVERT: r 23 PHE cc_start: 0.9298 (t80) cc_final: 0.8912 (t80) REVERT: r 26 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9358 (mm) REVERT: r 46 ILE cc_start: 0.9460 (mt) cc_final: 0.9203 (mp) REVERT: O 18 GLU cc_start: 0.9318 (pt0) cc_final: 0.9058 (pt0) REVERT: U 18 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8768 (mt-10) REVERT: b 3 LYS cc_start: 0.9169 (ptpp) cc_final: 0.8705 (mmpt) REVERT: k 9 LEU cc_start: 0.9254 (mm) cc_final: 0.8955 (mm) REVERT: k 14 ARG cc_start: 0.9139 (mtt90) cc_final: 0.8850 (mtt90) REVERT: k 42 ASN cc_start: 0.8950 (t0) cc_final: 0.8559 (t0) REVERT: J 25 GLN cc_start: 0.9438 (mt0) cc_final: 0.9107 (mp10) REVERT: f 15 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6541 (ttt-90) REVERT: f 38 ASN cc_start: 0.9271 (t0) cc_final: 0.9019 (t0) REVERT: E 14 GLN cc_start: 0.8956 (pm20) cc_final: 0.8654 (pm20) REVERT: E 18 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8849 (mm-30) REVERT: u 53 ARG cc_start: 0.8037 (mmt-90) cc_final: 0.7550 (mpp-170) REVERT: X 63 THR cc_start: 0.8802 (m) cc_final: 0.8587 (p) REVERT: s 6 LYS cc_start: 0.9559 (mmmm) cc_final: 0.9233 (mmmt) REVERT: s 25 PHE cc_start: 0.9436 (t80) cc_final: 0.9106 (t80) REVERT: s 42 ASN cc_start: 0.9090 (t0) cc_final: 0.8483 (t0) REVERT: s 45 ASP cc_start: 0.8934 (m-30) cc_final: 0.8211 (m-30) REVERT: R 27 MET cc_start: 0.8850 (ttp) cc_final: 0.8560 (mtp) REVERT: n 5 TYR cc_start: 0.8104 (p90) cc_final: 0.7814 (p90) REVERT: n 45 ASP cc_start: 0.8720 (m-30) cc_final: 0.8400 (m-30) REVERT: K 15 GLN cc_start: 0.9060 (mt0) cc_final: 0.8223 (mp10) REVERT: G 14 GLN cc_start: 0.9117 (pm20) cc_final: 0.8892 (pm20) REVERT: G 15 GLN cc_start: 0.8918 (mt0) cc_final: 0.8560 (mt0) REVERT: G 18 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8840 (mt-10) REVERT: j 3 LYS cc_start: 0.9040 (mmpt) cc_final: 0.8774 (ttpp) REVERT: j 42 ASN cc_start: 0.9261 (t0) cc_final: 0.8395 (t0) REVERT: j 45 ASP cc_start: 0.8936 (m-30) cc_final: 0.8515 (m-30) REVERT: I 15 GLN cc_start: 0.8635 (mt0) cc_final: 0.7903 (mt0) REVERT: I 18 GLU cc_start: 0.8500 (pp20) cc_final: 0.8111 (pp20) REVERT: I 19 LEU cc_start: 0.9250 (mp) cc_final: 0.8898 (mp) REVERT: L 213 GLU cc_start: 0.8734 (pm20) cc_final: 0.8332 (pm20) REVERT: L 272 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8424 (p90) REVERT: H 206 GLN cc_start: 0.9011 (mt0) cc_final: 0.8740 (pt0) REVERT: g 3 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8055 (tmmm) REVERT: g 38 ASN cc_start: 0.9360 (t0) cc_final: 0.9108 (t0) outliers start: 45 outliers final: 28 residues processed: 523 average time/residue: 0.4919 time to fit residues: 300.1447 Evaluate side-chains 519 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 484 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain t residue 33 LEU Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 34 MET Chi-restraints excluded: chain a residue 14 ARG Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain e residue 54 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain u residue 54 VAL Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain n residue 10 ILE Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 54 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain M residue 207 ILE Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain g residue 3 LYS Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain B residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 17 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 160 optimal weight: 0.0670 chunk 205 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... o 20 GLN N 15 GLN t 20 GLN e 20 GLN b 42 ASN A 25 GLN f 20 GLN ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN M 78 GLN H 93 ASN g 20 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.082964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.064076 restraints weight = 58307.880| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.19 r_work: 0.2782 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 23497 Z= 0.190 Angle : 1.196 38.174 32317 Z= 0.486 Chirality : 0.045 0.412 3242 Planarity : 0.004 0.053 3934 Dihedral : 21.842 179.987 3821 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.05 % Allowed : 21.79 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.18), residues: 2286 helix: 1.88 (0.13), residues: 1584 sheet: 2.74 (1.67), residues: 10 loop : -0.64 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG U 45 TYR 0.029 0.001 TYR M 304 PHE 0.018 0.001 PHE H 20 TRP 0.015 0.001 TRP U 44 HIS 0.006 0.001 HIS J 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 (23465) covalent geometry : angle 1.19604 / 0.49 (32317) hydrogen bonds : bond 0.05035 / 3.29 ( 1309) hydrogen bonds : angle 4.33699 / 3.17 ( 3705) Misc. bond : bond 0.00133 / 0.08 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8540.99 seconds wall clock time: 146 minutes 0.21 seconds (8760.21 seconds total)